Human Genome Meeting 2015
14 – 17 March 2015
Kuala Lumpur Convention Centre,
Malaysia
FINAL PROGRAMME
&
ABSTRACT BOOK
“Transforming Human Genomics for a Sustainable Tomorrow”
Human Genome Organisation
20 Bendemeer Road
#04-02 Cyberhub
Singapore 339914
Tel : +65 6411 6631 - Fax : +65 6496 5599
Email: admin@hugo-international.org
Website: www.hugo-international.org
TABLE OF CONTENTS
Welcome message from presidents........................................................ 3
Meeting information ............................................................................... 4
Scientific information .............................................................................. 5
HUGO Corporate Social Responsibility statement .................................. 5
Networking events .................................................................................. 6
Programme overview- Saturday, 14 March 2015 ................................... 7
Programme overview- Sunday, 15 March 2015 ...................................... 7
Programme overview- Monday, 16 March 2015 .................................... 8
Programme overview- Tuesday, 17 March 2015 .................................... 8
Satellite symposia programme ............................................................. 17
Posters session I – Saturday 14 March to Sunday 15 March................. 18
Posters session II – Monday 16 March to Tuesday 17 March ............... 22
Travel grants ......................................................................................... 28
Exhibition floor plan .............................................................................. 29
Sponsors & exhibitions list .................................................................... 31
Speakers biography ............................................................................... 32
Abstract book ........................................................................................ 40
2
WELCOME MESSAGE FROM PRESIDENTS
On behalf of the Kuala Lumpur local organizing committee, we would like to welcome delegates to the 2015 Human
Genome Meeting in Kuala Lumpur, or KL as it is more affectionately known, the beautiful and vibrant capital city of
Malaysia.
This conference is a platform for sharing research outcomes and the diverse cultural background which is rooted in
each and every one of our ‘DNA’. The theme of the HGM 2015 – “Transforming Human Genomics for A Sustainable
Tomorrow” relates to the foundations of scientific dynamics in formulating future agenda in human genetics for the
betterment of humankind.
The HGM 2015 provides geneticists, clinicians, bioinformaticians, and other health-care professionals a viable
platform to deliberate, exchange views and experiences in sharing and discussing the latest discovery of their
research to the world. We believe that you will gain related knowledge drawn from prominent speakers and experts
present here at this meeting.
On a final note, do take the opportunity to experience Malaysia as the colourful multi-ethnic cultures of the people,
the diverse tourist attractions, and the many mouth-watering cuisines and more; Malaysia is truly Asia.
Stylianos E. Antonarakis
President, Human Genome organization
Prof. Dr. Zilfalil Alwi
Chair of the Local Organising Committee, University Sains Malaysia and Chair of the Local Organizing Committee
LOCAL ORGANISING COMMITTEE
Zilfalil Alwi, Universiti Sains Malaysia (CHAIR)
Amir Feisal Merican bin. Aljunid Merican,
University of Malaya
Roziana Ariffin, Hospital Kuala Lumpur
Rosline Hassan, Universiti Sains Malaysia
Vijay Kumar, Universiti Malaysia Sabah
Zarina Abdul Latiff, Universiti Kebangsaan Malaysia
Muhammad Hamdi bin Mahmood,
University Malaysia Sarawak
Zahurin Mohamed, University of Malaya
Maude E. Phipps, Monash University, Malaysia
Rozita Rosli, Universiti Putra Malaysia
Ashley Edward Roy A/L Soosay,
Universiti Malaysia Sarawak
Sarina Sulong, Universiti Sains Malaysia
Wan Rohani Wan Taib, Universiti Sultan Zainal Abidin
Thong Meow Keong, University of Malaya
Narazah Mohd Yusoff, Universiti Sains Malaysia
Zubaidah Zakaria, Medical Research Institute
HUGO COUNCIL MEMBERS
Stylianos E. Antonarakis, Switzerland, President
Edison Liu, United States, President Emeritus
Partha Majumder, India
Julie Makani, Tanzania
John Mattick, Australia
Carmencita Padilla, The Philippines
Heidi Rehm, United States
Juergen Reichardt, Australia
Charles Rotimi, United States
Himla Soodyall, South Africa
Yik-Ying Teo, Singapore
Michael Snyder, United States
Martin Vingron, Germany
Ambroise Wonkam, South Africa
Huanming Yang, China
Karen B. Avraham, Israel
Piero Carninci, Japan
Ruth Chadwick, United Kingdom
Aravinda Chakravarti, United States
Kartiki Desai, India
Ada Hamosh, United States
Alfredo Hidalgo Miranda, Mexico
Dhavendra Kumar, United Kingdom
Charles Lee, United States
Klaus Linpaintner, United States
3
MEETING INFORMATION
BADGE & MEETING DOCUMENTS
The meeting documents (including name badges) should be collected on-site, during the official opening hours, from
the registration desk at the conference centre.
Your name badges must be visible at all times anywhere within the Kuala Lumpur Convention Centre (KLCC), level 3.
CERTIFICATE OF ATTENDANCE
The meeting participants will receive their own E-certificate of attendance by email after the meeting.
DISCLAIMER
HUGO and MCI Suisse SA, as the meeting organisers, claim no liability for the act of any supplier to this meeting, nor
liability for personal injury, the safety of any attendee while in transit to or from this event, for any loss or damage,
for delays in transport by air, sea, rail, road, weather, in case of strikes, sickness, war or other causes.
EXHIBITION INFORMATION
The HGM 2015 exhibition, featuring commercial displays of International Organisations, Life Science Companies,
Media Publishers and Scientific Societies, is located in conference hall 1 of the Kuala Lumpur Convention Centre.
Coffee breaks and lunch boxes will be distributed within and around the exhibition.
EXHIBITION SCHEDULE
Day
Saturday
Sunday
Monday
Tuesday
Date
14 March 2015
15 March 2015
16 March 2015
17 March 2015
Opening hours
11:00-17:00
09:30-17:00
09:30-17:00
08:30-12:30
FOOD & BEVERAGE
Coffee/tea during official breaks is included in the registration fees and will be served within the exhibition area. A
light lunch will be offered to each registered delegate on 14, 15, 16 and 17 March 2015.
LANGUAGES/OFFICIAL LANGUAGE
The official meeting language is English. No simultaneous translation is provided.
INSURANCE AND LIABILITY
It is recommended that participants obtain adequate cover for travel, health and accident insurance before they
depart from their countries. HUGO and MCI as organisers cannot accept responsibility for personal injuries, or loss of,
or damage to, private property belonging to the Meeting participants.
LOST AND FOUND
A lost-and-found service is available at the registration desk.
MOBILE PHONES
Delegates are kindly requested to keep their mobile phones in the off position in the rooms where scientific and
educational sessions are being held, as well as during poster sessions' rounds.
REGISTRATION DESK
The desk for registration, information and distribution of documents will be open as follows:
Day
Saturday
Sunday
Monday
Tuesday
Date
14 March 2015
15 March 2015
16 March 2015
17 March 2015
Opening hours
09:00 - 18:00
08:00 - 19:00
08:30 - 17:30
08:30 - 14:00
SMOKING POLICY
The HGM 2015 is a non-smoking event. It is forbidden to smoke in the conference venue, including the exhibition &
posters area.
4
SCIENTIFIC INFORMATION
POSTER SESSIONS
Posters sessions will take place in the exhibition area. Please go to the registration desk for any information and to
collect necessary hanging material. The author must be present in front of his/her poster during Poster viewing for
free discussion.
SPEAKER'S PREVIEW ROOM
The Speakers' Preview Room is located in Room 303. Speakers are kindly requested to provide their PC formatted
USB keys (PowerPoint presentations) to the Speaker's Preview Room centre at least two hours before their session.
All conference rooms contain state-of-the-art technical equipment.
The Speakers' Preview Room will be opened as follows:
Day
Date
Saturday
14 March 2015
Sunday
15 March 2015
Monday
16 March 2015
Tuesday
17 March 2015
Opening hours
09:00 - 19:00
08:00 - 18:30
08:00 - 17:30
08:00 - 14:00
HUGO CORPORATE SOCIAL RESPONSIBILITY STATEMENT
HUGO is aware of the environmental, economic and social impact of holding a large congress, and is working closely
with its partners to ensure that environmentally, economically and socially friendly policies are in place.
For the Kuala Lumpur Meeting, HUGO has made the following sustainable arrangements:
HEALTHY FOOD
All lunches and coffee breaks offer healthy options and local products have been prioritized
PRINTING
HUGO is committed to ensuring that printing is kept to a minimum to reduce the amount of waste paper.
Abstracts are included in the Final Programme, available on the USB stick and online, saving the printing of thousands
of pages.
LOCAL SUPPLIERS
HUGO wishes to have a positive local impact. When sourcing materials and supplies, HUGO considers local partners in
priority to avoid associated impacts of transportation and to positively impact the local economy.
SERVICES FOR THE DISABLED
HUGO wishes to make the meeting experience comfortable for all attendees. All the rooms and areas at the meeting
venue are fully accessible to participants with disabilities.
5
NETWORKING EVENTS
HGM 2015 provides delegates with numerous opportunities to network with colleagues and other professionals in
the field of human genome. The conference organizers are pleased to invite you to the following events:
HGM 2015 WELCOME LUNCH
Saturday 14 March 2015, 12:15 - 13:15
HGM 2015 will organize a networking lunch on the first day of the conference to welcome delegates and colleagues
coming from all over the world. This buffet lunch is held in the exhibition area of the venue.
 Venue:
Kuala Lumpur Convention Centre – Conference Hall 1, level 3
 Dress code:
Business casual
 Rate:
Included in the registration fee
6
PROGRAMME OVERVIEW- SATURDAY, 14 MARCH 2015
SATURDAY, 14 MARCH 2015
TIME
ROOM
Exhibition
Conference Hall 1
11:00 – 12:15
12:15 – 13:15
Conference Hall 3
Room 304-305
OPENING PLENARY
OPENING CEREMONY
& LUNCH
HUGO-OECD Joint Session - GENOMICS
FOR SUSTAINABLE DEVELOPMENT IN
EMERGING ECONOMIES: FOOD,
ENVIRONMENT, AND INDUSTRY
13:15 – 15:45
ETHICS & DATA SHARING
SPONSORED BY OECD
15:45 – 16:15
COFFEE BREAK
16:15 – 17:45
DISTINGUISHED SPEAKERS
MICROBIAL GENOMICS
PROGRAMME OVERVIEW- SUNDAY, 15 MARCH 2015
SUNDAY, 15 MARCH 2015
TIME
ROOM
Exhibition
Conference Hall 1
09:00 – 10:00
10:00 – 10:30
Conference Hall 3
Room 304-305
PLENARY LECTURE 2
COFFEE BREAK
EPIGENETICS
10:30 – 12:30
12:30 – 14:00
GLOBAL ALLIANCE & DATA SHARING
LUNCH
PERSONALISED
MEDICINE/PHARMACOGENOMICS
14:00 – 16:00
16:00 – 16:30
SPONSORED BY BLUEPRINT
LUNCH SYMPOSIUM
SPONSORED BY BIO-RAD
COFFEE BREAK
16:30 – 17:30
PLENARY LECTURE 3
17:30 – 18:30
SPONSORED SYMPOSIUM
SPONSORED BY PACIFIC BIOSCIENCES
7
ORAL PRESENTATIONS I
PROGRAMME OVERVIEW- MONDAY, 16 MARCH 2015
MONDAY, 16 MARCH 2015
TIME
ROOM
Exhibition
Conference Hall 1
09:00 – 10:00
10:00 – 10:30
Conference Hall 3
Room 304-305
PLENARY LECTURE 4
COFFEE BREAK
10:30 – 12:30
POPULATION GENETICS & STATISTICS
CANCER GENOMICS
13:30 – 15:00
GENETIC DISORDERS & GENOME
EDITING
ORAL PRESENTATIONS II
15:00 – 16:00
PLENARY LECTURE 5
12:30 – 13:30
16:00 – 16:30
LUNCH, VISIT OF THE
EXHIBITION & POSTERS
COFFEE BREAK
16.30 – 17:30
PLENARY LECTURE 6
17:30 – 18:30
HUGO MEMBERS' MEETING
PROGRAMME OVERVIEW- TUESDAY, 17 MARCH 2015
TUESDAY, 17 MARCH 2015
TIME
ROOM
08:30 – 09:00
Exhibition
Conference Hall 1
Conference Hall 3
COFFEE BREAK
USING HAEMOGLOBINOPATHIES TO
ADVANCE GENOMIC MEDICINE:
HUMAN VARIOME PROJECT'S GLOBAL
GLOBIN INITIATIVE
09:00 – 11:00
SPONSORED BY HVP MALAYSIA
11:00 – 12:00
12:00 – 14:00
Room 304-305
LUNCH
CHEN AWARD & HUGO-AFRICAN PRIZE
LECTURE
AWARDS PRESENTATION & CLOSING
CEREMONY
8
NON-CODING & RNA BIOLOGY
JOIN US AT HGM 2016!
9
SATURDAY, 14 MARCH 2015
11:00-12:15
OPENING PLENARY LECTURE
HALL 3
Chair: Stylianos Antonarakis (CH)
11:30- 12:15
OPENING PLENARY
Tan Sri Abdul Hamid (MY), Science Advisor to Malaysian PM
12:15-13:15
EXHIBITION, HALL 1
WELCOME LUNCH
13:15-15:45
SYMPOSIUM 1 – HUGO-OECD JOINT SESSION
HALL 3
Chair: Gerardo Jimenez-Sanchez (MX)
13:15-13:45
THE ROLE OF GENOMICS IN THE BIOECONOMY
Gerardo Jimenez-Sanchez (MX)
13:45-14:15
DEVELOPMENT OF SUBMERGENCE-TOLERANT RICE AND ITS SOCIOECONOMIC IMPACT
Abdelbagi M. Ismail (PH)
14:15-14:45
THE POTENTIAL OF BANANA GENOMICS INFORMATION AS A TOOL IN BREEDING
Hugo Alfried Volkaert (TH)
14:45-15:15
CONSERVING AND ENHANCING PRODUCTIVITY OF FORESTS IN GENOMICS ERA
Norwati Muhammad (MY)
15:15-15:45
OPPORTUNITIES FOR THE ENOMICS INDUSTRY IN SOUTH EAST ASIA
Mohd Nazlee Kamal (MY)
Panel discussion
SYMPOSIUM 2 - ETHICS & DATA SHARING
ROOM 304/305
Chair: Ruth Chadwick (UK)
13:15-13:45
HUGO STATEMENT ON SOLIDARITY AND BIG DATA
Ruth Chadwick (UK)
13:45-14:15
FRAGMENTATION, ANONYMISATION AND DIGITALISATION: IMPLICATIONS FOR RESEARCH ETHICS
Hub Zwart (NL)
14:15-14:45
GENOMIC DATA SHARING FOR THE BENEFIT OF PATIENTS AND CITIZENS - HOW CAN WE PROMOTE
IT IN ASIA?
Kazuto Kato (JP)
14:45-15:45
Panel discussion:
1. Himla Soodyall (ZA)
2. Maude E. Phipps (MY)
3. Benjamin Capps (CA)
15:45-16:15
EXHIBITION, HALL 1
COFFEE BREAK
16:15-17:45
SYMPOSIUM 3 - DISTINGUISHED SPEAKERS
16:15-16:45
Chair: Himla Soodyall (ZA)
SEQUENCING IN COHORTS REVEALS GENERALIZED GENETIC MODELS OF HUMAN DISEASE
Eric Boerwinkle (US)
16:45-17:15
TBA
Charles Lee (US)
17:15-17:45
SCALING METAGENOMICS FOR POPULATION STUDIES
Joseph Petrosino (US)
10
HALL 3
SYMPOSIUM 4 - MICROBIAL GENOMICS
ROOM 304/305
Chair: Ambroise Wonkam (ZA)
16:15-16:45
GENOMICS OF IMMUNE RESPONSE TO VACCINES FOR ENTERIC MICROBES
Partha P. Majumder (IN)
16:45-17:15
HUMAN GENOMICS AS A TOOL FOR DETERMINING SUCCESS OF VACCINE AND BIOMEDICAL TOOLS
FOR IMPACTING ON HEALTH OF DEVELOPING COUNTRY PEOPLE
Firdausi Qadri (BD)
17:15-17:45
DECIPHERING THE HOST-PATHOGEN INTERPLAY IN HUMAN MACROPHAGES INFECTED WITH
MYCOBACTERIUM TUBERCULOSIS
Kanury Rao (IN)
11
SUNDAY, 15 MARCH 2015
09:00-10:00
PLENARY LECTURE 2
HALL 3
Chair: Edison Liu (US)
09:00-10:00
ANALYSIS OF COMPLEX DISEASES USING INTEGRATIVE OMICS TECHNOLOGIES
Michael Snyder (US)
10:00-10:30
EXHIBITION, HALL 1
COFFEE BREAK
10:30-12:30
SYMPOSIUM 5 – EPIGENETICS – SESSION SPONSORED BY BLUEPRINT
Chair: Henk Stunnenberg (NL)
10:30-11:00
THE EPIGENOMIE BLUEPRINT OF BLOOD GENOMES: A GUIDE TO FUNCTION
Henk Stunnenberg (NL)
11:00-11:30
INSIGHTS FROM METHYLOME ANALYSIS
Stephan Beck (UK)
11:30-12:00
THE BLUEPRINT EPIVAR PROJECT
Nicole Soranzo (UK)
12:00-12:10
Oral presentations:
O01 - METHYLATION MAPPING IDENTIFIES GENES IMPLICATED IN DIABETES
Assam El-Osta (AU)
12:10-12:20
O02 - HDAC INHIBITION ATTENUATES CARDIAC HYPERTROPHY BY DEACETYLATION OF TARGET
GENES
Jenny Ooi (AU)
SYMPOSIUM 6 - GLOBAL ALLIANCE & DATA SHARING
Chair: Peter Goodhand (CA)
10:30-11:00
11:00-11:30
11:30-12:00
HALL 3
ROOM 304/305
THE GLOBAL ALLIANCE FOR GENOMICS AND HEALTH
Peter Goodhand (CA)
Partha P. Majumder (IN)
Kazuto Kato (JP)
12:00-12:30
Panel discussion:
1. Carlos Bustamente (US)
12:30-14:00
HALL 3
BIO-RAD LUNCH SYMPOSIUM
See details in related section on page 17
14:00-16:00
SYMPOSIUM 7 - PERSONALISED MEDICINE/PHARMACOGENOMICS
Chair: Klaus Lindpaintner(US)
14:00-14:30
PERSONALIZED MEDICINE IN CLINICAL PRACTICE: DELIVERING ON THE PROMISE
Thong Meow Keong (MY)
14:30-15:00
EPIGENETIC INFLUENCES ON GENE THERAPY
Syahrilnizam Abdullah (MY)
15:00-15:30
SYMPTOMS GENOMICS OF BREAST CANCER
Edison Liu (US)
15:30-15:40
HALL 3
Oral presentations:
O04 - A GENOME-WIDE POPULATION-SCALE MAP OF RARE AND COMMON PHARMACOGENETIC
VARIANTS IN MALAYSIA
Ambily Sivadas (IN)
12
15:40-15:50
O06 - COMBINED GAMMA-TOCOTRIENOL AND HYDROXYCHAVICOL ACTIVATED MULTIPLE
ANTICANCER PATHWAYS IN 1321N1, SW1783 AND LN18 GLIOMA CELL LINES: TRANSCRIPTOMIC
EVIDENCE OF SYNERGISTIC INTERACTION
Amirah Abdul Rahman (MY)
14:00-16:00
SYMPOSIUM 8 - ORAL PRESENTATIONS
Chair: Zahurin Mohamed (MY)
14:00-14:10
O07 - HOMOZYGOSITY DISEQUILIBRIUM IN THE HUMAN GENOME
Hsin-Chou Yang (TW)
14:10-14:20
O08 - SHUFFLING BETWEEN HYPOXIA AND VASCULAR HOMEOSTASIS PATHWAY GENES UNDER
HYPOBARIC HYPOXIA
Ma Qada Pasha (IN)
14:20-14:30
O09 - MEDICO-GENOMIC CHARACTERIZATION OF THE CHE WONG TRIO: AN ORANG ASLI
(INDIGENOUS GROUP) SUB-TRIBE OF MALAYSIA
Rose I. Ismet (MY)
14:30-14:40
O10 - ROLE OF N-METHYL D-ASPARTATE (NMDA) RECEPTORS IN ZEBRAFISH HEART DEVELOPMENT
Ramcharan A (IN)
14:40-14:50
O12 - WHOLE GENOME SEQUENCING OF KAZAKH INDIVIDUALS: INSIGHTS INTO THE GENETIC
ARCHITECTURE OF KAZAKH POPULATION.
Ainur Akilzhanova (KZ)
14:50-15:00
O13 - IN A GENOME-WIDE SEARCH, CNVS CONVEY PROTECTION AGAINST HAPE
Samantha Kohli (IN)
15:00-15:10
O14 - PHARMCOGENETIC VARIATION OF CLOPIDOGREL DRUG IN SOUTH INDIAN POPULATION
SUGGESTS DISTINCT INTERPOPULATION DIFFERENCES IN ALLELE FREQUENCIES
Arun Kiran Patnam (IN)
15:10-15:20
O15 - IMPACT OF CYP3A5 POLYMORPHISM ON TACROLIMUS TO PREDICT THE OPTIMAL INITIAL
DOSE REQUIREMENTS IN SOUTH INDIAN RENAL TRANSPLANT RECIPIENTS.
Sreeja S (IN)
15:20-15:30
O16 - INITIAL EXPERIENCE IN IMPLEMENTATION OF A CANCER GENE PANEL TEST TO DETERMINE THE
AETIOLOGY OF BREAST CANCER IN A DEVELOPING COUNTRY
Nirmala D. Sirisena (LK)
15:30-15:40
O17 - FINE-MAPPING EGFR SUSCEPTIBILITY LOCI THROUGH TRANS-ETHNIC META-ANALYSIS
Anubha Mahajan (UK)
15:40-15:50
O18 - SPECTRUM OF HEREDITARY SPASTIC PARAPLEGIA AND MUSCLE DISEASES IN QATAR
Alice Aleem (QA)
ROOM 304/305
16:00-16:30
EXHIBITION, HALL 1
COFFEE BREAK
16:30-17:30
PLENARY LECTURE 3
Chair: Partha Majumder (IN)
16:30-17.30
HALL 3
SINGLE CELL GENOMICS
Stephen Quake (US/SG)
17:30-18:30
HALL 3
PACIFIC BIOSCIENCES EVENING SYMPOSIUM
See details in related section on page 17
13
MONDAY, 16 MARCH 2015
09:00-10:00
PLENARY LECTURE 4
Chair: Charles Lee (US)
09:00-10:00
HALL 3
AUTISM SPECTRUM DISORDERS: NEW MUTATIONS, GENES AND SUBTYPES
Evan Eichler (US)
10:00-10:30
EXHIBITION, HALL 1
COFFEE BREAK
10:30-12:30
SYMPOSIUM 9 - POPULATION GENETICS & STATISTICS ( HUGO-PAPGI)
Chair: Lai Poh San (SG)
HALL 3
10:30-11:00
THE GENETIC STRUCTURE OF THREE INDIAN OCEAN ISLAND POPULATIONS: ZANZIBAR, MALDIVES
AND MADAGASCAR
Himla Soodyall (MY)
11:00-11:30
RARE VARIANTS AND MISSING HERITABILITY
Andrew Clark (US)
11:30-11:40
INDIGENOUS MALAYSIAN AND NEGRITOS
Maude Phipps (MY)
11:40-12:10
RECONSTRUCTING THE COLONISATION OF ASIA USING GENOMES AND SPATIALLY EXPLICIT MODELS
Andrew Eriksson (UK)
12:10-12:20
12:20-12:30
Oral presentations:
O22 - GENES REGULATED BY VITAMIN D IN BONE CELLS ARE POSITIVELY SELECTED IN EAST ASIANS.
Qasim Ayub (UK)
O23 - INSIGHTS FROM GENOME-WIDE DATA INTO THE PEOPLING OF NEAR AND REMOTE OCEANIA:
EXTENDING AND REFINING THE “DUAL-WAVE” MODEL
Mark Stoneking (DE)
SYMPOSIUM 10 - CANCER GENOMICS
Chair: Juergen Reichardt (AU)
10:30-11:00
11:00-11:30
ROOM 304/305
TRANSLATING GENETIC INFORMATION INTO PERSONALIZED THERAPY FOR CHILDHOOD LEUKEMIA
Hany Ariffin (MY)
MECHANISMS OF TUMORIGENESIS AND PROTECTION FROM TUMOURS BY STUDYING DOWN'S
SYNDROME
Dean Nizetic (UK/SGP)
11:30-12:00
THE SOMATIC GENETIC ARCHITECTURE OF CANCER- IMPLICATIONS FOR GENOMIC MEDICINE
Andy Futreal (US)
12:00-12:10
Oral presentations:
O25 - SMART SCREENING FOR CANCER DRUG DISCOVERY
Sukjoon Yoon (KR)
12:30-13:30
EXHIBITION HALL 1
LUNCH, EXHIBITION & POSTER VISIT
14
13:30-15:00
SYMPOSIUM 11 - GENETIC DISORDERS & GENOME EDITING
Chair: Rozita Rosli (MY)
HALL 3
13:30-14:00
TRANSCRIPTOME DYSREGULATION AND SINGLE CELL GENOMICS IN DOWN SYNDROME
Stylianos Antonarakis (CH)
14:00-14:30
CRISPR-Cas9
Haoyi Wang (US)
14:30-15:00
INHERITED NEUROMUSCULAR DISORDERS – IS NEXT-GEN SEQUENCING THE BEST SOLUTION FOR
CLINICAL DIAGNOSIS?
Lai Poh San (SG)
SYMPOSIUM 12 – ORAL PRESENTATIONS
Chair: Ashley Soosay (MY)
ROOM 304/305
13:30-13:40
O19 - COMPLETE MITOCHONDRIAL DNA SEQUENCE VARIATION IN ORANG ASLI OF PENINSULAR
MALAYSIA
Sean K. K. Eng (MY)
13:40-13:50
O20 - POPULATION GENETICS OF X-LINKED SNPS IN NORTH EURASIA AND ITS IMPLICATIONS FOR
HUMAN DNA IDENTIFICATION
Vadim Stepanov (RU)
13:50-14:00
O21 - HIGHLIGHTING NONLINEAR PATTERNS IN POPULATION GENETICS DATASETS
Timothy Ravasi (SA)
14:00-14:10
O29 - LEVERAGING GALAX-C, A NOVEL ASIAN GENOMIC VARIANT DATABASE TO ENHANCE
DIAGNOSTIC YIELD FOR PAEDIATRIC DEVELOPMENTAL DELAY
Tiew Yen Ling (MY)
14:10-14:20
O30 - MINING DNA: AN INVESTIGATION ON FEATURE-BASED CLASSIFICATION IN GENOME SCALE
MINING OF ENHANCERS
Sina Nazeri (MY)
14:20-14:30
O31 - NOVEL GENE IDENTIFICATION IN ALZHEIMER DISEASE
Zoran Brkanac (US)
14:30-14:40
O33 - GENOMEWIDE ASSOCIATION STUDY OF CANNABIS DEPENDENCE SEVERITY REVEALS NOVEL
RISK VARIANTS AND SHARED RISK WITH MAJOR DEPRESSIVE DISORDER
Joel Gelernter (US)
15:00-16:00
PLENARY LECTURE 5
Chair: Carmencita Padilla (PH)
15:00-16:00
HALL 3
RETINAL REGENERATIVE MEDICINE USING IPS CELLS
Masayo Takahashi (JP)
16:00-16:30
HALL 1
COFFEE BREAK
16:30-17:30
PLENARY LECTURE 6
Chair: Michael Snyder (US)
16:30-17:30
HALL 3
TBA
Carlos Bustamente(US)
17:30-18:30
ROOM 304/305
HUGO Members’ Meeting
15
TUESDAY, 17 MARCH 2015
09:00-11:00
SYMPOSIUM 13 - USING HAEMOGLOBINOPATHIES TO ADVANCE GENOMIC
MEDICINE: HUMAN VARIOME PROJECT'S GLOBAL GLOBIN INITIATIVE
HALL 3
SPONSORED BY HVP MALAYSIA
Chair: Christopher Arnold (AU)
09:00-09:20
Helene Robinson (AU)
09:20-09:40
Andreas Hadjisavvas (CY)
09:40-10.00
Zilfalil bin Alwi (MY)
10:00-10:20
Ming Qi (CN)
10:20-10:40
Raj Ramesar (ZA)
SYMPOSIUM 14 - NON-CODING & RNA BIOLOGY
Chair: Roziana Ariffin (MY)
ROOM 304/305
09:00-09:30
DECODING THE GENOME: DISSECTING THE REGULATORY REPERTOIRE OF THE GENOME THROUGH
HIGH RESOLUTION TRANSCRIPTOMICS
Marcel Dinger (AU)
09:30-10:00
MAGNIFIED VIEW OF THE GENOME WITH TARGETED SEQUENCING
Tim Mercer (AU)
10:00-10:30
INTRON RETENTION IS A CONSERVED GENE EXPRESSION CONTROL MECHANISM ASSOCIATED WITH
EPIGENETIC REGULATION
John E. Rasko (AU)
10:30-10:40
Oral presentations:
O34 - EXOME WIDE ASSOCIATION STUDY FOR CHILDHOOD OBESITY- AN ATTEMPT TO IDENTIFY
CODING VARIANTS
Dwaipayan Bharadwaj (IN)
10:40-10:50
O35 - RECONSTRUCTION OF SYNTHESIS PROTEIN THROUGH CODON UNIQUE REVISION (RESCUER)
FOR DMD GENE MUTATION CORRECTION IN MALAYSIAN PATIENTS WITH DUCHENNE MUSCULAR
DYSTROPHY
Abdul Qawee Rani (MY)
10:50-11:00
O36 - NOVEL THERAPEUTICS FOR CORONARY ARTERY DISEASE FROM GENOME-WIDE ASSOCIATION
STUDY DATA
Mani Grover (AU)
EXHIBITION, HALL 1
11:00-12:00
COFFEE BREAK & LIGHT LUNCH
12:00-14:00
CHEN AWARD & HUGO-AFRICAN PRIZE AWARD LECTURE
Chair: Stylianos Antonarakis (CH)
HALL 3
12:00-12:50
CHEN AWARD FOR DISTINGUISHED ACADEMIC ACHIEVEMENT IN HUMAN GENETIC AND GENOMIC
Jun Wang (CN)
12:50-13:40
HUGO-AFRICAN PRIZE AWARD
Alan Christoffels (ZA)
CONFERENCE CLOSING
16
SATELLITE SYMPOSIA PROGRAMME
Bio-Rad Lunch-time Symposium
Sunday 15 March 12:30-14:00 – Conference Hall 3
Practical high resolution Genomics via cell sorting and Droplet Digital™ PCR
Keynote Presentation:
Rapid and Ultra-Sensitive Single-Cell Transcript Profiling
Claudia Litterst, Ph.D.,
Staff Scientist, Bio-Rad Laboratories, Digital Biology Center
Pacific Biosciences Evening Symposium
Sunday 15 March 17:30-18:30 – Conference Hall 3
The Most Comprehensive View of The Human Genome
Speakers:
Jonas Korlach Ph.D., CSO, Pacific Biosciences
Mike Snyder Ph.D., Chair, Dept of Genetics, Stanford University
17
POSTERS SESSION I – SATURDAY 14 MARCH TO SUNDAY 15 MARCH
P001
SIGNATURES OF RAPID CHANGE IN PRDM9 BINDING TARGETS ARE EVIDENT IN ARCHAIC HUMANS / A. Tumian* R. Davies - S. Myers
P002
USING THE SEQUENCE CHROMATOGRAPHY TO ANALYZE THE QUANTITY OF COPY NUMBER VARIATION / C.-L. Tsai* Y.-S. Lee
P003
WIDE-RANGING SNAKE VENOM DATABASE / I. A. Tayubi* - A. S. A. Tawalah - F. J. Alzahrani - T. Khan
P004
BIOINFORMATIC APPROACH TO ANALYSE THE FUNCTIONAL EFFECT OF SNPS IN THE OLIGOMERISATION DOMAIN
"COILED-COIL" / K. Mohanasundaram* - M. Grover - A. Goscinski - T. Crowley - M. Wouters
P005
TBVAR 2.0: A COMPREHENSIVE DATABASE AND ANNOTATION RESOURCE FOR ANALYSIS OF CLINICAL RESEQUENCING
DATASETS OF MYCOBACTERIUM TUBERCULOSIS / K. Joshi* - H. Dhiman - V. Scaria
P006
FIRST TRIMESTER MATERNAL SERUM GLYCINE PREDICTS THE RISK OF GESTATIONAL DIABETES IN OBESE WOMEN /
M. Ryynanen* - M. Gissler - M. Vaarasmaki - T. Vaskivuo - S. Timonen
P007
LEARNING NEW BIOLOGY FROM GWAS BY MEANS OF NETWORK ANALYSIS AND LINK PREDICTION / T. Ravasi*
P008
FUNCTIONAL STUDY OF PEPTIDYLARGININE DEIMINASE TYPE 4 AS A GENETIC RISK FACTOR FOR RHEUMATOID
ARTHRITIS / A. Suzuki* - Y. Kochi - R. Yamada - K. Yamamoto
P009
LARGE-SCALE EXOME CHIP GENOTYPING REVEALS NOVEL CODING VARIATION ASSOCIATED WITH ENDOMETRIOSIS /
A. P. Morris* - R. Magi - N. Rahmioglu - A. Mahajan - N. Robertson - A. Salumets - K. Zondervan on behalf of UK Exome
Chip Consortium
P011
IL-6 GENE PROMOTER POLYMORPHISM IS ASSOCIATED WITH SUSCEPTIBILITY OF RHEUMATOID ARTHRITIS IN
DRAVIDIAN POPULATION / K. Priya* - S. Sathyan - L. Sreenivas - R. - S. Kesavarao - M. Banerjee
P012
LINKING LNCRNAS WITH ASSOCIATED LOCI IN GENOME-WIDE ASSOCIATION STUDIES / K. Po-Hsiu* - L. Ya-Chin - K.
Chung-Feng - C. Li-Chung
P013
LARGE SCALE GENOME-WIDE ASSOCIATION STUDY FOR BIRTH WEIGHT FINDS EIGHT NOVEL LOCI EXTENDING THE
GENETIC LINK BETWEEN EARLY GROWTH AND TYPE 2 DIABETES / M. Horikoshi* - A. P. Morris on behalf of EGG
Consortium
P014
GENETIC DETERMINANTS OF SUSCEPTIBILITY TO INFLAMMATORY BOWEL DISEASE IN A MOROCCAN COHORT /
N. Senhaji* - W. Badre - A. Serrano - N. Serbati - M. Karkouri - S. Nadifi - J. Martin
P015
CAN INSULIN LIKE FACTOR-3 (INSL3) BE A POTENTIAL CANDIDATE GENE FOR POLYCYSTIC OVARY SYNDROME (PCOS)
PATHOPHYSIOLOGY? / N. Shaikh* - N. Shah - S. Mukherjee
P016
HERITABILITY OF FOOD PREFERENCES AMONG UKRAINIANS / O. V. Filiptsova* - I. A. Timoshyna - M. N. Kobets - I. S.
Burlaka - P. V. Rakeev - I. A. Gurko
P017
GENE-GENE AND GENE-ENVIRONMENT INTERACTIONS IN THE ETIOLOGY OF TYPE 2 DIABETES MELLITUS IN THE
POPULATION OF HYDERABAD, INDIA / U. J. Kommoju* - B. Mohan Reddy
P018
APLN POLYMORPHISM INFLUENCES ITS EXPRESSION AND ASTHMA PHENOTYPES IN CHINESE / X. Ji* - W. Zhang - S. Jia R. Xu - J. Gao - W. Zhang
P019
INTEGRATING SEQUENCING ERRORS AND NON-CONVERSION RATES INTO METHYLATION CALLING / A. Salim*
P020
SEX DISTINGUISHES EPIGENETIC REGULATION BY NON-CODING RNA IN THE HEART / P. Mathiyalagan - H. KN - W. A.
Gold - J. Okabe - J. Christodoulou - X.-J. Du - A. El-Osta*
P021
HISTONE DEACETYLASE INHIBITORS INCREASE SMN2 EXPRESSION THROUGH METHYLATION / J. Mohseni* - Z.-H. Zamh
- T. H. Sasongko
18
P022
A NOVEL 19Q13.4 MICRODELETION INCLUDING THE IMPRINTED GENE PEG3 IS ASSOCIATED WITH SHORT STATURE,
DEVELOPMENTAL DELAY, CLEFT LIP AND PALATE, AND DYSMORPHIC FEATURES / L. Badalato* - A. C. Smith - G. E.
Graham
P023
THE PILOT STUDY FOR ASSOCIATION ASSAY OF METHYLATION OF NR3C1 AND CHILDHOOD MALTREATMENT WITH
MAJOR DEPRESSIVE DISORDER IN TAIWAN / L.-C. Chuang* - J.-H. Shen - Y.-C. Chung - P.-H. Kuo
P024
A GENOME-SCALE MAP OF THE EPIGENETIC PROGRAM IN EARLY ZEBRAFISH DEVELOPMENT / S. Kapoor* - S. Ghosh C. Sachidanandan - V. Scaria
P025
TRICHOSTATIN A ENHANCES SOCS-3 AND REDUCES STAT 6 EXPRESSION IN FLT3-ITD ACUTE MYELOID LEUKEMIC CELLS /
S. A. Mat Jusoh* - M. F. Johan
P026
OPINIONS OF HEARING PARENTS ABOUT THE CAUSES OF HEARING LOSS IN THEIR DEAF CHILDREN COMPARED WITH
GJB2 (CX26) GENETIC TESTING RESULTS IN RUSSIA / N. A. Barashkov - L. U. Dzhemileva - O. L. Posukh - A. V. Solovyev* M. S. Bady-Khoo - V. G. Pshennikova - F. M. Teryutin - S. L. Lobov - A. B. Neustroeva - K. A. Kurtanov - L. A. Klarov - L. M.
Vasilyeva - E. E. Fedotova - A. M. Rafailov - N. A. Solovyeva - S. K. Kononova - A. N. Alekseev - S. A. Fedorova - E. K.
Khusnutdinova
P027
EXPERIENTIAL PROCESS OF SECURING FREE PRIOR INFORMED CONSENT FOR GENETICS RESEARCH FROM AN
INDIGENOUS POPULATION IN THE PHILIPPINES / C. D. Padilla* - A. L. Sur - M. T. G. Padilla - M. Baluyot - E. M.
Cutiongco-de la Paz - S. Padilla
P028
EDUCATING FOR THE POTENTIAL GLOBAL CONSEQUENCES OF THE HUMAN GENOME PROJECT / J. Garrett*
P029
BIOETHICS AND GOVERNANCE OVER HUMAN GENOME RESEARCH IN SOUTH KOREA / S.-H. Kim* - S. Y. Kim
P030
PROTECTING PRIVACY THROUGH CONTROLLED ACCESS IN LARGE SCALE CANCER GENOMIC RESEARCH / Y. Joly* - E. de
Vries-Seguin
P031
MOLECULAR CHARACTERIZATION OF SCN1A GENE IN EPILEPTIC ENCEPHALOPATHIES CHILDREN IN MALAYSIA / A. W.
Siti Aishah* - Y. Yusnita
P032
CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS CLINICAL ISOLATES FROM KAZAKHSTAN BY SPOLIGOTYPING
/ U. Kozhamkulov - A. Akhmetova - Z. Zhumadilov - A. Akilzhanova*
P033
ASSOCIATION OF VITAMIN D RECEPTOR (FOKI, TAQI, APAI & BSMI) AND IFG GENES’ POLYMORPHISMS WITH RISK OF
DEVELOPING PULMONARY TB (PTB) AMONG KAZAKHSTANI POPULATION / D. Yerezhepov - M. Zhabagin - Z. Abilova - A.
Askapuli - A. Abilmazhinova - S. Rakhimova - U. Kairov - A. Molkenov - U. Kozhamkulov - A. Akhmetova - A.
Akilzhanova*
P034
INTERACTION BETWEEN FTO AND DRD2 GENE VARIANTS AND FOOD ENERGY DENSITY IN HUMAN BRAIN REWARD
SYSTEM RESPONSES TO FOOD PICTURES / A. M. Yiorkas* - C. G. Prechtl - M. L. Sleeth - A. D. Miras - S. Scholtz - N. M.
Daud - G. Durighel - S. F. M. Alberts - G. S. Frost - J. D. Bell - A. I. F. Blakemore - A. P. Goldstone
P035
GERMLINE MUTATIONS IN BRCA1/2 IN PATIENTS FROM CEMIC AND THE UNIVERSITY OF BUENOS AIRES REVEALS HIGH
HETEROGENEITY AND NOVEL VARIANTS: CONSTRUCTING THE INSTITUTIONAL GENETIC VARIANT BASE AND THE FIRST
IN THE COUNTRY / A. R. Solano* - F. C. Cardoso - F. Poletta - V. Romano - S. Quiroga - J. Lopez Camelo - O. Mando
P036
RESISTIN RS1862513 [-420 C/G] POLYMORPHISM IN PSORIASIS IN SOUTH INDIAN POPULATION / A. Sudhesan* M. Rajappa - A. PH - D. M. Thappa - S. Satheesh - A. C
P037
INVERSE ASSOCIATION BETWEEN MPJ6_1I3008 OF THE NR1I3 GENE AND NEONATAL HYPERBILIRUBINEMIA IN THE
MALAY FEMALES / C. Tian Pei* - S. Yusoff - R. Ismail - N. N. Nawawi - N. A. Abdullah - N. Ramli - N. R. Ibrahim - N. Hj.
Abd Majid - N. M. Yusoff - H. Nishio - H. Van Rostenberghe
P038
NON-INVASIVE PRENATAL SCREENING PLUS (NIPS+): DETECTION OF FETAL 22Q11.2 MICRODELETION AND
MICRODUPLICATION SYNDROMES / C.-C. Hung* - Y.-N. Su
P039
TARGETED NEXT-GENERATION SEQUENCING PANEL FOR DETECTION OF MUTATIONS IN HEARING IMPAIRMENT / C.-C.
Hung* - Y.-N. Su
19
P040
P041
WHOLE-EXOME SEQUENCING IDENTIFIED FLJ22184 NON-SYNONYMOUS MUTATION COMMON IN TWO TYPE 1
DIABETES CORE FAMILIES WITH MULTIPLE CASES / C.-H. Lin* - I. J. Tsai - Y.-S. Lee - Y.-Y. Huang - F.-S. Lo - Z.-S. Chen - C.N. Tsai
FOK1 AND TAQ1 POLYMORPHISMS OF VDR GENE AND STUNTED GROWTH IN TRANSFUSION DEPENDENT
THALASSEMIA PATIENT: A PRELIMINARY STUDY / D. Rashid* - W.-Z. Abdullah - A. Nasir - P. Yahya - N. F. Azman - S.
Hanafi - M. F. Johan - R. Bahar - R. Hassan - B. Zilfalil
P042
MUTATIONS OF THE SCN1A GENE IN VIETNAMESE CHILDREN WITH DRAVET SYNDROME / D. T. T. Hang* - B. Chi Bao V. Diem My
P043
ACUTE ENCEPHALOPATHY IN TWO CHILDREN WITH DRAVET SYNDROME / D. Thi Thu Hang* - H. Thi Thuy Kieu - L. Thi
Khanh Van
P044
CLASSIFICATION OF HBE/BETA – THALASSAEMIA DISEASE SEVERITY BASED ON SCORING SYSTEM AND MOLECULAR
GENOTYPE / H. Alsaleh* - A. Nasir - Z. Alwi - S. Hanafi - D. Rashid - R. Hassan
P045
COMPARISON OF MLPA WITH FISH TECHNIQUE IN DETECTION OF CHROMOSOME 22Q11.2 MICRODELETION
SYNDROME AMONG ATRIAL SEPTAL DEFECTS PATIENTS /
S. Maran - S. A. Faten - H. Hashim - N. A. Mohd Nawi - N. Ramli - W. P. Wan Ibrahim - A. R. Wong - M. R. Mohd Zain - W.
R. Wan Taib - R. Ankathil - H. L. Tan*
P046
FEATURES OF THE FIRST REFERENCE SEQUENCE OF SAUDI / I. Alabdulkareem* - W. Alharbi - M. Ballow - Y. Alhaidan - A.
AlAbdulrahman - Z. Rabhan - M. Aljumah - M. Albalwi
P047
TNF-LTA GENE VARIATIONS AND THE RISK OF DEVELOPING RHEUMATOID ARTHRITIS IN THE MYEIRA STUDY / L. K. Tan*
- S. Sulaiman - J. S. Dhaliwal - S. Murad - C. L. Too
P048
THE NON-GENOMIC ACTION OF DIHYDROTESTOSTERONE (DHT) IN SKELETAL MUSCLE FIBRE TYPES / M. H. Mahmood*
P049
FREQUENCY OF HUMAN INTERLEUKIN 28B RS12979860 C>T AND RS8099917 T>G VARIANTS IN FILIPINO PATIENTS
WITH NON-ALCOHOLIC FATTY LIVER DISEASE / M. Baclig* - J. Gopez-Cervantes on behalf of St. Luke’s Liver Diseases
Study Group
P050
TRANSCRIPTIONAL PROFILING OF AGEING IN MICE REVEALS EFFECTIVENESS OF SHORT- AND LONG-TERM PIPER BETLE
SUPPLEMENTATION / M. F. A. Shukor* - W. Z. Wan Ngah - N. A. Abdul Hamid
P051
EVIDENCE OF HAPLOTYPE ASSOCIATION OF SLC2A9 POLYMORPHISMS IN GOUTY MALAY POPULATION / N. Mohd
Yunus* - M. Adanan - W. S. Wan Ghazali - T. Huay Lin - W. R. Wan Taib
P052
PTPN11 GENE ANALYSIS IN TUNISIAN PATIENTS WITH NOONAN SYNDROME / N. G. Abroug* on behalf of Nehla
Ghédira, Natacha Fillot, Emna Kerkeni, Sana Sfar, Sofiene Bouaziz, Rania Sakka, Fatma-Zohra Chioukh, Karim Ben
Ameur, Hayet Ben Hmida, Hélène Cavé, Kamel Monastiri
P053
MUTATIONS IN ARYLSULFATASE A GENE OF MALAYSIAN PATIENTS WITH METACHROMATIC LEUKODYSTROPHY / N. A.
B. Abdul Azize* - A. B. Omar - Y. B. Yakob - Z. B. Md Yunus
P054
IDENTIFICATION OF RS9960767 AT TCF4 GENE IN MALAYSIAN SCHIZOPHRENIA AND RHEUMATOID ARHTRITIS
PATIENTS: A PRELIMINARY STUDY / N. S. Ab Rajab* - M. R. Salleh - M. A. Mohd Yasin - W. S. Wan Ghazali - N. Abdul
Talib - W. R. Wan Taib - S. Sulong
P055
GENOME WIDE ASSOCIATION STUDIES (GWAS) ON TRANSFUSION DEPENDENT HBE/ BETA THALASSEMIA PATIENT IN
KELANTAN, A PRELIMINARY REPORT / N. F. Azman* - R. Hassan - S. Hanafi - D. Rashid - A. Nasir - P. Yahya - W.-Z.
Abdullah - M. F. Johan - R. Bahar - B. Zilfalil
P056
IDENTIFICATION OF THE SUSCEPTIBILITY GENETIC MARKERS FOR PRIMARY OPEN ANGLE GLAUCOMA IN MALAYS / R.
Thambiraja* - M. Imran Bukhari - L. S. Ahmad Tajudin - K. Chiea Chuen - Z. Bin Alwi - S. Sulong
P057
PARTIAL TRISOMY 22(PTER-Q11.23): CASE REPORT OF A RARE SYNDROME / R. A. Adnan* - Z. Abu Bakar - S. M. Ismail N. Ramli - N. M. Z. Mat Zin - N. A. Nawi - M. Q. Abu Bakar - H. Hashim - R. H. Razali - N. Mohd Yunus - I. H. Ibrahim - M.
H. Mohd Jamil - R. Ankathil
20
P058
CHEMICAL SYNTHESIS OF A RECOMBINANT HUMAN GRANULOCYTE COLONY STIMULATING FACTOR (RHG-CSF) CDNA
AND ITS EXPRESSION ANALYSIS / S. A. Alrokayan*
P059
MOLECULAR CHARACTERISATION AND FREQUENCY OF GΓ XMN I POLYMORPHISM IN TRANSFUSION DEPENDENT
HBE/Β-THALASSEMIA PATIENTS IN KELANTAN, WEST OF MALAYSIA / S. Hanafi* - R. Hassan - R. Bahar - M. F. Johan - W.
Z. Abdullah - N. D. Rashid - N. F. Azman - A. Nasir - N. Mohamad - N. K. Nik Yussof - S. Salleh - B. A. Zilfalil
P060
MOLECULAR PHYLOGENETIC OF SELECTED ORANG ASLI TRIBES (ABORIGINES) IN PENINSULAR MALAYSIA INFERRED
FROM BETA FIBRINOGEN GENE. / S. Mat Yasin* - N. Mohd Nasir - E. Ismail - Z. Alwi - R. Zainudin - M. T. Abdullah
P061
TRANSCRIPTOME PROFILE OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA IN KAZAKHSTAN / S. Rakhimova* A. Akilzhanova - U. Kairov - A. Molkenov - Y. Zhukov - J. Y. Shin - Z. Zhumadilov
P062
DNA SEQUENCING SERVICE AT IMCB / S. N. H. B. Mohamed Haron Narasib* - C. Ah Keng - L. Debbie - T. Alice
P063
RELATIONSHIP BETWEEN CHEMOKINE (C-X-C MOTIF) LIGAND 12 GENE VARIANT RS1746048 AND CARDIOVASCULAR
DISEASES / S. Ikeda* - K. T. T. Zaw - T. Arai - M. Mieno-Naka - M. Sawabe - M. Muramatsu
P064
GENETIC POLYMORPHISMS OF SMAD7 IN MALAY PATIENTS WITH VENTRICULAR SEPTAL DEFECTS / S. A. F. Mohamed
Sadom* - H. Hashim - S. Maran - T. Hern-Tze - M. R. Mohd Zain - W. P. Wan Ibrahim - T. Huay Lin
P065
INHIBITION OF SIRT1 AND TREATMENT WITH TOCOTRIENOL-RICH FRACTION MODULATE THE EXPRESSION OF GENES
INVOLVED IN THE REGULATION OF CELL CYCLE AND APOPTOSIS / S. Makpol* - F. Jaafar - Y. A. Mohd Yusof - W. Z. Wan
Ngah
P066
INDISPUTABLE DOUBLE PATERNITY IN TWINS CAUSING BY SUPERFECONDATION / W. Manoubi* - A. Mili - A. M’sakni A. Saad - M. Gribaa
P067
IDENTIFICATION OF CAUSAL GENES THROUGH WHOLE EXOME SEQUENCING IN A MALAYSIAN COHORT OF CHARCOTMARIE-TOOTH PATIENTS / A. Ahmad-Annuar* - S. Tey - N. Shahrizaila - K.-J. Goh - G.-S. Ch'ng - G. Nicholson M. Kennerson
P068
CBS GENE MUTATIONS DETECTED IN A FILIPINO INDIVIDUAL WITH HOMOCYSTINURIA / C. L. T. Silao* - T. D. F. Fabella K. I. D. Rama - S. C. Estrada
P069
CHARACTERIZATION OF MUTATIONS THROUGH WHOLE GENE SEQUENCING OF THE GLUCOSE-6-PHOSPHATE
DEHYDROGENASE GENE AMONG FILIPINO CHILDREN WITH G6PD DEFICIENCY / E. M. C. Cutiongco De La Paz* - C.
David-Padilla - M. M. P. Baluyot
P070
COMBINED PITUITARY HORMONE DEFICIENCY: MUTATION ANALYSIS OF POU1F1 AND PROP1 GENES IN A COHORT OF
MALAYSIAN PATIENTS / J. Mohd Ali* - F. Harun - L. Kha Chin
P071
A PATIENT WITH AORTIC DISSECTION AS A RESULT OF MUTATIONS IN TGFBR2 AND ACTA2 GENES / M. Dvorakova* - P.
Cibulkova - R. Krenkova - P. Vanickova - A. Boday
P072
POPULATION STUDY OF A CLASSICAL MENDELIAN GENETIC MARKER FOR A TASTE SENSITIVITY TO
PHENYLTIOCARBAMIDE IN UKRAINE / O. V. Filiptsova* - I. A. Timoshyna - Y. N. Kobets - I. S. Burlaka - H. F. Chechui - P.
V. Mirenkova
P073
FKRP GENE SCREENING SHOULD BE CONSIDERED IN DIAGNOSIS OF PATIENTS WITH DUCHENNE/BECKER-LIKE
PHENOTYPES / K. L. Ng - I. S. Tan - C. J. Y. Chia - S. Zhou - C. Liu - P.-S. Low - S. Tay - P.-S. Lai*
P074
FINDING THE CAUSATIVE GENE MUTATION IN A CONSANGUINEOUS FAMILY WITH CHARCOT-MARIE-TOOTH (CMT)
DISEASE / S. Tey* - N. Shahrizaila - A. Drew - K. J. Goh - G. Nicholson - M. Kennerson - A. Ahmad Annuar
P075
SEVERE OBESITY, TYPE 2 DIABETES MELLITUS, INTELLECTUAL DISABILITY AND HYPOGONADOTROPHIC HYPOGONADISM
IN A FAMILY SEGREGATING WITH A TRUNCATING MUTATION IN THE CARBOXYPEPTIDASE-E (CPE) GENE / S. I. Alsters* A. P. Goldstone - J. L. Buxton - A. Zekavati - A. Sosinsky - A. M. Yiorkas - S. Holder - R. E. Klaber - N. Bridges - M. M. van
Haelst - C. W. le Roux - A. J. Walley - R. G. Walters - A. I. Blakemore
P076
GENUS RATIO OF PREVOTELLA TO BACTEROIDES AS A MICROBIAL MARKER IN OBESITY / A. Shafiq* - T. Lay Kek - I. Rose
Iszati - L. Lian Shien - Y. Hartini - A. Aminuddin - O. Mazlifah - R. Thuhairah - S. Mohd Zaki
21
P077
DIVERSITY OF HELICOBACTER PYLORI CAGA EPIYA MOTIFS IN DIFFERENT DIFFERENT ETHNIC GROUPS/
H. A. Osman* - H. Hasan - R. Suppian - A. Abdul Rahim - S. Hassan - D. Z. Andee - N. Abdul Majid - B. A. Zilfalil
P078
UNDERSTANDING THE GENOME OF BURKHOLDERIA TO UNRAVEL THE EVOLUTION OF PLANT-MICROBE INTERACTION /
N. Najimudin* - A. H. Ahmad Ghazali - S. Shaffie - N. Ab. Aziz - A. F. Mohamad - A. Y. Abdul Rahman
P079
MCP-1−2518 A/G, 336A/G CD209, AND CCR2 V64 A/G GENES POLYMORPHISMS INCREASES THE LIKELIHOOD RISK OF
DEVELOPING TUBERCULOSIS OR AGAINST WITH LTBI INDIVIDUALS IN PENINSULAR MALAYSIA / O. S. Elmi* - H. Hasan S. Abdullah - M. Z. Mat Jeab - B. Zilfalil - N. N. Naing on behalf of non
P080
WHOLE GENOME SEQUENCING AND COMPARATIVE ANALYSIS OF BARTONELLA ELIZABETHAE / S. T. Tay* - K. L. Kho W. Y. Wee - S. W. Choo
P081
MOLECULAR EVOLUTION AND INDIVIDUALITY OF DETOXIFICATION SYSTEM IN HUMAN MICROBIOME / W. Y. Low* - N.
S. Che Wahid - C. Luo
POSTERS SESSION II – MONDAY 16 MARCH TO TUESDAY 17 MARCH
P082
CLOUD-BASED VARIANT ANALYSIS SOLUTION USING CONTROL-ACCESSED SEQUENCING DATA / C. Xiao* - E. Yaschenko
- S. Sherry
P083
SYSTEMATIC ANALYSIS OF BIG DATA FOR CANCER DRUG DISCOVERY / N. Kim* - S. Yoon
P084
ICLIKVAL: COMMUNITY RESOURCE FOR CURATING THE VAST WEALTH OF SCIENTIFIC LITERATURE THROUGH THE
POWER OF CROWDSOURCING / T. D. Taylor* - N. Kumar
P085
GIGADB：PROMOTING DATA DISSEMINATION AND REPRODUCIBILITY / X. Sizhe* - C. I. Hunter - P. Li - R. Davidson –
S. C. Edmunds - L. Goodman
P086
7X LOW-DEPTH GENOMIC SEQUENCING IS SUFFICIENT FOR CLINICAL ANALYSIS OF A GIST FFPE TUMOUR SAMPLE / A.
Amin* - S. Abdul Karim - S. M. Ching - H. Isa - Y. S. Leong - J. Y. Chia - K. W. Chong - F. Wahid - T. M. Pasupati - R. G.
Hercus - P. Suwinski - L. Croft
P087
DETECTION OF EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR) MUTATIONS IN NON-SMALL-CELL LUNG CANCER
PATIENTS IN MALAYSIA / C. W. Tay* - S. B. Yousoof - Y. K. Cheah - P. Rajadurai
P088
EXTRACELLULAR MATRIX PROTEINS SECRETED BY MESENCHYMAL STEM CELLS INDUCE PROSTATE CANCER CELL
MIGRATION IN VITRO / C. Maercker* - M. Boutros - F. Graf
P089
AP-1-MEDIATED CHROMATIN LOOPING REGULATES ZEB2 TRANSCRIPTION: NEW INSIGHTS INTO TNF -INDUCED
EPITHELIAL–MESENCHYMAL TRANSITION IN TRIPLE-NEGATIVE BREAST CANCER / C. Zhao*
P090
RESECTABLE VX-2 RABBIT BRAIN TUMOR MODEL FOR DEVELOPMENT OF INTRAOPERATIVE LOCAL ADMINISTRATION
OF DRUGS / F. Ahmad* - A. Pacholska - V. Tuppurainen - S. Ylä-Herttuala - A. Hyvarinen
P091
CIRCULATING MICRORNAS AS BIOMARKER FOR THE DIAGNOSIS OF NASOPHARYNGEAL CARCINOMA / G. W. Tan* - A. S.
B. Khoo - T. Y. Tan - L. P. Tan on behalf of The Malaysian Nasopharyngeal Carcinoma Study Group
P092
ADRA2A GENE POLYMORPHISM IS ASSOCIATED WITH BREAST CANCER SEVERITY / G. Belaaloui* - B. Kaabi - W.
Benbrahim - K. Hamizi - M. Sadelaoud - W. Toumi - H. Bounecer
P093
ANALYSIS OF CANCER SUSCEPTIBILITY GENES IN CASES OF FAMILIAL NASOPHARYNGEAL CARCINOMA / H. Akmal
Hisham* - T. Lu Ping - K. W. Ric - L. C. Lun - P. K. Choo - Y. Y. Yap - D. B. Dass - T. T. Yong - G. K. Govindasamy - A. Khoo
Soo Beng on behalf of The Malaysian Nasapharyngeal Carcinoma Study Group#
P094
PREVENTING BREAST AND OVARIAN CANCERS IN MALAYSIAN BRCA MUTATION CARRIERS / H. Sa'at* - Y. Sook-Yee - W.
Yin-Ling - K. Rahmat - Y. Cheng-Har - T. Soo-Hwang - T. Hassan - T. Gie-Hooi - S. Mee-Hoong - S. Jamaris - T. MeowKeong - N. A. Taib
22
P095
CCND1 REARRANGEMENT AS A SECONDARY MOLECULAR EVENT IN MANTLE CELL LYMPHOMA / H. Elghezal* - A.
alzahrani - I. ben abdallah - K. alfayez - S. sobki - G. Elyamany
P096
MICRORNA EXPRESSION PROFILES AND COPY NUMBER ALTERATIONS IN ACUTE PROMYELOCYTIC LEUKAEMIA
PATIENTS: A PRELIMINARY STUDY / I. Ismail* - S. Sulong - M. F. Md Ahid - S. Ghazali - A. Cheng Yong - N. A. F. Abdullah
- N. M. K. Nik Man - Z. Zakaria - A. Mansoor - R. Hassan
P097
EXPRESSION DATA IDENTIFIES DEREGULATED IMPRINTED GENES IN NASOPHARYNGEAL CARCINOMA / I. M. Alhwij* A. Soosay
P098
IDENTIFICATION OF BRCA1 AND BRCA2 MUTATIONS IN BREAST CANCER IN BRUNEI DARUSSALAM / F. N. Mohd Jaya - S.
N. I. Haji Matusin - D. N. H. Pg Haji Mumin - H. Zainal Abidin - X. Y. Lim - H. M. S. Abdullah - D. B. Sukumaran - M. R. W.
Haji Abdul Hamid*
P099
IMAGE-BASED HIGH THROUGHPUT SIRNA LIBRARY SCREENING PLATFORM FOR CANCER TARGET DISCOVERY / M.
Song* - S. Yoon
P100
AMPLIFICATION OF CHROMOSOME 1Q AND DELETION OF CHROMOSOME 8Q WAS ASSOCIATED RECURRENCE IN
EARLY STAGE OF HCC AFTER RESECTION- ANALYSIS OF FFPE SPECIMEN BY AFFYMETRIX ONCOSCAN PLATFORM / M.-C.
Yu* - Y.-S. Lee - C.-N. Tsai
P101
INFLUENCED OF HTERT MRNA EXPRESSION AND TELOMERASE ACTIVITY IN MALAYSIAN CML PATIENTS TREATED WITH
IMATINIB MESYLATE / M. S. watihayati* - A. husin - R. Hassan - A. ravindran - A. A. baba - S. Sulong
P102
GENE COPY NUMBER STATUS OF TERC IN CANCER CELL LINES MODEL WITH SPECIAL EMPHASIS ON FLUORESCENCE IN
SITU HYBRIDIZATION (FISH) ANALYSIS / N. Mohd Adam* - S. Sulong - J. Mohamed
P103
DETECTION OF MLH1 AND MSH2 BY IMMUNOHISTOCHEMISTRY ASSESSMENT IN NEPALESE PATIENT WITH
HEREDITARY NONPOLYPOSIS COLORECTAL CANCER / N. A. Gandah* - M. Bhattarai - B. A. Zilfalil - T. R. Shrestha
P104
A COMBINATORIAL APPROACH TO CUSTOMIZE PIPELINE FOR IDENTIFICATION OF GENOMIC ALTERATIONS USING NEXT
GENERATION SEQUENCING DATA / P. Narang* - A. Lynn
P105
TREATMENT-FOCUSED GENETIC TESTING (TFGT). IS IT TOO SOON FOR MALAYSIA? / R. A. Mazlan* - K. Barlow-Stewart M. Gleeson - T. Soo Hwang - Y. Sook Yee - T. Gie Hooi - T. Meow Keong - N. A. Mohd Taib
P106
DETECTION OF PDGFRA MUTATIONS AT EXON 12 AND 18 AMONG MALAYSIAN CHRONIC MYELOID LEUKEMIA
PATIENTS TREATED WITH IMATINIB MESYLATE / R. H. Razali* - R. Hassan - A. Husin - S. Sulong
P107
TRANSFER RNA SIGNATURES AS PROGNOSTIC MARKERS FOR BREAST CANCER / S. Damaraju* - P. Krishnan - S. Ghosh J. Mackey - O. Kovalchuk
P108
PROTEOMIC DYNAMICS IN CERVICAL CANCER TUMORS FROM THE CANCER CELL LINES REVEALS AN IMPORTANT ROLE
OF GLUTATHIONE -S-TRANFERASES / S. M. Encarnacion* - A. Checa-Rojas - L. Delgadillo-Silva
P109
THE PROGNOSTIC IMPLICATIONS OF OVER-EXPRESSION OF MLH1 AND MSH2 FOR STAGE I-II COLON CANCER PATIENTS
/ S.-F. Huang* - S.-C. Huang
P110
WHOLE GENOME GENE EXPRESSION PROFILING IDENTIFIES KEY BIOLOGICAL PATHWAYS DIFFERENTIAL IN EARLY AND
LATE ONSET BREAST CANCER / S. Malvia* - S. A. R. Bagadi - D. Arora - R. Sarin - C. Chintamani - S. Saxena
P111
MLH1 AND MSH2 GENE POLYMORPHISMS IN MALAYS WITH HEREDITARY NONPOLYPOSIS COLORECTAL CANCER
(HNPCC) / W. K. Wan Juhari* - K. B. Ahmad Amin Noordin - W. F. Wan Abdul Rahman - A. S. Mohd Sidek - M. R. Abu
Hassan - J.-P. Plazzer - F. Macrae - A. D. Zakaria - B. A. Zilfalil
P112
MRI OF THE BRAIN IN CORNELIA DE LANGE SYNDROME AND CORRELATION WITH BEHAVIOUR / T. R. Roshan Lal* - A.
Kline
P113
GENOTYPE IMPUTATION IN THAI POPULATION / W. Lert-Itthiporn* - P. Suriyaphol
P114
ASSOCIATION BETWEEN ACE GENE VARIATION AND PHYSICAL FITNESS PARAMETERS OF MALAY FEMALE ATHLETES
AND NON ATHLETES IN MALAYSIA / X. Li* - F. K. Ooi - Z. Bin Alwi - Y. Surini
23
P115
TITLE: DRTA AND SAO IN MALAYSIA: CLINICAL AND MOLECULAR FEATURES / Y. Raman* - N. M. Yusoff - Z. Alwi
P116
PHARMACOGENETIC ASPECTS OF PLANT AND ANIMAL PRODUCTS CONSUMPTION / O. V. Filiptsova - M. N. Kobets - Y.
N. Kobets* - I. A. Timoshyna
P117
GENERATION AND CHARACTERISATION OF TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASES (TALENS)
TARGETING TNFR1 GENOME EDITING / A. Alotiby* - L. Fairclough - I. Todd - P. Tighe
P118
ACCURATE VARIANT DETECTION USING MOLECULAR BARCODES / C. Y. Lee* - H. Johansson - J. Chi - K. Zobeck - L.
Forsmark - M. Isaksson - H. Hogrefe
P119
SHOTGUN METAGENOME SEQUENCING FOR SCREENING OF CURRENCY NOTES FOR MICROBIAL PATHOGENS AND
ANTIBIOTIC RESISTANCE GENES / S. Jalali* - S. Kohli - C. Latka - S. Bhatia - S. K. Vellarikal - S. Sivasubbu - V. Scaria - S.
Ramachandran
P120
DIFFERENTIAL UPREGULATION OF THE HYPOTHETICAL TRANSMEMBRANE PROTEIN 66 (TMEM66) IN BAHRAINI
MULTIPLE SCLEROSIS PATIENTS WITH POTENTIAL INFLAMMATORY RESPONSE / S. M. Taha* - M. O. Bakhiet - M. J.
Aljishi
SHORT- AND LONG-TERM TOCOTRIENOL RICH FRACTION (TRF) SUPPLEMENTATION MODULATES GENE EXPRESSION
DURING AGEING IN MICE / S. M. Abdul Ghani* - W. Z. Wan Ngah - N. A. Abdul Hamid
P121
P122
MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (MLPA) FOR DETECTION AND QUANTIFICATION OF
MITOCHONDRIAL DNA MUTATIONS IN PATIENTS WITH MITOCHONDRIAL DISORDERS / Y. Yakob* - H. Ruslan - N. A. Abd
Azize - C. Yew Sing - N. Lock Hock
P123
TOCOTRIENOL-RICH FRACTION PROMOTES DIFFERENTIATION OF HUMAN SKELETAL MUSCLE MYOBLAST / A. M. Binti
Razak* - N. Binti Abdul Karim - S. Binti Makpol
P124
GENOME-WIDE MAP OF POTENTIAL LONG NONCODING RNA MEDIATED DNA:DNA:RNA TRIPLEXES IN THE HUMAN
GENOME / S. Jalali* - V. Scaria
P125
DISTINCT AND MODULAR ORGANIZATION OF PROTEIN INTERACTING SITES IN LONG NON-CODING RNAS / S. Jalali* - V.
Scaria
P126
A SPATIO-TEMPORAL MAP OF LONG NONCODING RNAS IN ZEBRAFISH DEVELOPMENT / S. Kapoor* - V. E. Leonard - A.
Sivadas - S. Sivasubbu - C. Sachidanandan - V. Scaria
P127
NOVEL AND RARE FUNCTIONAL GENOMIC VARIANTS IN MULTIPLE AUTOIMMUNE SYNDROME / H. R. Patel* - A. Johar M. Arcos-Burgos
P128
PREVALENCE OF 16P11.2 DELETION CARRIERS AMONG UK OBESITY SURGERY PATIENTS AND IMPLICATIONS FOR THEIR
WEIGHT LOSS OUTCOMES / N. H. Ramzi* - N. A. Nor Hashim - S. I. M. Alsters - J. L. Buxton - A. M. Yiorkas - J. Murphy H. S. Chahal - S. Purkayastha - A. R. Ahmed - C. W. le Roux - R. G. Walters - A. I. F. Blakemore
P129
PREDICTING INSULIN USE IN CHINESE PATIENTS WITH TYPE 2 DIABETES USING CLINICAL AND GENETIC INFORMATION /
R. C. W. Ma* - C. Tam - G. Jiang - Y. Wang - H. M. Lee - C. Lim - W. Y. So - J. C. Chan
P130
GENETIC POLYMORPHISMS AT INTRON 1 OF OPRD1 ARE ASSOCIATED WITH SEVERITY OF DEPENDENCE, DIASTOLIC
BLOOD PRESSURE, CHEMOKINE IP-10 AND DRY MOUTH SIDE EFFECT / C.-P. Fang* - S.-C. Wang - H.-H. Tsou - Y.-S.
Chang - I.-K. Ho - H.-W. Kuo - S.-W. Liu - Y.-L. Liu
P131
GENETIC ASSOCIATION OF PDYN POLYMORPHISMS AMONG MALAYSIAN OPIOID DEPENDENTS / D. Nagaya* - Z. Zahari M. Salem - B. H. Yahaya - T. S. Choon - R. Ismail - N. Mohd Yusoff
P132
ASSOCIATION STUDY BETWEEN THE DPYD GENETIC VARIANTS AND DPYD ENZYME ACTIVITY IN KOREAN POPULATION
/ J.-G. Shin* - T. S. Kang - H. S. Cheong - H. D. Shin - M. W. Chung
P133
THE PREVALENCE OF CYP2D6 GENE POLYMORPHISMS AMONG FILIPINOS AND THEIR USE AS BIOMARKERS FOR CANCER
RISK AMONG THOSE WITH LUNG CANCER / R. J. B. Luna* - E. M. C. de la Paz - J. Nevado Jr. - C. L. Silao - C. Ngelangel A. D. Wang - R. H. Sebastian - R. Ceniza - L. L. P. Simpao - L. F. Beratio - E. Dominguez - A. Albay
24
P135
P136
PATHWAY-BASED METHADONE DOSE ASSOCIATION ANALYSES DISCOVERED CDH2 GENETIC POLYMORPHISMS
ASSOCIATION WITH BLOOD PRESSURE / Y.-L. Liu* - R.-H. Chung - S.-W. Liu - S.-C. Wang - H.-W. Kuo - H.-C. Yang - I.-K.
Ho
CYP2D6 GENE POLYMORPHISMS AND COLD PRESSOR PAIN SENSITIVITY: LACK OF ASSOCIATION AMONG HEALTHY
MALAY MALES / Z. Zahari* - L. Chee Siong - M. A. Ibrahim - N. Musa - M. A. Mohd Yasin - L. Yeong Yeh - T. Soo Choon N. Mohamad - R. Ismail
P137
LINEAGE-MEDIATED MYELOTOXICITY AND CHROMOSOME ABERRATION STATUS OF HYDROQUINONE-EXPOSED
MURINE BONE MARROW DERIVED-HEMATOPOIETIC STEM AND MYELOID PROGENITOR CELLS / Z. Abdul Hamid* C. Paik Wah - N. Khen Eng - J. Mohd Idris
P138
LRRK2 N551K AND R1398H VARIANTS: A GENETIC AND FUNCTIONAL STUDY / A. Gopalai* - S.-Y. Lim - L. L. Chua - Y.
Zhao - E.-K. Tan - A. Ahmad-Annuar
P139
TUMOUR NECROSIS FACTOR GENE POLYMORPHISM AMONG CHRONIC RHINOSINUSITIS PATIENTS WITH OR WITHOUT
NASAL POLYPS OF HOSPITAL USM / A. Ahmad* - K. Misron - S. Sheikh Abdul Hamid - R. R. Ramli
P140
VARIATION AND MUTATION DATABASE OF MALAYSIAN NODE OF HUMAN VARIOME PROJECT: AN UPDATE / B. H.
Halim-Fikri* - B. Atif Amin - A. Nurul Fatihah - W. J. Wan Khairunnisa - A. Mia Yang - H. Sarifah - A. R. Nur-Shafawati - W.
I. Hatin - B. Rosnah - J. Muhammad Farid - A. W. Zaidah - B. A. Zilfalil - A. L. Ahmad Zubaidi
P141
IDENTIFICATION OF SIGNATURE OF POSITIVE NATURAL SELECTION AMONG THE INDIGENOUS POPULATIONS FROM
PENINSULAR MALAYSIA / Y. Yunus - X. Liu - D. Lu - F. Aghakhanian - W.-Y. Saw - L. Deng - M. Ali - X. Wang - F. Mohd Nor
- T. Abdul Rahman - S. A. Shaari - M. Z. Salleh - P. Maude - R. T.-H. Ong - S. Xu - Y.-Y. Teo - B. P. Hoh*
P142
POPULATION STRUCTURE OF FIVE INDIGENOUS ETHNIC GROUPS IN SABAH, NORTH BORNEO, AND THEIR HISTORICAL
MIGRATION RELATIONSHIPS TO SOUTHERN CHINA AND SOUTHEAST ASIAN POPULATIONS / C. W. Yew* - M. Z. Hoque J. Pugh-Kitingan - C. L. Y. Voo - J. Ransangan - S. T. Y. Lau - X. Wang - W. Y. Saw - T. H. Ong - Y. Y. Teo - S. H. Xu - B. P.
Hoh - M. E. Phipps - S. V. Kumar
P143
ANALYSIS OF GENETIC STRUCTURE IN INDIGENOUS POPULATIONS OF PENINSULAR MALAYSIA / F. Aghakhanian* Y. Yunus - T. Jinam - A. Manica - R. Naidu - B. P. Hoh - M. E. Phipps
P144
ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNP) IN PCSK9 GENE WITH LIPID ANALYSIS AMONG IBAN
AND BIDAYUH ETHNIC GROUPS IN SARAWAK POPULATION / H. H. Hood* - Y. T. Siaw - S. P. Sim - H. Helmy - M. M.
Aminudin
MITOCHONDRIAL HAPLOGROUP M9A1A1C1B IS ASSOCIATED WITH HYPOXIC ADAPTION IN TIBETAN / Q. Li - H. Sun - K.
Lin - X. Huang - Z. Yang - J. Chu*
P145
P146
POLYMORPHISMS AND HAPLOTYPES OF INTERFERON-GAMMA RECEPTOR GENES ARE ASSOCIATED WITH THE RISK OF
PULMONARY TUBERCULOSIS / J.-G. Shin* - B. L. Park - L. H. Kim - C. S. Park - H. D. Shin
P147
GENE GEOGRAPHY OF KAZAKH POPULATIONS FROM THE Y-CHROMOSOMAL DATA / M. Zhabagin* - O. Balanovsky –
Z. Sabitov - I. Tazhigulova - A. Askapuli - K. Dibirova - M. Chukhryaeva - A. Agdzhoyan - N. Markina - Y. Yusupov - P.
Tarlykov - E. Zholdybaeva - A. Akilzhanova - Z. Zhumadilov - E. Balanovska
P148
PARP15 POLYMORPHISMS ASSOCIATED WITH FIRST INDUCTION CHEMOTHERAPY IN ACUTE MYELOID LEUKEMIA / M.
K. Lee* - H. S. Cheong - H. D. Shin - S.-S. Yoon
P149
ASSOCIATION BETWEEN DEPRESSION AND 5,10-METHYLENETETRAHYDROFOLATE REDUCTASE (MTHFR) GENE
POLYMORPHISMS IN THE TUNISIAN POPULATION / M. A. S. Sayadi* - O. ACHOUR - A. Ezzaher - A. Omezzine - W. Douki
- A. Bousslama - L. Gaha - M. F. Najjar
P150
THE MULTI-DIMENSIONAL SCALE ANALYSIS OF THE ORANG ASLI INDIVIDUALS IN PENINSULAR MALAYSIA / N. Mohd
Nasir* - W. I. Hatin - P. Yahya - S. Mat Yasin - E. Ismail - N. N. Nik Hassan - B. A. Zilfalil
P151
POPULATION GENETIC STRUCTURE OF THE EIGHT MALAY SUB-ETHNIC GROUPS IN PENINSULAR MALAYSIA / P. B.
Yahya* - N.-S. Ab Rajab - H. Wan Isa - S. Sulong - A. Harun - Z. Bin-Alwi
P152
GENETIC STRUCTURE AND DIVERSITY OF INDIGENOUS POPULATIONS IN SABAH, EAST MALAYSIA / B. P. Kee - L. H. Lian K. H. Chua - E. T. J. Chong - P. C. Lee*
25
P153
A NOVEL STATISTICAL APPROACH TO SELECT APPROPRIATE SUSCEPTIBILITY GENES AND IMPROVE PREDICTIVE ABILITY
OF DISEASES / S. Balan - A. Sunder - L. Musmade - H. Pallikarana Tirumala - S. Mohammed* - P. Mankad
P154
POTENTIAL ASSOCIATION BETWEEN TRA2B POLYMORPHISMS AND TOTAL COLONIC AGANGLIONOSIS OF
HIRSCHSPRUNG DISEASE / S.-G. Lee* - J.-H. Kim - H. D. Shin
P155
TARGETED EXOMING IN SEARCH OF HUMAN NEURAL TUBE DEFECTS GENE(S) / S. W. Mohd-Zin* - A. Ahmad-Annuar M.-K. Thong - Y. Osman - L. Niswander - N. M. Abdul-Aziz
P156
TRACING LINKS BETWEEN NEGRITOS IN SOUTHEAST ASIA USING GENOME-WIDE SNPS / T. Jinam* - M. Phipps - S.
Naruya
DISTRIBUTION OF MC1R ARG163GLN VARIANT IN MODERN JAPANESE, RECENT AINU AND JOMON INDIVIDUALS /
T. Motokawa* - N. Adachi - H. Kanzawa-Kiriyama - K.-I. Shinoda
P157
P158
GENOME-WIDE SEARCH FOR SIGNALS OF HUMAN ADAPTATION TO CLIMATE / V. Stepanov* - V. Kharkov - A. Markov A. Cherednichenko - K. Vagaitseva - E. Trifonova
P159
GENOMIC REGIONS INVOLVED IN THE DETECTION OF DIFFERENT PATHOGENS REQUIRES ACCUMULATION OF RARE
VARIANTS / I. Uktverytė - I. Domarkienė - L. Ambrozaitytė - V. Kučinskas*
P160
SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) OF LOW-DENSITY LIPOPROTEIN RECEPTOR GENE (LDLR) IN LIPID
RELATED GENE-ASSOCIATED FAMILIAL HYPERCHOLESTEROLAEMIA AMONG IBAN AND BIDAYUH ETHNIC GROUPS IN
SARAWAKIAN POPULATION: PRELIMINARY DATA ANALYSIS / Y. Siaw* - H. Hood - S. P. Sim - H. Helmy - M. M. Aminudin
P161
DIFFERENTIAL EXPRESSION OF MICRO-RNA’S AND MRNA’S IN PBMCS OF SPINOCEREBELLAR ATAXIA1 PATIENTS / D.
Kumaran* - G. Hasan
P162
ISODIOSPYRIN DOES NOT ALTER SPLICING ACTIVITY OF DYSTROPHIN GENE EXON 53 / R. Rashid* - M. Mustapha - Z. A.
Mohd Hussin - H. Abdul Wahab - T. H. Sasongko
P163
DYNAMICS OF MYOGENIC REGULATORY FACTORS REVEALED THE POTENTIAL IMPLICATION OF VITAMIN E IN
MEDIATING DIFFERENTIATION DURING SKELETAL MUSCLE AGING / S. C. K. Khor* - N. Abdul Karim - W. Z. Wan Ngah - S.
Makpol
P164
A BLOOD BASED GENE EXPRESSION AND SIGNALING PATHWAY ANALYSIS TO DIFFERENTIATE BETWEEN HIGH GRADE
*
AND LOW GRADE GLIOMAS. / S.N. Ponnampalam - M.F. Zulkifle - N.A. Azami - S. Ponnusamy - N.R. Kamaluddin - Z.
Zakaria
26
27
TRAVEL GRANTS
The Human Genome Meeting 2015 and HUGO would like to express its gratitude to Prof Kazuto Kato and Prof Charles
Lee for offering travel grant to enable the attendance of the following researchers:
Assam El-Osta (Australia)
BakerIDI Heart & Diabetes Institute, Melbourne, Australia
Abstract N°O01
Title: METHYLATION MAPPING IDENTIFIES GENES IMPLICATED IN DIABETES
MA Qadar Pasha (India)
CSIR-INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY (CSIR-IGIB), DELHI, INDIA
Abstract N°O08
Title: SHUFFLING BETWEEN HYPOXIA AND VASCULAR HOMEOSTASIS PATHWAY GENES UNDER HYPOBARIC HYPOXIA
Arif Anwar (Malaysia)
Sengenics
Abstract N°O29
Title: LEVERAGING GALAX-C, A NOVEL ASIAN GENOMIC VARIANT DATABASE TO ENHANCE DIAGNOSTIC YIELD FOR
PAEDIATRIC DEVELOPMENTAL DELAY
Sina Nazeri (Malaysia)
SARAWAK UNIVERSITY
Abstract N°O30
Title: MINING DNA: AN INVESTIGATION ON FEATURE-BASED CLASSIFICATION IN GENOME SCALE MINING OF
ENHANCERS
Dwaipayan Bharadwaj (India)
CSIR-Institute of Genomics and Integrative Biology
Abstract N°O34
Title: EXOME WIDE ASSOCIATION STUDY FOR CHILDHOOD OBESITY- AN ATTEMPT TO IDENTIFY CODING VARIANTS
28
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Analisa Resources (M) Sdn Bhd
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HUGO International
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N°01
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N°04
Theragen Etex
N°05
Genotypic Technology
DNA Genotek
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31
SPEAKERS BIOGRAPHY
This is a non-exhaustive list of HGM speakers’ biographies
Syahril Abdullah
Hany Ariffin
Syahril is an Associate Professor at Universiti Putra Malaysia.
He is currently the head of the Genetics and Regenerative
Medicine Research Centre of the Faculty, and also a member
of the Young Scientists Network-Academy of Sciences
Malaysia. He holds a DPhil from University of Oxford for his
work at the Gene Medicine Research Group, John-Radcliffe
Hospital, UK. His primary research interest is in the field of
gene therapy, focusing on ways to extend the duration of
therapeutic gene expression.
Dr Hany Ariffin is Professor of Paediatrics at the University of
Malaya and Senior Consultant Paediatric Oncologist at the
University of Malaya Medical Centre, Kuala Lumpur. Her main
research interest is in childhood leukaemia and she has
collaborated in the Malaysia-Singapore Leukemia Study
Group since 2003. Her other research interests include
inherited cancer syndromes especially related to TP53
mutations.
Stylianos E. Antonarakis
Stephan Beck
Professor and Chairman of Genetic Medicine, University of
Geneva, and the founding director of iGE3 (institute of
Genetics and Genomics of Geneva). He studies the
relationship between genomic and phenotypic variation. MD
(1975) and DSc (1982) University of Athens; Medical Genetics
at Johns Hopkins, Baltimore with H. Kazazian and V. McKusick
(1980-1983). Faculty of Johns Hopkins since 1983; full
professor of Genetics and Medicine in 1990. In 1992 he
moved to Geneva, Switzerland to chair Genetic Medicine. Has
published >660 papers and is listed as one of the highly cited
by ISI (>49,000 citations; h-index 105). President of the
European Society of Human Genetics (2001-2002), President
of HUGO for 2013-2016, foreign member of the Acad Athens
(2003), EMBO member (2006). Co-organizer of the Eur Sch of
Genetic Medicine, and for 32 years taught in the Bar Harbor
Genetics Course. Soc Ped Res Young Investigator Award
(1984), Jerome Lejeune Prize (2004), Eur Soc of Hum Genetics
Award (2005), Soc^Scholars of the Johns Hopkins (2006), Am.
Acad Physicians (2010). Member of the Swiss Science
Research Council, Chair of the Review Panel of ERC. Funded
by the NIH, EU (including the ERC), Swiss National Science
Foundation.
Stephan Beck is Professor of Medical Genomics at the
University College London (UCL) Cancer Institute. Using
experimental and computational approaches, his laboratory
has broad interests in the genomics and epigenomics of
phenotypic plasticity in health and disease. He has over 30
years experience in high-throughput genomics and has
(co)authored over 250 publications that have attracted over
45,000 citations to date. He received his PhD in 1985 from the
University of Konstanz where he studied DNA structure. After
appointments at the MRC Laboratory of Molecular Biology in
Cambridge, Millipore Corporation in Boston and the Imperial
Cancer Research Fund in London, he joined the Wellcome
Trust Sanger Institute in 1996. During his tenure as Head of
Human Sequencing (1998-2006), he played a leading role in
the sequencing and analysis of the human, mouse and
zebrafish genomes. He has co-founded and led a number of
international efforts, including the Human Epigenome
Project, the UK Personal Genome Project and serves on
numerous national and international advisory boards. He is a
Fellow of the Academy of Medical Sciences and recipient of a
Royal Society Wolfson Research Merit Award.
32
Eric Boerwinkle
Alan Chistoffels
Eric Boerwinkle is the Director of the Human Genetics Center
and Department Chair of Epidemiology, Human Genetics and
Environmental Sciences at the University Of Texas School Of
Public Health. In 2011, he joined Dr. Richard Gibbs at Baylor
College of Medicine and became Associate Director of the
Human Genome Sequencing Center at Baylor. Dr. Boerwinkle
is an internationally-recognized expert on the genetics of
common chronic disease, especially cardiovascular
disease. He has published over 700 peer-reviewed articles on
the subject. Dr. Boerwinkle’s group has pioneered methods to
identify genes or genomic regions that are protective from
disease, which has fueled the development of novel inhibitors
for disease treatment. With the transition from exome
sequencing to whole-genome sequencing, he and his group
are exploring novel methods for analyzing whole-genome
sequence data with respect to a complex trait.
Alan Christoffels completed his studies in genetics and
pharmacology in South Africa followed by doctorial studies in
Bioinformatics at the University of the Western Cape. In his
PhD thesis he developed a method to analyze large volumes
of expressed sequence tags. He expanded his genomics skills
by completing a 3-year postdoctoral fellowship in the
laboratory of Venkatesh and Brenner in Singapore. He
proceeded to establish his first research lab at Tamesk
LifeSciences Laboratory. In 2008 he returned to South Africa
and established his second laboratory at the South African
National Bioinformatics Institute (SANBI). In 2009, he became
the director of SANBI. He was also awarded the DST/NRF
Research Chair in Bioinformatics and Public Health Genomics.
Alan serves on the board of the International Society for
Computational Biology and was a founding member of the
Southern African Human Genome Programme in 2010. Alan’s
research interests lie in genome evolution and adaptations at
the host-pathogen interface while contributing to annotation
of four international genome projects. During this time he has
been actively involved in delivering genomics methods and
training researchers working on African trypanosomiasis
through the World Health Organisation Tropical Disease
Research Programme. . In recognition of his commitment to
training quality researchers in the health sciences, Alan was
awarded the 2014 Silver Medical by the South African
Medical Research Council. His group is committed to building
open-source tools for sustainable genomics resources
through the H3Africa consortium.
Ruth Chadwick
Professor Ruth Chadwick is Professor of Bioethics at the
University of Manchester. From 2002-2013 she directed the
ESRC Centre for Economic and Social Aspects of Genomics
(Cesagen). She co-edits Bioethics and Life Sciences, Society
and Policy and has served on the Council of the Human
Genome Organisation, the Panel of Eminent Ethical Experts of
the Food and Agriculture Organisation of the United Nations
(FAO), and the UK Advisory Committee on Novel Foods and
Processes (ACNFP). She is Fellow of the Academy of Social
Sciences; of the Hastings Center, New York; of the Royal
Society of Arts; and of the Society of Biology. In 2005 she won
the World Technology Network Award for Ethics and in 2014
she was elected Fellow of the Learned Society of Wales.
Andrew Clark
Dr. Andrew G. Clark is the Schurman Professor of Molecular
Biology & Genetics at Cornell. His Ph.D. is from Stanford in
Population Genetics (with Marc Feldman). He is a member of
the U.S. National Academy of Sciences. His work centers on
use of genome-wide polymorphism data for population
genetic inference (times of common ancestry, inference of
natural selection, admixture), inference of genotypephenotype association, and genetic impacts of recent rapid
population expansion.
33
Ravasi’s group at King Abdullah University of Science and
Technology (KAUST). His recent work on human population
genetics has focused on using past climate and spatially
explicit models to reconstruct the out-of-Africa expansion of
anatomically modern humans. He has also worked on the
effect of ancient population structure on patterns of genetic
similarity between human genomes and the Neanderthal,
domestication of the horse, and the spread of malaria.
Marcel E. Dinger
Andrew Futreal
Marcel Dinger is the Head of Genome Informatics at the
Garvan Institute of Medical Research and conjoint Associate
Professor at UNSW Australia. After completing his PhD at the
University of Waikato (New Zealand), he was awarded a NZ
FoRST Postdoctoral Fellowship to join Professor Mattick’s
group at The University of Queensland to study the role of
long noncoding RNAs in mammalian development and
disease. He was recruited to the Garvan Institute in 2012.
Andy Futreal, PhD, is a professor of Genomic Medicine and
the Robert A Welch Distinguished University Chair as well as
holding an Honorary Faculty position at the Wellcome Trust
Sanger Institute. Dr. Futreal's work includes the identification
of BRCA1 and BRCA2, BRAF mutations in melanoma and
chromatin modifier gene mutations in human cancer. He codirected the Sanger Cancer Genome Project that pioneered
application of systematic genome-wide approaches to the
study of human cancer. His work at MD Anderson focuses on
the integration of clinical and comprehensive genomic data to
improve patient outcomes, with particular emphasis on
tumor heterogeneity and evolution.
Evan E. Eichler
Evan Eichler, Ph.D., is a Professor and Howard Hughes
Medical Institute Investigator in the Department of Genome
Sciences, University of Washington School of Medicine. He
graduated with a B.Sc. Honours degree in Biology from the
University of Saskatchewan, Canada, in 1990. He received his
Ph.D. in 1995 from the Department of Molecular and Human
Genetics at Baylor College of Medicine, Houston. After a
Hollaender postdoctoral fellowship at Lawrence Livermore
National Laboratory, he joined the faculty of Case Western
Reserve University in 1997 and later the University of
Washington in 2004. He was a March of Dimes Basil O’Connor
Scholar (1998-2001), appointed as an HHMI Investigator
(2005), awarded an AAAS Fellowship (2006) and the American
Society of Human Genetics Curt Stern Award (2008), and
elected to the National Academy of Sciences (2012). He is an
editor of Genome Research and has served on various
scientific advisory boards for both NIH and NSF. His research
group provided the first genome-wide view of segmental
duplications within human and other primate genomes and
he is a leader in an effort to identify and sequence normal
and disease-causing structural variation in the human
genome. The long-term goal of his research is to understand
the evolution and mechanisms of recent gene duplication and
its relationship to copy number variation and human disease.
Peter Goodhand
Peter Goodhand is a leader in the global health sector as a
senior executive and board member in the health research
advancement community.
Goodhand played a key role in the creation of the Global
Alliance to accelerate progress in genomic research and
medicine and in June 2013, he was appointed acting
Executive Director of the Alliance for its critical development
phase.
He is currently Chair of the Board of HTX; Chair of the
Steering Committee of the Occupational Cancer Research
Center; Board Member, MaRS EXCITE (Excellence in Clinical
Innovation and Technology Evaluation); and works with the
Institute of Corporate Directors to advance governance within
the not-for-profit sector.
He served as board Chair and President of Canada’s Medical
Device Industry association (MEDEC), chaired the
Government of Canada’s Expert working group on the future
Anders Eriksson
Anders Eriksson obtained his PhD from University of
Gothenburg. He now has a postdoc shared between Andrea
Manica’s group at University of Cambridge and Timothy
34
of medical isotope production, and was a member of the
Canadian delegation to the UN summit on non-communicable
diseases.
Goodhand had a 12-year experience as a patient advocate,
caregiver and navigator throughout his family’s battle with a
rare cancer.
at Biofields, and Council Member in Biotechnology to the
United Nations Secretary General.
Kazuto Kato
Abdelbagi M. Ismail
Kazuto Kato, PhD is Professor of Biomedical Ethics and Public
Policy at the Graduate School of Medicine, Osaka University,
Japan. He is also Project Professor of the Institute for
Integrated Cell-Material Sciences (iCeMS) at Kyoto University.
He has a PhD degree in developmental biology from Kyoto
University. After finishing postdoctoral research at the
University of Cambridge with Sir John Gurdon, he started to
work on the ethical and social issues of genomics and stem
cell research. He has been serving as members of various
international projects/academic societies such as Ethics
Committee of Human Genome Organization (HUGO)
(Currently, HUGO Committee on Ethics, Law and Society), ELSI
group of the International HapMap Project. In 2010, he was
appointed as a member of the Expert Panel on Bioethics of
the Council for Science, Technology and Innovation Policy
(CSTP) of the Cabinet Office, Japan.
Principal Scientist at IRRI, Philippines. His research focuses on
developing rice varieties adapted to less favorable
environments. Holds a PhD in Botany, University of California,
Riverside (UCR), worked at UCR (1993-2000) and joined IRRI
in 2000. Associate Editor for the Annals of Botany-PLANTS
and Guest Editor for several other journals. Recipient of two
Medals and 3 Best Scientific Article Awards. Member of
several international societies including ISPA, CCSA, ASA and
ASPB
Gerardo Jimenez-Sanchez
Partha P. Majumder
Professor Gerardo Jimenez-Sanchez is the Executive President
of Global Biotech Consulting Group and an Adjunct Professor
of Genomics and Bioeconomy in the Department of
Epidemiology at Harvard School of Public Health. He is a
certified pediatrician, with a PhD in Human Genetics and
Molecular Biology from Johns Hopkins University, and has a
degree in business administration. He serves the Chairman of
the Board of Genomica y Bioeconomia, as a Council member
to the Human Genome Organization (HUGO), and chairs its
Committee on Genomics and Bioeconomy. He is a member of
the Medical and Scientific Board to the Social Security and
Social Services Institute in Mexico, and a member of the
National Academy of Medicine. At the Organization for
Economic Cooperation and Development (OECD), he served
as President of the Working Party on Biotechnology (20062013), and he was a Member of the Scientific Council for the
Grand Challenges in Genomics at the World Health
Organization. He was the founder Director General of the
National Institute of Genomic Medicine in Mexico, Director of
the Mexican Genomic Diversity Project, Chief Scientific Officer
PARTHA MAJUMDER is the founding Director of the National
Institute of Biomedical Genomics, India, and Professor of the
Indian Statistical Institute. He has made seminal contributions
to human and population genetics He is an elected Fellow of
all science academies of India, of The World Academy of
Sciences and the International Statistical Institute. He is a
Council Member of the Human Genome Organisation. He is
the Indian National Coordinator on the International Cancer
Genome Consortium.
35
followed by a Ph.D. degree in microbiology and immunology
from Baylor College of Medicine in 1998, where he was hired
as a tenure-track faculty member in 2006. As a Principal
Investigator for the Human Microbiome Project, Dr. Petrosino
assisted in the lead of consortium efforts for standardized
clinical sample preparation, sequencing, and analysis, which
are now being implemented in new studies internationally.
Dr. Petrosino launched the CMMR in January 2011. Currently,
the CMMR is pursuing over 230 metagenomics projects in
humans and model systems with the goal to improve human
health through detection and modulation of the microbes
that reside on and in us and to translate these efforts into
new diagnostics and therapeutics. Among the latest CMMR
projects initiated is an $11.8M microbiome analysis of Type 1
Diabetes samples from the NIH/NIDDK TEDDY (The
Environmental Determinants of Diabetes in the Young) study.
Timothy Mercer
Dr. Mercer leads a research team at the Garvan Institute of
Medical Research (Sydney), with interests in genome and
RNA biology (including long noncoding RNAs, gene
organization and splicing), and bioinformatic and sequencing
innovations. Dr. Mercer received his PhD at the University of
Queensland (Brisbane) and has undertaken research at
Harvard University (Cambridge), Max Planck Institute for
Molecular Cell Biology and Genetics (Dresden) and Centre for
Genome Regulation (Barcelona).
Firdausi Qadri
Dean Nizetic
Dr. Firdausi Qadri is the Director, Centre for Vaccine Sciences
at the International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b). She obtained her PhD in Biochemistry
from the University of Liverpool in 1980. Dr. Qadri began her
academic career in 1981 as faculty in the Department of
Biochemistry, University of Dhaka and then joined icddr,b in
1986 as a postdoctoral research fellow and since then has
worked her way up to her current title of Senior Scientist and
to lead researchers in the Centre for Vaccine Sciences. She
and her team have made significant contributions to
international scientific research, particularly in the field of
infectious diseases with emphasis on infections which are
very common in children in developing countries. Her work
includes basic and applied immunology of infectious diseases
but also clinical and large field based studies on enteric
vaccines. In the last 3 years she has been leading the largest
field studies in over 400,000 participants of an oral cholera
vaccine in an urban slum in Bangladesh-to pave the way
forward for introducing cholera vaccine in high risk people in
the country and in the near future in the region and globally.
Her work also involves her devotion to an initiative that she
has set up known as the “Institute for developing science and
health initiatives” (ideSHi). The primary focus at ideSHi is on
the development of science and technology in Bangladesh
and encouraging scientists to work in the field of biomedical
sciences and also by using the facilities in the ideSHi and
icddr,b laboratories and through networking with other
institutions in the government and private sector. A large part
of her career has been focused in developing leaders in the
field infectious disease research from different disciplines and
institutions. She also has inspired many young scientists
through her teaching and research activities. Her penchant
for mentoring can be seen in her lab and field sites where
Prof. Nizetic M.D., Ph.D. is one of the leading researchers and
opinion-makers in molecular research into Down’s Syndrome
(DS), in particular its relation to stem cell pathology, ageing
and cancer (Nature Rev. Cancer 2012, AJHG2008). His team
generated isogenic induced-pluripotent-Stem-cells (iPSC)
from an adult with mosaic DS. Prof. Nizetic is currently
leading the iPSC–cellular modelling stream within the
LonDownS
consortium
(see
http://www.ucl.ac.uk/londowns/research-themes/cellular).
Joseph Petrosino
Joseph F. Petrosino, Ph.D., is an Assistant Professor of
Molecular Virology and Microbiology at Baylor College of
Medicine where he is also the director of the Alkek Center for
Metagenomics and Microbiome Research (CMMR). He
obtained his undergraduate degree in microbiology and
immunology from the University of Rochester in 1993
36
aspiring fellows from both local and international universities,
join her team as interns and later move on to faculty
positions globally.Research Areas: Her major interests are on
vaccine and infectious disease research and implementation
of findings in developing country settings. Emphasis is on
cholera, enterotoxigenic Escherichia coli diarrhea, enteric
fever due to S. Typhi/Paratyphi and other pathogens common
in the setting and for which knowledge is needed.
Understanding the natural course of immune responses
involving innate immunity, adaptive immunity, T and B cell
responses, genomic, proteomic and high throughput studies.
Implementation of vaccines and rapid diagnostics in
developing countries including technology transfer is her aim
and aspiration so as to benefit the LDCs.
Michael Snyder
Michael Snyder is the Stanford Ascherman Professor and
Chair of Genetics and the Director of the Center of Genomics
and Personalized Medicine. Dr. Snyder received his Ph.D.
training at the California Institute of Technology and carried
out postdoctoral training at Stanford University. He is a leader
in the field of functional genomics and proteomics, and one
of the major participants of the ENCODE project. His
laboratory study was the first to perform a large-scale
functional genomics project in any organism, and has
developed many technologies in genomics and proteomics.
These including the development of proteome chips, high
resolution tiling arrays for the entire human genome,
methods for global mapping of transcription factor binding
sites (ChIP-chip now replaced by ChIP-seq), paired end
sequencing for mapping of structural variation in eukaryotes,
de novo genome sequencing of genomes using high
throughput technologies and RNA-Seq. These technologies
have been used for characterizing genomes, proteomes and
regulatory networks. Seminal findings from the Snyder
laboratory include the discovery that much more of the
human genome is transcribed and contains regulatory
information than was previously appreciated, and a high
diversity of transcription factor binding occurs both between
and within species. He has also combined different state-of–
the-art “omics” technologies to perform the first longitudinal
detailed integrative personal omics profile (iPOP) of person
and used this to assess disease risk and monitor disease
states for personalized medicine. He is a cofounder of several
biotechnology companies, including Protometrix (now part of
Life Tehcnologies), Affomix (now part of Illumina), Excelix,
and Personalis, and he presently serves on the board of a
number of companies.
Kanury V. Rao
Dr. Kanury Rao's primary research interest is to use the tools
of systems analysis to understand the mechanisms by which
Mycobacterium tuberculosis adapts within the hostile
intracellular milieu of the host macrophage. To this end, he
integrates a range of high-throughput biology approaches
including genome-wide RNAi screen, proteomics, lipidomics,
and metabolomics, by employing computational and
mathematical tools.
John Rasko
Professor Rasko is an Australian pioneer in the application of
adult stem cells and genetic therapy. He directs the
Department of Cell and Molecular Therapies at Royal Prince
Alfred Hospital and heads the Gene and Stem Cell Therapy
Program at the Centenary Institute, University of Sydney.
John Rasko is a clinical hematologist, pathologist and
scientist. In over 150 publications he has contributed to the
understanding of stem cells and haemopoiesis, gene transfer
technologies, oncogenesis, human aminoacidurias and noncoding RNAs.
He serves on Hospital, state and national bodies including
Chair of GTTAC, Office of the Gene Technology Regulator –
responsible for regulating all genetically-modified organisms
in Australia. He is the recipient of national and international
awards in recognition of his commitment to excellence in
medical research, including appointment as an Officer of the
Order of Australia.
Himla Soodyall
Himla is a Medical Scientist in the Division of Human Genetics
at the NHLS and holds a joint appointment as Associate
Professor at Wits.
37
Nicole Soranzo
Meow-Keong Thong
Nicole uses genetic analysis of high-dimensional phenotypic
and genetic datasets to unravel genetic predisposition to
quantitative traits that are risk factors for cardiometabolic
diseases, principally coronary artery disease and type 2
diabetes. The aim of this research is to advance
understanding of biologic processes underlying disease
aetiology addressing genetic and physiologic influences, and
to explore the use of this genetic information in clinical
care.Nicole graduated in biological sciences at the University
of Milano, Italy, with a dissertation on plant population and
evolutionary genetics. She later obtained a PhD in genetics
from the University of Dundee, and undertook post-doctoral
training in human population and statistical genetics at
University College London, conducting applied and
methodological work in evolutionary genetics and association
studies. In 2005 Nicole joined the pharmacogenomics
department at Johnson and Johnson Pharmaceutical
Research and Development (Raritan, USA). In 2007 she joined
the Wellcome Trust Sanger Institute, and since 2009 she has
led her own team. In 2013 Nicole was additionally appointed
as Principal Research Associate at the School of Clinical
Medicine of the University of Cambridge.
Dr THONG Meow-Keong is a Professor of Paediatrics and
Consultant Clinical Geneticist at the University of Malaya
Medical Centre. He is a board-certified clinical geneticist, and
was a Fulbright scholar and the current President of the AsiaPacific Society of Human Genetics and Vice-President of the
Medical Genetics Society Malaysia. He established the first
Genetics Clinic in 1995. He published extensively and worked
with the WHO and Ministry of Health in developing genetic
management modules.
Hugo A. Volkaert
M. Sc. Degree in Agricultural Engineering - Forestry, from
Katholieke Universiteit Leuven, Belgium, 1988
Ph. D. degree (Forest Resources) from the University of
Maine, USA, 1995.
I have been researching genetic diversity in Thailand at MaeJo
University in ChiangMai (1996-1999), at the Rice Gene
Discovery Center (1999-2001) and since than at Center for
Agricultural Biotechnology, Kasetsart University.
Interest in forest trees (teak, Xylia, Dalbergia,
Dipterocarpaceae), bananas, stingless bees etc.
Masayo Takahashi
Jun Wang
Masayo Takahashi Project leader, Laboratory for Retinal
Regeneration Research at RIKEN. She received her M.D. from
Kyoto University in 1986, and her Ph.D. in 1992. After serving
as an assistant professor in the Department of
Ophthalmology, Kyoto University Hospital, she worked in the
Salk Institute for two years, where she discovered the
potential of stem cells as a tool for retinal therapy. After she
went back and begun her research in Kyoto University, she
joined RIKEN in 2006.
Jun Wang is the Director of the BGI (previously known as the
Beijing Genomics Institute). He was instrumental in the 1999
founding and the growth of the BGI Bioinformatics
Department, which is now widely recognized as one of
world’s premier research facilities committed to excellence in
genome sciences. Dr. Wang also holds a position as an Ole
Römer professor at the University of Copenhagen. He has
authored 200+ peer-reviewed original papers – of which 100+
are published in Cell, Nature (including Nature series), N Engl
38
J Med., and Science (26 as cover story). He has been
recognized with an award from His Royal Highness Prince
Foundation, Nature’s 10 - the year in Science (2012); “Highly
Cited Researchers (2013/2014)” “The Hottest Scientific
Researchers of 2012” (by Thomson Reuters), “Rebels, leaders,
innovators for the next 25 years” (by CNBC), “Fortune’s 40
under 40” from Fortune Magazine (2013), Lundbeck Talent
Price, Outstanding Science and Technology Achievement from
the Chinese Academy of Sciences, Outstanding Technical
Talent, ZhouGuangZhao Award, TanJiaZeng Life Science
Innovation Award, Top 10 Scientific Achievements In China,
Major Award from Shenzhen Municipal Government, The first
“TopSUN” Scientific Paper Award from Peking University, Tan
Jiazhen Life Science Award from Fudan University, and Prize
for Important Innovation and Contribution from Chinese
Academy of Sciences. His research focuses on genomics and
related bioinformatics analysis of complex diseases and
agricultural crops, with the goal of developing applications
using the genomic information.
Hub Zwart
Hub Zwart (1960) is Philosophy Professor at the Science
Faculty, RU Nijmegen (Netherlands). He established / directed
the Centre for Society and Genomics (CSG) and the Institute
for Science, Innovation & Society (ISIS) and joined the HUGO
Committee on Ethics (CELS). He studies the philosophical
dimensions of life sciences (genomics, synthetic biology,
neuro-science). Special attention is given to genres of the
imagination (novels, cinema, drama, art) as laboratories for
philosophical
research.
39
ABSTRACT BOOK
SPEAKERS ABSTRACTS
SPK01 - SPK27
ORAL PRESENTATIONS
Sunday 15 March 2015
Epigenetics
Personalised Medicine / Pharmacogenomics
Oral Presentations I
O01 - O03
O04 - O06
O07 - O18
Monday 16 March 2015
Population Genetics & Statistics
Cancer Genomics
Oral Presentations II
O22 - O24
O25
O19 - O21
&O29 - O33
Tuesday 17 March 2015
Non-Coding & RNA Biology
O34 - O36
POSTER PRESENTATIONS
Poster Session 1 – Saturday 14 to Sunday 15 March 2015
Bioinformatics
Complex Genetics
Epigenetics
Ethics and Genomics
General Genetics & Genomics
Mendelian Genetics
Microbial Genomics
P001 - P007
P008 - P018
P019 - P025
P026 - P030
P031 - P066
P067 - P075
P076 - P081
Poster Session 2 – Monday 16 to Tuesday 17 March 2015
Big Data
Cancer Genomics
General Genetics & Genomics
Genomics Technologies
Non-Coding RNA
Personalised Medicine
Pharmacogenomics
Populations Genetics
RNA Biology
P082 - P085
P086 - P111
P112 - P116
P117 - P122
P123 - P126
P127 - P129
P130 - P137
P138 - P160
P161 - P163
40
SPK01
THE ROLE OF GENOMICS IN THE BIOECONOMY
1 2,*
G. Jimenez-Sanchez
1
Global
Biotech
Consulting
Group,
Mexico,
2
Mexico Genomica y Bioeconomia, Mexico, ,
productivity and combating poverty. This presentation
will discuss our progress in developing varieties tolerant
of complete submergence for 1 to 2 weeks, which
regularly devastate over 20 million ha of rice in Asia.
Significant progress was made in identifying tolerant
donors and several tolerant breeding lines were
developed through standard breeding methods over the
past three decades, but were not widely adopted. An
important turning point was the mapping of the SUB1
locus in mid 1990s, followed by its cloning and functional
analyses. SUB1 harbors 3 ethylene responsive factors
(ERFs), with SUB1A as the primary provider of tolerance.
Cloning of SUB1A facilitated the development of
functional markers used for its transfer into high-yielding
varieties; and their subsequent deployment to farmers.
SUB1 confers tolerance of complete submergence for 4
to 20 days, with no undesirable consequences, from a
week after seeding until just before heading. Its
effectiveness was validated in farmers’ fields with yield
-1
advantages of 1 to over 3 t ha . Eight Sub1 varieties were
developed in the background of varieties popular in Asia;
most of them were commercialized in several countries.
These varieties are spreading fast since the release of the
first one in India in 2009, currently grown by over 4
million farmers. The choice of popular varieties for
deploying SUB1 and its consistent performance over
variable environments contributed considerably to this
success. Adoption of these varieties in flood-affected
areas significantly contributed to production stability and
food security, and provided opportunities for new
livelihood options. These varieties are benefiting
extremely poor farmers and low social groups who are
forced to live in less favorable areas at high population
densities. Our goal is to develop more resilient varieties
that can withstand multiple stresses and produce more
rice from worsening natural resources to meet the everincreasing global demand for food
Abstract: The impact of genomics on the economy is
becoming more and more significant in the industrialized
world. The drop in sequencing costs and the increase in
the number of species sequenced had propelled
genomics-based innovation. Applications to improve
healthcare, agriculture, environment, meet, and milk
production, and the generation of valuable chemical
molecules are beginning to emerge. The wide range of
potential applications suggests that genomics can
contribute to meet global challenges and become a
valuable component to the economy. Recent studies
show that the investment made by the United States
government in the Human Genome Project since 1988
has led to a return close to $140 for every dollar, a sum
close to one trillion dollars. In 2009, the Organization for
Economic Cooperation and Development (OECD)
published a policy agenda to develop a bioeconomy and
interest has been growing since. In 2012, the United
States published its bioeconomy blueprint, and the
European Union elaborated a similar strategy. Several
other nations, including Belgium, Canada, Germany, the
Netherlands and South Africa, have also developed their
own bioeconomy strategies. In all of them, genomics is
predicted to play a major role in economic development.
To turn the aspirations of genomics into real products
and services there are a number of challenges to
overcome. These include a qualified workforce, sustained
investments, public-private partnerships, the ability to
coordinate efforts around multidisciplinary initiatives, as
well as a forward-looking political and societal vision to
ensure the appropriate and timely development of
genomics applications that will contribute to meet basic
human needs in the coming future (Jimenez-Sanchez G &
Philp J. EMBO Rep. 2015 Jan;16(1):17-20).
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
SPK03
THE POTENTIAL OF BANANA GENOMICS INFORMATION
AS A TOOL IN BREEDING.
1 2,*
H. A. Volkaert
1
Plant Research Unit, NSTDA-BIOTEC, Pathumthanee,
2
Center of Excellence in Agricultural Biotechnology,
Kasetsart University, Kamphaengsaen, Thailand
SPK02
DEVELOPMENT OF SUBMERGENCE TOLERANT RICE AND
ITS SOCIOECONOMIC IMPACT
1,*
A. M. Ismail
1
Crop and Environmental Sciences, INTERNATIONAL RICE
RESEARCH INSTITUTE, Metro Manila, Philippines
Abstract: Bananas are a very important subsistence crop
for 100s of millions of people living in tropical regions of
Asia, Africa and Latin America. Bananas are also a very
important fruit commodity on the international market,
even though that represents a mere 15-20% of the total
production. Bananas originated from wild ancestors
growing in the forests of Southeast Asia, mostly Musa
acuminata (A genome) with or without hybridization
with M. balbisiana (B genome) and some other species,
generating diploid and triploid seedless fruit-bearing
cultivars with AA, AAA, AAB, ABB, AB, BB genome
Abstract: Flooding is one of the major abiotic stresses
constraining rice production in Asia and in Africa, and its
effects are foreseen to worsen progressively with climate
change. Early floods can lead to poor crop establishment,
and during vegetative stage, even partial floods can be
devastating if they persist for long duration. Transient
complete submergence causes high mortality and large
yield losses. Breeding varieties tolerant of these different
types of floods is of high priority for enhancing
41
compositions. Since the time of their origin, these plants
were propagated vegetatively and carried across the
lands and oceans by wandering human populations to
Hawai, Madagascar, East Africa and West Africa in prehistoric times and more recently to Latin America. This
vegetative propagation over long times and large areas
has severely restricted genetic diversity and made
bananas vulnerable to various diseases (Fusarium,
Mycosphaerella, viruses) and limited their adaptation to
adverse climatic conditions such as drought. As bananas
are seedless and for most important cultivars also
triploid, plant improvement through crossing and
selecting among segregating populations is extremely
difficult. In such situations molecular tools, including
marker assisted selection, association mapping or
genome-wide selection could probably be used to
increase the efficiency of selection. Although the genetic
diversity of cultivated bananas has been studied in some
detail, the relationships between the diversity in the
cultivars and the wild populations have not been
clarified. Until this has been done properly, it will be
extremely difficult to introduce beneficial traits that exist
in the wild populations into the cultivated bananas.
Disclosure of Interest: None Declared
epistemological level (i.e. the level of the ‘desire to
know’), this complies with Lacan’s understanding of
science as the relentless ‘symbolisation of the real’,
culminating in the representation of living beings in
digital formats, that is: in terms of 1s and 0s (denoting
presence or absence of elementary constituents). This
will be elucidated using three post-HGP case studies:
epigenomics (BLUEPRINT), connectomics (HBP) and
“complexomics”. Subsequently, I will address the
implications for the ethical domain. The composite
generalised reference human of the HGP, I will argue,
corresponded with the generalised reference agent of
standard (‘normal’) ethics. We are now moving away
from this in two directions. On the one hand towards a
micro-ethics of the life-world (focussing on practices of
the self, self-management and identity); on the other
hand towards a macro-ethics of large-scale, automated
data management, where human agency becomes
increasingly marginalised (focussing on transparency,
accessibility and cost reduction). Question: if the current
human condition can indeed be assessed in terms of
fragmentation and anonymisation, what does this entail
for moral virtues such as solidarity?
Disclosure of Interest: None Declared
SPK04
TOWARDS A HUGO STATEMENT ON SOLIDARITY AND
BIG DATA
1,*
R. Chadwick
1
University of Manchester, Manchester, United Kingdom
SPK06
SEQUENCING IN COHORTS REVEALS GENERALIZED
GENETIC MODELS OF HUMAN DISEASE
1 2,*
E. Boerwinkle
1
Human Genetics Center, The University of Texas Health
2
Science Center at Houston (UT Health), Human Genome
Sequencing Center, Baylor College of Medicine, Houston,
United States
Abstract: The era of big data has brought with it changes
in the way that research is conducted, and associated
modifications in types and level of risk, privacy and
storage issues. In this context it is necessary to explore
the ways in which ethical principles are applicable. This
Statement will examine, in particular the principle of
solidarity in relation to big data. Solidarity has,
historically, been a very important principle for HUGO.
When and how should data be shared, and what are the
contra-indications? How can the use of genomic data be
maximised for public good? The Statement will consider
a number of scenarios including the use of genomic and
methylation data.
Disclosure of Interest: None Declared
Abstract: The relative contribution of variants of
different frequencies to common chronic diseases is a
central question in human genetics. We formalized this
discussion with the clan genomics hypothesis that
recognizes that rare alleles with large effects on disease
risk and pathology arose in recent ancestors and have
profound impact on human health and disease (PMID:
21962505). Accumulated exome and whole genome
sequences from deeply-phenotyped individuals provide
data to test this hypothesis, since the model is supported
if rare alleles can be detected and shown to greatly
influence phenotypes related to common disease risk
and risk factor levels. Two complimentary study designs
are informative: family-based whole exome sequencing
(WES) in both our CLIA/CAP certified clinical sequencing
laboratory and in the research arena (N >10,000 cases)
and WES/WGS in large multiethnic longitudinal cohort
studies (N>20,000 participants). Each provides
supportive data for the clan genomics hypothesis. Family
studies reveal complex phenotypes arising from
compounded mutations at multiple loci; contributions
from rare CNVs; an under-appreciated burden of de novo
mutations; and an excessive carrier burden that explains
some syndromic cases without simple Mendelizing
disease. The data from large cohorts show examples of
SPK05
FRAGMENTATION,
ANONYMISATION
AND
DIGITALISATION: IMPLICATIONS FOR RESEARCH ETHICS
1,*
H. Zwart
1
Faculty of Science; Department of Philosophy, RADBOUD
UNIVERSITY NIJMEGEN, Nijmegen, Netherlands
Abstract: In the post-HGP era, the focus has shifted
towards big systematic data analysis in various –omics
fields: a style of research that is captured in metaphors
of fluidity, such as: ‘trawling’ data, ‘drowning’ in data and
the shift from ‘substance’ to ‘data flow’. On the
42
rare alleles that contribute to endophenotypes, including
metabolite fluctuations (PMID: 25575548) and protective
variants that lower disease risk (PMID: 25587968).
Together these detailed genetic and phenotypic data sets
are substantiating generalized models for the genetic
architecture of common disease.
Disclosure of Interest: None Declared
SPK08
GENOMICS OF IMMUNE RESPONSE TO VACCINES FOR
ENTERIC MICROBES
1,*
P. P. Majumder
1
NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS,
Kalyani, India
Abstract: To assess the role of genomic factors
associated with immunological response to typhoid and
cholera vaccines, we have conducted two large studies in
India. Typhoid: Significant associations of response with
SNPs in 7 genes (DEFB1, TLR1, IL1RL1, CTLA4, MAPK8,
CD86, IL17D) were discovered and cross-validated. These
genes are involved in polysaccharide recognition, signal
transduction, inhibition of T-cell proliferation, proinflammatory signaling and eventual production of
antimicrobial peptides. Cholera: Significant associations
of SNPs and haplotypes in three genes (MARCO,
TNFAIP3, CXCL12) with response were discovered and
validated. LPS, present in the vaccine, is a potent
activator of innate immune responses and a ligand of
MARCO. CXCL12 is a neutrophil and lymphocyte
chemoattractant that is upregulated in response to V.
cholerae infection. LPS in the vaccine possibly provides
signals that mimic those of the live bacterium. TNFAIP3
promotes intestinal epithelial barrier integrity and
provides tight junction protein regulation; possible
requirements for adequate vaccine-response.
SPK07
SCALING METAGENOMICS FOR POPULATION STUDIES
1,*
J. Petrosino
1
Baylor College of Medicine, Houston, United States
Abstract: The Alkek Center for Metagenomics and
Microbiome Research (CMMR) at Baylor College of
Medicine is leading research and development efforts in
the study of how commensal microbes (ie. the
microbiome) impact health and disease. Among these
efforts are the benchmarking and validation of preanalytical (i.e. biospecimen collection and stabilization),
in vitro and in silico strategies to engage large, complex
cohorts and unique sample sources. Through local and
international collaboration, CMMR researchers are also
advancing over 230 diverse clinical and basic research
projects. Among the study of various GI diseases,
autoimmune disease, neurodevelopmental disorders,
and cancer, among others, we have multiple ongoing
efforts
looking
at
the
link
between
the
microbiome/virome and type 1diabetes (T1D, also known
as juvenile diabetes).
Disclosure of Interest: None Declared
The incidence of T1D and other immunity-related
diseases has increased dramatically in the world in the
last 50 years while infectious diseases have declined.
These trends cannot be explained by genetic factors
alone, but suggest that the modern environment has
changed leading to this increased risk. The link between
our genetic blueprint, in utero exposures, and the
development of our microbiome in early life sets our
baseline health state. Increased gut permeability,
intestinal inflammation and deregulated oral tolerance
have all been observed in children with T1D.
Furthermore, data support the hypothesis that an
infectious trigger may be responsible for the emergence
of autoantibodies that ultimately lead to the decline to
T1D. In the largest clinical microbiome study to date,
including virus culturing and mycobiome components,
we explore the comprehensive taxonomic and functional
changes in the microbiome between birth and T1D onset
in over 13,403 stool and 6,380 plasma samples from a
subset of cases and controls (1:1; n=820) from the TEDDY
international prospective cohort. Preliminary results
examining 16S rRNA gene, and bacterial/viral
metagenomic data exploring the developmental
microbiome in this cohort, including the impact of
country of origin and breastfeeding have identified a
significant difference in microbial richness and evenness
across countries (p
Disclosure of Interest: None Declared
SPK09
DECIPHERING THE HOST-PATHOGEN INTERPLAY IN
HUMAN
MACROPHAGES
INFECTED
WITH
MYCOBACTERIUM TUBERCULOSIS
1,*
K. V. Rao
1
Immunology, International Centre for Genetic
Engineering and Biotechnology, Delhi, India
Abstract: Despite decades of intervention programs,
Mycobacterium tuberculosis (Mtb) persists as an
enduring pathogen in the human population. Infection is
initiated through inhalation of the pathogen as an
aerosol, following which Mtb enters the lung and infects
alveolar macrophages. Although macrophages constitute
the primary defense against microbial invasion, the
pathogen Mycobacterium tuberculosis (Mtb) has evolved
effective mechanisms to attenuate or inhibit the diverse
anti-microbial pathways initiated by the host cell. This
attenuation is mediated through active engagement with
several biochemical pathways of the host cell. Resolution
of these interactions is important for the development of
more effective strategies for TB control. To this end, we
performed a genome-wide siRNA screen to identify host
factors that regulated pathogen load in human
macrophages infected with a virulent strain of
Mycobacterium tuberculosis. Iterative rounds of
confirmation, followed by validation, identified 275 such
molecules that were all found to functionally associate
43
with each other through a dense network of interactions.
This network then yielded to a molec- ular description of
the host cell functional modules that were both engaged
and perturbed by the pathogen. Importantly, a
subscreen against a panel of field isolates revealed that
the molecular composition of the host interface varied
with both genotype and the phenotypic properties of the
pathogen. An analysis of these differences, however,
permitted identification of those host factors that were
invariantly involved, regardless of the diversification in
adaptive mechanisms employed by the pathogen.
Interestingly, these factors were found to predominantly
function through the regulation of autophagy.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
SPK12
THE GLOBAL ALLIANCE FOR GENOMICS AND HEALTH
1
2
3
4
M. Bobrow , D. Altshuler , K. North , P. Goodhand , P.
5
6
7
8,*
Flicek , D. Haussler , T. Hudson , K. Kato , B. Knoppers
9
10
11
12
, B. Margus , E. Nabel , C. Sawyers
1
University of Cambridge, Cambridge, United Kingdom,
2
Broad Institute of Harvard MIT, Cambridge, United
3
States, Murdoch Childrens Research Institute, Parkville,
4
Australia, Global Alliance for Genomics and Health,
5
Toronto, Canada, European Bioinformatics Institute,
6
Cambridge, United Kingdom, University of California,
7
Santa Cruz, United States, Ontario Institute for Cancer
8
Research, Toronto, Canada, Osaka University, Osaka,
9
10
Japan, McGill University, Montréal, Canada, A-T
11
Children’s Project, Coconut Creek,
Brigham and
12
Women’s Hospital, Boston, Memorial Sloan Kettering
Cancer Center, New York, United States
SPK10
INSIGHTS FROM METHYLOME ANALYSIS
1,*
S. Beck
1
UCL Cancer Institute, University College London, London,
United Kingdom
Abstract: What determines a phenotype is one of the
fundamental questions in biology and medicine. In
addition to genetic variants, epigenetic variants such as
altered DNA methylation have been shown to play
important roles. To understand the rules governing DNA
methylation and their functional consequences in health
and disease requires genome-wide analysis of
methylome dynamics. I will present our efforts using
array- and sequencing-based platforms for methylome
analysis and discuss insights for translational,
regenerative and personalized medicine.For further
details,
please
see:
http://www.ucl.ac.uk/cancer/medical-genomics/me
Disclosure of Interest: None Declared
Abstract: The Global Alliance for Genomics and Health is
an international, non-profit alliance formed to help
accelerate the potential of genomic medicine to advance
human health. Bringing together over 250 leading, global
organizations working in healthcare, research, disease
and patient advocacy, life science, and information
technology, members in the Global Alliance are working
together to create a common framework of standards
and harmonized approaches to enable the responsible,
voluntary, and secure sharing of genomic and clinical
data. There are currently four active Working Groups:
Regulatory and Ethics, Data, Security, and Clinical. These
Working Groups are charged with producing thoughtful,
actionable conclusions and products in their respective
work
areas.
Learn
more
at:
http://genomicsandhealth.org.
Disclosure of Interest: None Declared
SPK11
THE BLUEPRINT EPIVAR PROJECT
1 2,*
N. Soranzo
and BLUEPRINT EpiVar Working Group
1
2
Wellcome Trust Sanger Institute, Department of
Haematology, NHS Blood and Transplant, University of
Cambridge, Cambridge, United Kingdom
SPK13
PERSONALIZED MEDICINE IN CLINICAL PRACTICE:
DELIVERING ON THE PROMISE
1,*
M.-K. Thong
1
Paediatrics, University of Malaya, Kuala Lumpur,
Malaysia
Abstract: Homeostatic regulation of the hematopoietic
system is tightly controlled within a healthy individual by
a host of genetic and non-genetic factors. The
BLUEPRINT EpiVar project aims to elucidate how genetic
variants affect hematopoietic development through
transcriptional programs, focusing on the three most
abundant cells of the immune cell system, and namely
monocytes, neutrophils and CD4+ T-cells. We have
purified the three cell types from 200 healthy blood
donors, and used sequencing-based assays to
characterise their genomes, methylation status,
epigenetic marks and transcriptomic changes. Here I will
present results of interim analyses for this project,
discussing how these data impacts on understanding of
the genetic predisposition to common, complex disease.
Abstract: Personalized medicine is determined by an
individual’s unique clinical, genomic and environmental
information. The molecular understanding of diseases
allowed development of preventive healthcare strategies
and medical treatments at the pre-symptomatic or
earliest stage of the disease. To achieve this promise,
DNA-based risk assessment, molecular profiling, targeted
therapies and dose selection of therapeutic agents were
developed to facilitate customization of patient care.
Commercially available genomic tests routinely are
applied across a wide range of disease states in
predictive or prognostic applications.
Many clinicians were concerned about the lack of
progress in the clinical application of genomic medicine.
The development of genomic diagnostic tools such as
44
array comparative genomic hybridization, exome and
whole genome sequencing had a vital role to play in the
delineation of new Mendelian loci for previously
unrecognized syndromes or identification of additional
genes or loci contributing to known disease entities.
While the costs of these tests had decreased, the
interpretation of information of uncertain significance
may
require
increased
‘genomic
counseling’
consultations to allay anxiety.
Personalized medicine at present has limited roles in
complex disorders or used as a tool lifestyle change
decisions as public health or primary care professionals
who may not be sufficiently ‘genomic-trained’. Genomic
health risk assessments and statistical probabilities are
difficult for clients to understand and personalized
medicine must be integrated into the existing health
systems and clinical workflow with significant changes
required in regulatory and reimbursement policies as
well as legislative protection related to patient’s
confidentiality. The difficulties with use of genome-wide
association studies in clinical practice, with its limited
phenotype-genotype impact is known.
Personalized medicine is unlikely to revolutionize
traditional clinical practice; it will evolve to deliver on the
promise of a safer and effective healthcare for the
individual patient.
Disclosure of Interest: None Declared
transgene expression using vectors with zero CpG,
chromatin insulators, and by selecting appropriate cells
will also be discussed.
Disclosure of Interest: None Declared
SPK15
AUTISM SPECTRUM DISORDERS: NEW MUTATIONS,
GENES AND SUBTYPES
1,*
E. E. Eichler
1
Department of Genome Sciences and Howard Hughes
Medical Institute, University of Washington, Seattle,
United States
Abstract: I will summarize our recent findings regarding
the discovery of genetic mutations and their contribution
to autism spectrum disorder (ASD) and intellectual
disability (ID). Our analysis of 30,000 children with
ASD/ID suggests that between 8-14% of disease is caused
by inherited or de novo deletions and duplications of
large segments of the genome involving multiple genes. I
will present evidence from exome and molecular
inversion probe sequencing of more than 10,000 children
with simplex autism and show how these data may be
used to pinpoint specific genes. The emerging data
strongly argue that the development of the human brain
is particularly sensitive to the timing and expression of
many different genes; multiple genetic perturbations
within specific neurodevelopmental pathways related to
long-term potentiation, chromatin remodeling and WNT
signaling appear particularly important; and that the
maternal and paternal contributions differ significantly. I
will present data on how grouping patients based on a
specific gene can be used to predict clinical subtypes of
autism. The flood of recent data and candidates provides
a powerful path forward for understanding the genetic
architecture of these diseases but the heterogeneity
demands an unprecedented level of global cooperation
and networking.
Disclosure of Interest: None Declared
SPK14
EPIGENETIC INFLUENCES ON GENE THERAPY
1,*
S. Abdullah
1
Genetics & Regenerative Medicine Research Centre,
Faculty of Medicine & Health Sciences, Universiti Putra
Malaysia, Kuala Lumpur, Malaysia
Abstract: Much attention and considerable promise has
been given to the field of gene therapy since its first
successful clinical trial in 1990. Since then, a great
number of in vitro and animal studies have provided
proofs of concept for many potential disease curative
applications. Unfortunately, the clinical progress has
been very slow due to many setbacks. One of the major
challenges for gene therapy is the short-lived expression
of the therapeutic DNA (transgene), in both episomal and
integrating gene delivery contexts. In addition, variation
in the levels of transgene expression from integrating
system is also observed among the individual clones of
transgene-harboring cells. Growing evidence indicates
that these phenomena are due to the host’s epigenetic
influences on the therapeutic DNA at transcriptional
level. Verification on the importance of epigenetics in the
regulation of therapeutic DNA gene expression comes in
part from the study of reporter transgene. This talk
reviews the different factors, both host-dependent and
vector dependent, and the interplay between DNA
methylation and chromatin modification which are
known to contribute to the attenuated and variegated
transgene expression based on in vitro and animal
studies. Strategies to prevent short-lived and stochastic
SPK16
THE GENETIC STRUCTURE OF THREE INDIAN OCEAN
ISLAND POPULATIONS: ZANZIBAR, MALDIVES AND
MADAGASCAR
1,*
H. Soodyall
1
Human Genetics, NHLS & University of the
Witwatersrand, Johannesburg, South Africa
Abstract: The peopling of the islands of Zanzibar,
Maldives and Madagascar has been largely influenced by
economic trade networks in the wider Indian Ocean Rim.
We have used haploid genetic markers – mitochondrial
DNA (mtDNA) and Y chromosome DNA - to trace the
genetic trails of the parental populations that have
contributed to the gene pool of the islanders.
We analysed Y chromosome variation in 434 males from
Zanzibar. About 65% of Y chromosomes trace back to
45
Africa; 15% to North Africa (including Middle East) and
17% to
Europe/Asia (Eurasian). In the sample of 518 individuals
we examined for mtDNA variation, ~ 98% of the mtDNA
lineages resolved traced to African origins, whilst others
traced to Asian (~2%) and Eurasian (0.2%) sources.
We resolved the Y chromosomes in 218 Maldivian males
into 16 sub-haplogroups; 57.8% traced to Eurasian origin,
41.7% to Asian origin and only 0.5% to African origin. On
the other hand, mtDNA data on 220 individuals shows a
stronger genetic affinity of the Dhivihi with South Asians,
with haplogroup M and its sub-haplogroups being found
at a frequency of 55.9%.
Mitochondrial studies conducted on 984 individuals
revealed that ~40% of the Malagasy mtDNA lineages
were derived from African origins and ~60% from nonAfrican sources. However, about two-thirds of the Y
chromosome variation was traced to sub-Saharan Africa
and the rest to Asian and European sources.
Disclosure of Interest: None Declared
Objectives The availability of next-generation sequencing
data offers the possibility of asking sophisticated
questions about the colonisation history of Asia. But the
wealth of information available from complete genomes
needs to be matched with clear, hypothesis driven
approaches that allow us to distinguish among the
sometimes subtly different scenarios that have been
proposed by anthropologists.
Methods In this talk, I will present a new climate-driven
spatially explicit framework for describing the
colonisation of Asia. Simpler versions of this framework
has been used successfully to look at the out of Africa
expansion of anatomically modern humans and their
possibly hybridisation with Neanderthal, and thus offer
great promise in helping us unravel the details of the
colonisation of the Asian continent.
Results Testing of the framework using simulated data
reveals that it has high power to detect multiple waves
into the same area using combinations of genetic
differences between populations (such as f4 statistics). I
will also present results using a global panel of highquality genomes from the Pan-Asian Genomics Initiative
(PAPGI) to test the hypothesis of separate waves of
colonisation of Eurasia and the extent of gene flow
between the waves.
Conclusion The combination of next-generation
sequencing data and climate-informed spatially explicit
models of past demography allows for disentangling
subtle patterns of shared genetic variation. In addition,
the best-fitting models generate explicit predictions for
key demographic events such as first arrival time and
areas of common ancestry between populations, which
can be compared to other lines of evidence such as
archaeology.
SPK17
RARE VARIANTS AND MISSING HERITABILITY
1,*
A. Clark
1
CORNELL UNIVERSITY, Ithaca, United States
Abstract: Genome-wide association studies have
provided a plethora of genetic variants that contribute to
the risk of chronic complex diseases. One of the
surprises from these studies is that even with sample
sizes exceeding 100,000, the variability that is explained
by statistical predictions based on associated SNPs is
typically quite small. Many reasons have been given for
this “missing heritability.” This talk will articulate why
heritability is actually of little relevance in medical
genetics, and that individual risk prediction based on
genotype data is largely decoupled from classical
heritability. In particular, heritability predicts properties
of population means, for which additive genetic variation
is all important, whereas individual prediction can rely
heavily on knowledge of dominance, epistasis and
GxE. We will see why methods for individual prediction
that are used in agriculture, such as genomic prediction,
are largely ineffective for human populations. Finally,
even the classical way of representing genotype x
environment interaction is not very useful in human
genetics, and another approach for quantifying context
dependence will be shown to be more useful for
individual prediction.
Disclosure of Interest: None Declared
The availability of next-generation sequencing (NGS) data
offers the possibility of asking sophisticated questions
about the colonisation history of Asia. But the wealth of
information available from complete genomes needs to
be matched with clear, hypothesis driven approaches
that allow us to distinguish among the sometimes subtly
different scenarios that have been proposed by
anthropologists. In this talk, I will present a climatedriven spatially explicit framework for describing the
colonisation of Asia. Using a global panel of high-quality
genomes from the Pan-Asian Genomics Initiative (PAPGI)
I test the hypothesis of separate waves of colonisation of
Eurasia and the extent of gene flow between the waves.
This framework has been used successfully to look at the
out of Africa expansion of anatomically modern humans
and their possibly hybridisation with Neanderthal, and
thus offer great promise in helping us unravel the details
of the colonisation of the Asian continent.
Disclosure of Interest: None Declared
SPK18
RECONSTRUCTING THE COLONISATION OF ASIA USING
GENOMES AND SPATIALLY EXPLICIT MODELS
1 2,*
2
1
A. Eriksson , A. Manica , T. Ravasi
1
King Abdullah University of Science and Technology,
2
Thuwal, Saudi Arabia, University of Cambridge,
Cambridge, United Kingdom
46
SPK19
TRANSLATING
GENETIC
INFORMATION
INTO
PERSONALISED THERAPY FOR CHILDHOOD LEUKAEMIA
1,*
H. Ariffin
1
Paediatrics, University of Malaya, Kuala Lumpur,
Malaysia
and/or mutations in chromatin remodellers and
lymphocyte differentiation factors. Remarkably, in 2/3
relapsed cases, there is a switch from a primary JAK2- or
PTPN11-mutated sub-clone to a RAS-mutated sub-clone
in relapse. These results provide important new insights
informing the patient stratification strategies for
targeted therapeutic approaches for DS–ALL. Possible
mechanisms protecting people with DS from most other
cancer types will be discussed.
Disclosure of Interest: None Declared
Abstract:
The evolution of childhood acute lymphoblastic
leukaemia from an inevitably fatal disease in the 1950’s
to its current form where more than 80% of patients
attain long-term cure has been one of modern
medicine’s best success stories. This outstanding
achievement has been largely due to better
understanding of the genetic heterogeneity of leukaemia
cells , and hence their biology, leading to the
development of risk-stratified treatment protocols. In
tandem with the recognition of individual patient
pharmacogenomics, chemotherapy of appropriate
intensity has managed to achieve the balance between
efficacy and organ toxicity – key components of
personalized medicine.
Disclosure of Interest: None Declared
SPK21
THE SOMATIC GENETIC ARCHITECTURE OF CANCERIMPLICATIONS FOR GENOMIC MEDICINE
1,*
A. Futreal
1
Genomic Medicine, The University of Texas MD
Anderson Cancer Center, Huston, United States
Abstract: The somatic genetic architecture of cancerimplications for genomic medicine The past decade has
seen remarkable advances in our understanding of the
molecular genetic underpinnings of human cancer.Efforts
spanning from international consortia to single labs are
contributing to data fueling insights into processes
sculpting cancer genomes, the heterogeneity between
and within cancer types and that found within individual
patients and within single tumours. My talk will focus on
the what we are learning in these areas and how they
may impact the burgeoning field of genomic medicine. I
will focus on recent work in several tumor types,
including sarcoma, lung cancer and hematopoietic
malignancies, with particular focus on intra-tumour
heterogeneity.
Disclosure of Interest: None Declared
SPK20
MECHANISMS OF TUMORIGENESIS AND PROTECTION
FROM TUMOURS BY STUDYING DOWN’S SYNDROME
1,*
D. Nizetic
1
Genetics and Genomics, Lee Kong Chian School of
Medicine, Nanyang Technological University, Singapore,
Singapore, Singapore
Abstract: Individuals with Down’s syndrome (DS) are
protected from most common solid tissue cancers in
childhood and adulthood. This is paradoxical, as trisomy
21 confers biological features expected to increase
cancer incidence. On the other hand, children with
Down’s Syndrome (DS) have an approximately 50-fold
higher overall incidence of leukaemias, than normal
children, including all types of acute myeloid leukaemia
(AML) and B-cell acute lymphocytic leukaemia (ALL). The
role of trisomy 21 and the nature of mutations and
acquired changes (oncogenic driver events) in this
disease have recently been discovered for both DS-AMKL
and DS-ALL in the exome-sequencing studies co-directed
by D.Nizetic (Nikolaev et al. Blood 2013, Nature
Communications 2014). For pre-leukaemic DS-transient
myeloproliferative disorder (TMD), the exome
sequencing confirmed that an acquired mutation in
GATA1-exon2 is usually the sole event found, and for
evolution from DS-TMD to DS-AMKL, the exomesequencing did not find a common, recurrently mutated
driver gene. For DS-ALL, CRLF2, JAK2 and RAS mutations
were predominant leukaemia drivers. RAS mutations are
almost completely mutually exclusive with JAK2
mutations (P<0.016), driving a combined total of 70% of
analysed DS-ALL cases. Clonal architecture analysis
revealed that both RAS and JAK2 drove sub-clonal
expansions primarily initiated by CRLF2 rearrangements,
SPK22
TRANSCRIPTOME DYSREGULATION AND SINGLE CELL
ANALYSIS IN TRISOMY 21
1,*
S. E. Antonarakis
1
Genetic Medicine, University of Geneva, Geneva,
Switzerland
Abstract: Trisomy 21 is the most frequent genetic cause
of cognitive impairment. To assess the perturbations of
gene expression in trisomy 21, and to eliminate the noise
of genomic variability, we studied the transcriptome of
fetal fibroblasts from a pair of monozygotic twins
discordant for trisomy 21. The differential expression
between the twins is organized in domains along all
chromosomes that are either upregulated or
downregulated. These gene expression dysregulation
domains (GEDDs) are well conserved in induced
pluripotent stem cells derived from the twins' fibroblasts.
Comparison of the transcriptome of the Ts65Dn mouse
model of Down's syndrome and normal littermate mouse
fibroblasts also showed GEDDs along the mouse
chromosomes that were syntenic in human. The GEDDs
47
correlate with the lamina-associated (LADs) and
replication domains of mammalian cells. The overall
position of LADs was not altered in trisomic cells;
however, the H3K4me3 profile of the trisomic fibroblasts
was modified and accurately followed the GEDD pattern.
These results indicate that the nuclear compartments of
trisomic cells undergo modifications of the chromatin
environment influencing the overall transcriptome, and
that GEDDs may therefore contribute to some trisomy 21
phenotypes.
The study of gene expression in mammalian single cells
via genomic technologies now provides the possibility to
investigate the patterns of allelic gene expression. We
used single-cell RNA sequencing to detect the allelespecific mRNA level in 203 single human primary
fibroblasts over 133,633 unique heterozygous singlenucleotide variants (hetSNVs). We observed that at the
snapshot of analyses, each cell contained mostly
transcripts from one allele from the majority of genes;
76.4% of the hetSNVs displayed stochastic monoallelic
expression in single cells. Remarkably, adjacent hetSNVs
exhibited a haplotype-consistent allelic ratio. Moreover,
the allele-specific expression in single cells correlated
with the abundance of the cellular transcript. We
observed that genes expressing both alleles in the
majority of the single cells at a given time point were
rare and enriched with highly expressed. Overall, these
results have direct implications in cellular phenotypic
variability. Single cell transcriptome analysis in trisomy
21 will be discussed.
Disclosure of Interest: None Declared
medicine, the visual function might stay low even after
the successful treatment, so that the regenerative
medicine will be accomplished with following
rehabilitation (low vision care).
In Japan pharmaceutical law has been changed and a
new chapter for regenerative medicine was generated.
This is the first law specific for regenerative medicine in
the world. It was determined in the co-operation with
ministry & academia and its success will depend on the
co-operation with ministry and academia. I will discuss
about the future regenerative medicine in Japan.
Disclosure of Interest: M. Takahashi Grant / Research
Support from: Healios, NIDEK
SPK24
DECODING
THE
GENOME:
DISSECTING
THE
REGULATORY REPERTOIRE OF THE GENOME THROUGH
HIGH RESOLUTION TRANSCRIPTOMICS
1,*
M. E. Dinger
1
Kinghorn Centre for Clinical Genomics, Garvan Institute
of Medical Research, Sydney, Australia
Abstract: Approximately 98% of the human genome
comprises noncoding DNA, the function of which is
largely unknown. Transcriptomic studies, empowered by
increasingly sophisticated molecular techniques, reveal
that the majority of these noncoding regions are
expressed as noncoding RNAs. However, as many of
these transcripts are either lowly expressed or expressed
only in very specific cell or tissue types, their annotation
and functional study has proved very challenging.
To improve our understanding of these noncoding
regions of the genome, we have developed novel
methods to experimentally interrogate the transcripts
that are expressed from them. First, we developed a
technique termed RNA-Capture-Seq, which targets RNA
sequencing to specific areas of the genome. This
technique dramatically increases the sensitivity of RNASeq analysis and improves the qualitative and
quantitative analysis of rare transcripts. Second, to
identify the presence and measure the regulation of
transcripts that are dynamically transcribed, we have
developed approaches to interrogate high-resolution
temporal transcriptomic profiles. This method provides a
means to dissect driver and passenger changes through
key biological transitions in both disease progression and
development.
The implementation of these approaches in several
experimental contexts challenges traditional definitions
of the gene and brings an intriguing perspective into our
understanding of how information in the genome is
encoded. As well as improving our understanding of
cellular regulatory processes, these approaches show
considerable potential in the identification of biomarkers
and therapeutic targets.
Disclosure of Interest: None Declared
SPK23
RETINAL REGENERATIVE MEDICINE USING IPS CELLS
1,*
M. Takahashi
1
Laboratory for Retinal Regeneration, CDB, RIKEN, Kobe,
Japan
Abstract: The first in man application of iPS-derived cells
started in September 2014 targeted the incurable retinal
disease called age-related macular degeneration
(AMD). AMD is caused by the senescence of retinal
pigment epithelium (RPE) that affect the center of the
retina (macula). It is the major cause of visual
impairment in advanced countries. We aim to develop a
treatment that replace damaged RPE with normal, young
RPE made from patients’ own iPS cells to rescue
photoreceptors in the neural retina.
In the clinical study, we judge the outcome 1 year after
the surgery. Grafted cell sheet went though various tests
and tumorigenicity test using immunodeficient mice to
check the safety. Primary endpoint is the safety and
mainly the tumor formation and immune rejection will
be checked.
One of the issues of regenerative medicine is that
expectation become hype. In this clinical study the
efficacy such as retinal sensitivity increase is secondary
endpoint. Hype comes from the way of thinking that cure
is the only way of solution. In retinal regenerative
48
SPK25
MAGNIFIED VIEW OF THE GENOME WITH TARGETED
SEQUENCING
1,*
T. Mercer
1
GARVAN INSTITUTE OF MEDICAL RESEARCH, Sydney,
Australia
Abstract: We have developed targeted sequencing
approaches that use oligonucleotide probes to capture
genetic features of interest for sequencing (CaptureSeq),
achieving unprecedented read coverage, sensitivity and
resolution. CaptureSeq can target any RNA, enabling
more sensitive gene discovery, more precise
measurement of gene abundance, and more accurate
isoform assembly. We have used CaptureSeq to (i)
annotate long noncoding RNAs, (ii) profile the expression
and aberrant splicing of oncogenes in tumors, (iii)
discover new genes in ‘empty’ disease-associated
genome intervals and (iv) map transient RNA
intermediates in the splicing pathway. An analysis of
transcription from human chromosome 21 reveals a
massive abundance and diversity of splicing, coding and
noncoding RNAs, well beyond current annotations. This
complexity is complemented by a similarly a highresolution view of the chromatin landscape using
targeted DNase- and ChIP-Seq. Further comparison to
the syntenic mouse transcriptome distinguishes the
evolutionary forces shaping this transcriptional and
regulatory complexity.
measured differential IR in FACS purified cells at three
progressive stages of normal mature mouse
granulopoiesis;
promyelocytes,
myelocytes
and
granulocytes. We found that IR is a widespread
mechanism that reduces gene expression (mRNA and
protein) via nonsense-mediated decay (NMD). Genes
affected were conserved between human and mouse,
including those specific to granulocytes (Lyz2 and MMP8)
and nuclear architecture (Lmnb1 and Lbr). IR was
associated with lower levels of splicing factors
responsible for exon definition. Chemical and siRNA
inhibition of NMD resulted in marked accumulation of
many intron retaining mRNAs, indicating that IR triggers
NMD to downregulate gene expression. Analysis of
nascent RNA transcripts demonstrated that IR-mediated
NMD occurred independently of transcriptional
regulation.
IR is of broad significance in mammalian biology. Our
improved IRFinder algorithm reveals that one or more
introns in >80% mRNA genes have >10% IR in at least 10
different tissue types (500 human samples with mRNA
data downloaded from the short read archive). IR
frequently regulates the expression of functionally
related genes. Higher GC content was a conserved
feature of retained introns. Putative enhancer regions
and intronic regions contained more than half of all
differential methylated sites. In agreement with previous
studies, enhancer methylation was negatively related to
gene expression levels. We have now demonstrated that
methylation levels at exon-intron boundaries sufficiently
distinguish retained and non-retained introns. In
addition, 5-deoxyazacytidine treatment led to reduced
boundary methylation levels and increased levels of IR.
We conclude that IR coupled with NMD is a significant
widespread mechanism by which gene expression is
1
normally controlled in mammalian biology .
1
Wong et al. Cell, 2013;154(3):583-95
Disclosure of Interest: None Declared
Disclosure of Interest: T. Mercer Grant / Research
Support from: Dr Mercer has been awarded a Discovery
Grant funded by Roche/Nimblegen
SPK26
INTRON RETENTION IS A CONSERVED GENE EXPRESSION
CONTROL MECHANISM ASSOCIATED WITH EPIGENETIC
REGULATION.
1,*
J. Rasko
1
Gene & Stem Cell Therapy Program , Centenary Institute,
University of Sydney, Sydney, Australia
SPK27
A MILLION GENOMES AHEAD
1,*
J. Wang
1
BGI, China
Abstract: Intron retention is a conserved gene
expression control mechanism associated with
epigenetic regulation.
1,3
1
1,3
Justin Wong , Dadi Gao , Robert Middleton1, Amy Au ,
1,3
1,3
1,3
Trung Nguyen , Charles Bailey , Jeff Holst , William
1,3
1,2,3
Ritchie , John EJ Rasko
1
Gene & Stem Cell Therapy Program, Centenary Institute,
2
Australia; Cell and Molecular Therapies, Royal Prince
3
Alfred Hospital, Australia; University of Sydney, Australia
Abstract: While it is definitely a question whether
different types of cancer have similar genomic
alterations, we do not even have sufficient samples to
understand a single type of cancer. Individuals with
different genetic and environmental factors, such as
carcinogen exposure, commensal or pathogenic bacteria
and viruses, life style and mental health, all have to be
sampled, both horizontally and longitudinally. The
interpretation of cancer genomes relies on the scale and
quality of the sequencing data, innovative handling of
such big data and detailed clinical and pre-clinical
information. Early and routine tests would be possible
with accurate and ultra-low input next-generation
sequencing
technologies,
which
necessitate
Intron retention (IR) is the least understood mechanism
by which alternative splicing contributes to genetic
diversity. IR is known as a pathological failure in the
splicing machinery’s excision of intronic sequences from
pre-messenger RNAs, but its widespread role in normal
physiology is only now coming into focus. Using mRNAseq of polyA+ RNA and a novel algorithm, IRFinder, we
49
development of non-invasive sampling approaches. Each
sample should be analyzed in a multi-omic fashion to be
truly reliable and informative. Single-cell sequencing is
necessary for elucidating the heterogeneity and
reconstructing the evolution of a cancer sample.
Biological investigations with optimized humanized
mouse models and conditional reprogramming tumors
cells would be instrumental for development and
evaluation of drugs. While we envision a million
‘personalized’ cancer genomes to come, the hope is to
integrate the large-scale, multi-dimensional data in order
to stratify each patient or at-risk individual, for efficient
diagnosis, prognosis and treatment.
significance of DNA methylation on mTOR was confirmed
using the DNA methylation inhibitor, 5-aza-2'deoxycytidine (5adC). We show exon-specific mTOR
expression is DNA methylation dependent. The results of
our ChIP assays show DNA methylation of mTOR
regulates CTCF binding in cells stimulated by
hyperglycemia and 5adC.
Conclusion: Our results are particularly novel for several
reasons bringing together strong clinical detection with
experimental validation in primary human cells. The
approach of unbiased methylation sequencing identified
epigenetic predictors coordinating transcription factors
in the regulation of novel and relevant genes implicated
in diabetes are conferred by hyperglycemia and
regulated by DNA methylation.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
ORALS
EPIGENETICS
O01
METHYLATION
MAPPING
IDENTIFIES
GENES
IMPLICATED IN DIABETES
1
2
1
1
I. Khurana , A. Syreeni , M. Ziemann , A. Kaspi , M.
1
2
1,*
Cooper , P.-H. Groop , A. El-Osta
1
BakerIDI Heart & Diabetes Institute, Melbourne,
2
Australia, Folkhälsan Institute of Genetics, Folkhälsan
Research Center, Biomedicum Helsinki, Helsinki, Finland
O02
HDAC
INHIBITION
ATTENUATES
CARDIAC
HYPERTROPHY BY DEACETYLATION OF TARGET GENES
1,*
1
1
2
J. Ooi , N. Tuano , H. Rafehi , X.-M. Gao , M. Ziemann
1
2
1
, X.-J. Du , A. El-Osta
1
2
Human Epigenetics & Disease Laboratory, Experimental
Cardiology Laboratory, BAKER IDI HEART AND DIABETES
INSTITUTE, Melbourne, Australia
Objectives: Although significant progress has recently
been made in elucidating the genetics of diabetes and its
complications, the non-genetic component remains
poorly defined. In the last five years, approximately 600
GWAS studies have examined over 100 human diseases,
uncovering more than 800 genetic variants associated
with one or more diseases. However, in nearly every
case, the majority of factors that cause the disease are
still unknown. This has led to interest in studying nongenetic factors that could impact on disease. In this
paper we present key data examining genome-wide DNA
methylation of the FinnDiane type 1 diabetes cohort.
Methods: Informed consent was obtained from
FinnDiane-200 study participants before sampling. Agematched males and females were also recruited. Methylcapture coupled with massive parallel sequencing
(Methyl-seq) was used to identify differential methylated
regions (DMRs) and bisulfite sequencing was used to
validate these regions. Chromatin immunoprecipitation
(ChIP) techniques were used to validate transcription
factor interactions subject to methylation at target
genes.
Results: We map human differential methylation of key
transcription factors in the FinnDiane type 1 diabetes
cohort. Genes implicated in diabetes such as mTOR,
EPHA1, EFNB2, FGFR4 and BGN were subject to
epigenetic changes. Methyl-seq identified mTOR gene
regulation was subject to differential methylation at the
CTCF consensus-binding site. These clinical findings were
tested ex vivo in primary human aortic endothelial cells
and confirm low glucose (LG) transition to high glucose
(HG) conditions increased mTOR expression. The
Objectives: Pharmacological histone deacetylase (HDAC)
inhibitors attenuate pathological cardiac remodeling and
hypertrophic gene expression yet the direct histone
targets remain poorly characterized. Since the inhibition
of HDAC activity is associated with suppressing
hypertrophy we hypothesized histone acetylation would
target genes implicated in cardiac remodeling.
Trichostatin A (TSA) regulates cardiac gene expression
and attenuates transverse aortic constriction (TAC)
induced hypertrophy.
Methods: We used chromatin immunoprecipitation
(ChIP) coupled with massive parallel sequencing (ChIPseq) to map for the first time genome-wide histone
acetylation changes in a preclinical model of pathological
cardiac hypertrophy and attenuation of pathogenesis
with TSA.
Results: Pressure overload-induced cardiac hypertrophy
was associated with histone acetylation of genes
implicated in cardiac contraction, collagen deposition,
inflammation and extracellular matrix identified by ChIPseq. Gene set enrichment analysis identified NF-kappa B
(NFkB) transcription factor activation with load induced
hypertrophy. Increased histone acetylation was observed
on the promoters of NFkB target genes (Icam1, Vcam1,
Il21r, Il6ra, Ticam2, Cxcl10) consistent with gene
activation in the hypertrophied heart. Surprisingly, TSA
attenuated
pressure
overload-induced
cardiac
hypertrophy and the suppression of NFkB target genes
by broad histone deacetylation.
Conclusion: Our results suggest a mechanism for
cardioprotection subject to histone deacetylation as a
previously unknown target implicating the importance of
50
inflammation by pharmacological HDAC inhibition. The
results of this study provides a framework for HDAC
inhibitor function in the heart and argues the long held
views of acetylation is subject to more flexibility than
previously thought.
response is blunted in CaMKIIδ-KO. We also document
that the chaperone protein 14-3-3 binds phosphorylated
H3 in response to stress, allowing proper elongation of
fetal cardiac genes by RNA polymerase II (RNAPII), as well
as elongation of transcription factors regulating cardiac
hypertrophy. These processes are impaired in CaMKIIdKO mice.
Conclusion: These findings reveal a novel in vivo function
of CaMKIIδ in regulating H3 phosphorylation and suggest
a novel epigenetic mechanism by which CaMKIIδ controls
cardiac hypertrophy.
Disclosure of Interest: None Declared
O03
REGULATION OF HISTONE H3 PHOSPHORYLATION BY
CAMKII IN RESPONSE TO PATHOLOGICAL CARDIAC
STRESS
1,*
1
2
1
S. Mahmoud , K. Al-Haffar , P. Quijada , M. Kunhi ,
1
3
4
N. Al-Yacoub , G. Sutherland , ,. A. Assiri , M. Sussman
5
6
7
1
, D. Bers , W. Al-Habeeb , C. Poizat
and Kamar
Mohamed Adib Al-Haffar 1, Qussay Marashly 2, Pearl
Quijada 3, Muhammad Kunhi 1, Nadya Al-Yacoub 1,
George Sutherland 4, Abdullah Assiri 5, Mark Sussman 3,
Donald Bers 6, Waleed Al-Habeeb 7, Coralie Poizat 1
1
Cardiovascular Research Program, King Faisal Specialist
2
Hospital and Research Center, Riyadh, Saudi Arabia,
Department of Biology, San Diego State University,
3
4
California, United States, Heart Centre, Comparative
Medicine, King Faisal Specialist Hospital and Research
5
Center, Riyadh, Saudi Arabia, Department of Biology,
6
San Diego State University,
Department of
Pharmacology, University of California at Davis,
7
California, United States, Medicine College, King Saud
University, Riyadh, Saudi Arabia
Disclosure of Interest: None Declared
PERSONALISED MEDICINE /
PHARMACOGENOMICS
O04
A GENOME-WIDE POPULATION-SCALE MAP OF RARE
AND COMMON PHARMACOGENETIC VARIANTS IN
MALAYSIA
1,*
1
A. Sivadas , V. Scaria
1
GN Ramachandran Knowledge Center for Genome
Informatics, CSIR INSTITUTE OF GENOMICS AND
INTEGRATIVE BIOLOGY (CSIR-IGIB), DELHI, India
Objectives: Expanding the scope of pharmacogenomic
research by including multiple global populations is
integral to building robust evidence for its clinical
translation. Deep whole-genome sequencing of diverse
ethnic populations provides a unique opportunity to
study rare and common pharmacogenomically relevant
markers which often vary in frequency across population.
In this study, we aim to build a diverse map of
pharmacogenetic variants in Malay population using
deep whole genome sequencing of 100 healthy Malay
individuals.
Methods: We analyzed the genomic variants identified
from the whole-genome sequences of 100 healthy Malay
individuals belonging to the Singapore Sequencing Malay
Project (SSMP). We used SIFT and PolyPhen2 to identify
potentially deleterious, non-synonymous coding variants.
Clinically relevant pharmacogenetic variants were
obtained from PharmGKB and DrugBank. Global and
population-specific variant allele frequencies were
obtained from 1000 Genomes Project and International
Hapmap consortium to understand the differential
frequency distribution of the Malay pharmacogenetic
variants across populations.
Results: We analysed the frequency distribution of highconfidence clinically significant pharmacogenetic variants
in the Malay population in comparison with global
populations and was observed to be largely characteristic
of the Asian ethnic groups. Our analysis revealed 218
common and 429 rare potentially deleterious nonsynonymous coding variants in 415 pharmacogenomic
genes which are involved in drug metabolism, transport
and drug target genes, including 67 novel variants.
Objectives: Heart failure is associated with the
reactivation of a fetal cardiac gene program which has
become a hallmark of cardiac hypertrophy and
maladaptive ventricular remodeling. Yet the mechanisms
that regulate this transcriptional reprogramming are not
fully understood. In this study we investigated the in vivo
role of nuclear CaMKIIδ in transcriptional reprograming
of cardiac muscle.
Methods: Human failing hearts and mice with genetic
ablation of CaMKIIδ (CaMKIIδ-KO) were used. In addition
to comprehensive experimental approaches including
chromatin immunoprecipitation assays (ChIP), q-PCR, in
vitro transcription assay, siRNA technology and
fluorescent microscopy.
Results: We show that calcium/calmodulin-dependent
protein kinase II delta (CaMKIIδ) regulates the
phosphorylation of histone H3 at serine-10 during
pressure overload hypertrophy. H3 S10 phosphorylation
is strongly increased in the adult mouse heart in the early
phase of cardiac hypertrophy . This response strongly
correlates with up-regulation of CaMKIIδ and increased
expression of transcriptional drivers of pathological
cardiac hypertrophy and of fetal cardiac gene. Similar
changes are detected in patients with end-stage heart
failure where CaMKIIδ specifically interacts with
phospho-H3. Mechanistically, fetal cardiac genes are
activated by increased recruitment of CaMKIIδ and
enhanced H3 phosphorylation at hypertrophic promoter
regions both in mice and in human failing hearts, and this
51
Conclusion: This study has created one of the most
comprehensive map of pharmacogenetic markers in any
population from whole genome datasets and will hugely
benefit clinical pharmacokinetic investigations and drug
dosage recommendations in Malay population.
treatment alone, and/or by inducing the expression of
other genes.
Disclosure of Interest: None Declared
ORAL PRESENTATIONS I
Disclosure of Interest: None Declared
O07
HOMOZYGOSITY DISEQUILIBRIUM IN THE HUMAN
GENOME
1,*
1
H.-C. Yang , Y.-T. Lin
1
Institute of Statistical Science, ACADEMIA SINICA, Taipei,
Taiwan, Province of China
O06
COMBINED GAMMA-TOCOTRIENOL AND
HYDROXYCHAVICOL ACTIVATED MULTIPLE ANTICANCER
PATHWAYS IN 1321N1, SW1783 AND LN18 GLIOMA
CELL LINES: TRANSCRIPTOMIC EVIDENCE OF
SYNERGISTIC INTERACTION
1,*
1
1
A. Abdul Rahman , W. Z. Wan Ngah , R. Harun , R.
1
1
Jamal , N. Mokhtar
1
UKM Medical Molecular Biology Institute, Kuala Lumpur,
Malaysia
Objectives: Homozygosity disequilibrium (HD), which
was first coined by Yang et al [1], indicates a non-random
pattern of run of homozygosity in the genome. Our
previous studies investigated HD through whole-genome
analyses of SNP microarray data and next-generation
sequencing data. We derived the distribution of HD in
the human genome, found a familial aggregation of HD,
and identified regions of HD associated with cancers and
complex disorders [1-3]. The present study aimed to
examine HD in global populations by analyzing wholegenome sequencing data.
Methods: The data contained more than 38 million
single nucleotide variants of 1,092 individuals from 14
global populations in the 1000 Genomes Project - Phase
I. Software LOHAS [2-3] developed by our team were
applied to estimate the whole-genome homozygosity
intensity and detect regions of HD. Singular value
decomposition and phylogenetic analysis based on
homozygosity intensity were used to determine the
major configurations of homozygosity intensity and
display the relative coordinates and proximity of global
populations in terms of HD.
Results: We derived the whole-genome profiling of
homozygosity intensity for every individual and
characterized the distribution of HD in the human
genome. Singular value decomposition analysis
suggested a large discrepancy of HD distributions in
continental populations. Phylogenetic analysis revealed a
large population differentiation between continental
populations. Furthermore, among the subpopulations in
the same continent, the molecular proximity of HD
coincided with evolutionary history of the study
subpopulations.
Conclusion: This whole-genome sequencing analysis of
HD provides a blueprint to understand genomic
homozygosity in the human genome in global
populations. The results are helpful for human evolution
discovery in population genomics and for disease gene
mapping in medical genomics.
References: [1] Yang, H.-C., Chang, L.-C., Liang, Y.-J., Lin,
C.-H. and Wang, P.-L. (2012). A genome-wide
homozygosity association study identifies runs of
homozygosity associated with rheumatoid arthritis in the
human Major Histocompatibility Complex. PLoS ONE 7,
e34840.
Objectives: Increasing evidence revealed that specific
combinations of phytochemicals may be more effective
in chemoprevention than isolated compounds by
targeting different pathways and achieving lower
biologically available concentrations. However, our
understanding of the molecular mechanisms underlying
such synergistic effects is still limited. Gammatocotrienol (GTT) are powerful antioxidants, possess
anticancer and neuroprotective properties. Meanwhile,
hydroxychavicol (HC) selectively kills cancer cells via ROS
generation without affecting normal cells.
Methods: Using RNA-sequencing approach, we identified
the genes modulated by combined GTT and HC
treatment in human glioma 1321N1 (grade II), SW1783
(grade III), and LN18 (grade IV) cell lines.
Results: A total of 1616, 674, and 652 genes were
differentially expressed in 1321N1, SW1783 and LN18
cells respectively (FDR P<0.05, fold-change>1.5), when
treated with combined GTT+HC, where only 146 genes
were found to be commonly expressed in all treatments.
Only five genes were commonly expressed in all cell lines
treated with GTT alone, whereas 81 genes were
commonly expressed in all cell lines treated with HC
alone. The differential expression of genes in GTT+HC
treated cells clustered into cell cycle functions, response
to endoplasmic reticulum stress, autophagy, DNA repair,
toll-like receptor signaling pathway, regulation of
apoptosis and chemokine production. Furthermore,
subnetwork analysis of differentially expressed genes in
1321N1, SW1783 and LN18 cells revealed two similar
central genes, ATF4 and XBP1.
Conclusion: Our results suggested that the anticancer
effect of combined GTT+HC on different grades of glioma
cell lines are influenced by both common and unique
genes and pathways. This may be due to the different
characteristics of each cell lines tested. Additionally, the
combination of GTT+HC was shown to synergize and
enhance the effects of each individual bioactive by
increasing the expression of genes present in GTT or HC
52
[2] Yang, H.-C., Chang, L.-C., Huggins, R. M., Chen, C.-H.
and Mullighan, C. G. (2011). LOHAS: Loss-ofheterozygosity analysis suite. Genetic Epidemiology 35,
247-260.
[3] Yang, H.-C. and Li, H.-W. (2014). Analysis of
homozygosity disequilibrium using whole-genome
sequencing data. BMC Proceedings 8, S15.
adaptation. Our own study associated two of the loci of
the EGLN1 gene with HAPE (p<0.05).
Conclusion: To summarize, adaptation and or
maladaptation at HA is of multifactorial origin that stems
from complex interactions between genes of vascular
system and hypoxia pathway with environmental factors.
Our findings make significant contribution to the ongoing
research in the field of HA, establishing the possible
predisposing markers in relation to HA adaptation and
disorders.
Disclosure of Interest: None Declared
O08
SHUFFLING BETWEEN HYPOXIA AND VASCULAR
HOMEOSTASIS PATHWAY GENES UNDER HYPOBARIC
HYPOXIA
1,*
M. Q. Pasha
1
CSIR-Institute of Genomics and Integrative Biology (CSIRIGIB), Delhi, India, Delhi, India
Disclosure of Interest: None Declared
O09
MEDICO-GENOMIC CHARACTERIZATION OF THE CHE
WONG TRIO: AN ORANG ASLI (INDIGENOUS GROUP)
SUB-TRIBE OF MALAYSIA
1,*
12
12
1
R. I. Ismet , M. Z. Salleh , L. K. Teh , N. Mohamad ,
1
3
3
L. S. Lee , A. Ahmad , T. Abdul Rahman , F. Mohd Nor @
3
1 4
1 4
5
Ghazali , A. I. Ismail , K. M. Isa , V. Scaria , S.
6
7
Sivasubbu , H. Salleh and LRGS Orang Asli
1
Integrative Pharmacogenomics Institute (iPROMISE),
2
Faculty of Pharmacy, Universiti Teknologi MARA (UiTM),
3
Puncak Alam, Faculty of Medicine, Universiti Teknologi
4
MARA (UiTM), Sungai Buloh, Faculty of Art and Design
(FSSR), Universiti Teknologi MARA (UiTM), Shah Alam,
5
Malaysia, GN Ramachandran Knowledge Center for
6
Genome Informatics, Genomics and Molecular Medicine,
CSIR Institute of Genomics and Integrative Biology (CSIR7
IGIB), Delhi, India, Institut Alam Sekitar dan
Pembangunan
(LESTARI),
Universiti
Kebangsaan
Malaysia (UKM), Bangi, Malaysia
Objectives: The hypoxic environment at high-altitude
(HA), while renders the performance of sojourners
difficult, hardly affects the routine physical activities of
the natives because of adaptation to the environment.
Acquisition of HA phenotype over generations by natural
selection is a possible explanation. Taking into account
the candidate gene and genome-wide studies (GWAS),
last one decade has made phenomenal contribution to
our knowledge on genetic aspects. Genes of the vascular
system, owing to their relevance in blood pressure
homeostasis, and genes of the hypoxia pathway, owing
to their role in cellular oxygen homeostasis, accentuate
their significance at HA. Hence, in a case-control design
to study adaptation and maladaptation at HA, we
evaluated the genes of vascular system, with special
reference to Renin-Angiotensin-Aldosterone System
(RAAS) and hypoxia pathway.
Methods: We genotyped potential single nucleotide
polymorphisms (SNPs) in the genes of vascular system
and hypoxia pathway. The investigated genes include
Angiotensin-converting enzyme (ACE), Angiotensinogen
(AGT), Angiotensin II receptor1 (AT2R), Aldosterone
synthase (CYP11B2), endothelial nitric oxide synthase
(NOS3), neuronal NOS (NOS1) and Egl nine homolog 1
(EGLN1).
Results: Our results revealed a significant association of
alleles such as I of ACE I/D, T174 of AGT T174M, G894,
4b, –922A and –786T of NOS3 G894T, 4b/4a, –922A/G,
and –786T/C, respectively, with adaptation (p<0.05) that
may facilitate routine physical activities at HA. On the
other hand, allele D of ACE, M174 of AGT, intron-2
conversion of CYP11B2, and longer CA-repeats (34-45),
T894 and 4a of NOS3 associated with HAPE (p<0.05). ACE
activity, aldosterone and NO levels correlated with
respective alleles (p<0.05). Novel variations, 5'UTR
1598C/T, exon 1 1773C/T and intron 1 GT- and CArepeats and intron 3 GT-repeat in NOS2 have also been
scored (p<0.05). Recent GWAS from different parts of the
world have reported positive selection of EPAS1, EGLN1
and PPARA, whose products are likely, involved in HA
Objectives: We aim to characterize the genomic
architecture of the unique group of indigenous tribe in
Malaysia. We aim to explore the disease risk and
protection conferred by genetic traits via sequencing the
whole genome of a trio sample of Che Wong, an
alarmingly small Orang Asli population.
Methods: A parent-offspring trio genome study was
designed. Their genomes were sequenced and mapped
to the human reference genome (hg19) with an objective
of achieving a coverage depth of ≥30x for each genome.
Genomic bioinformatics analysis included the discovery
of variants, determination of structural variants,
discovery of novel variants, polymorphism classification,
and identification of disease associated variants. The
genomic findings were then correlated to biochemistry
and metabolite analysis findings.
Results: Approximately 6.2 million variants were
identified for the trios with 624,775 of these variants
being unique to the Che Wong trio. Upon selection of
functional and conserved regions as well as filtering with
known databases, variants with the potential of
increasing one’s disease susceptibility and were unique
to the Che Wong were identified. These variants were
associated to genes involved in ageing, cardiovascular,
psychological, metabolic, neurological, vision, cancer,
immune, pharmacogenomics, renal, infection, normal
53
variation, and other disease class. Genetic traits
associated with metabolic syndrome and cardiovascular
diseases were observed among the trio.
Conclusion: We report here for the first time the
catalogue of the genomics composition of the Malaysian
Orang Asli together with its medico-genomic findings.
This data provides new perspective of the genomics
background of the indigenous population in South East
Asia (SEA) which we believed would be useful for the
scientific and health community.
NMDAR gene. We observed up-regulation of key
hypertrophic and sarcomeric genes. Calcium handling
genes were also upregulated in the mutant animals.
Presently, we are validating the differentially expressed
genes via qRT-PCR and investigating the role of NMDA
receptors in cardiac function.
Conclusion: GBT mediated insertional mutant exposed
the novel role of NMDAR in the zebrafish heart function.
NMDAR regulates key calcium handling genes for
2+
maintaining intracellular Ca
homeostasis in the
zebrafish heart.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
O10
ROLE OF N-METHYL D-ASPARTATE (NMDA) RECEPTORS
IN ZEBRAFISH HEART DEVELOPMENT
1,*
1
1
1
1
R. A , S. K , A. Patowary , K. Kaushik , M. Singh , A.
1
1
1
1
1
Sabharwal , E. Leonard , S. Vellarikkal , A. V , R. J , R.
1
1
1
1
Chauhan , A. Joshi , V. Scaria , S. Sivasubbu
1
CSIR Institute of Genomics and Integrative Biology,
Delhi, India
O12
WHOLE
GENOME
SEQUENCING
OF
KAZAKH
INDIVIDUALS:
INSIGHTS
INTO
THE
GENETIC
ARCHITECTURE OF KAZAKH POPULATION.
1,*
1
1
A. Akilzhanova , U. Kairov , S. Rakhimova , A.
1
2
3
3
1
Molkenov , A. Rhie , J.-I. Kim , J.-S. Seo , Z. Zhumadilov
1
Department of Genomic and Personalized Medicine,
NAZARBAYEV UNIVERSITY, CENTER FOR LIFE SCIENCES,
2
Astana, Kazakhstan, Genomic Medicine Institute (GMI),
Department of Biochemistry and Molecular Biology,
3
Genomic Medicine Institute (GMI), Department of
Biochemistry and Molecular Biology, Seoul National
University College of Medicine, Seoul, Korea, Republic Of
Objectives: NMDA receptors are a subtype of ionotropic
2+
glutamate receptors mediating Ca uptake. NMDAR
comprises of three classes which exhibit distinct patterns
of developmental expression in the central nervous
system. Several groups have illustrated the cellular
distribution of different subtypes of glutamate receptors
in non-neural tissues including heart. The role of NMDAR
has been previously implicated in brain function but its
function in heart still remains elusive. In zebrafish one of
the NMDAR paralogs is expressed at low levels in the
heart. Mutant zebrafish models for NMDA receptor
genes provide excellent template for understanding their
function in heart development.
Methods: We carried out a large-scale insertional
mutagenesis screen in zebrafish using a transposonbased gene breaking trap (GBT) approach. Molecular
characterization of the GBT mutant was done using
inverse PCR, RACE (5’ and 3’) and next generation
sequencing techniques. The functional characterization
of GBT mutant was carried out using microscopy, MO
knockdown, western blotting, calcium imaging, qRT-PCR,
and In-situ hybridization etc. Deep sequencing of the
transcriptome of the mutant heart permitted us to
identify differentially expressed transcripts.
Results: GBT mediated insertional mutagenesis identified
a viable adult zebrafish mutant, which displayed
pronounced cardiac arrhythmia (bradycardia) in embryos
followed by chamber enlargement and cardiac
hypertrophy. Functional studies revealed an enlarged
atrium in the mutant animals. Molecular characterization
revealed the GBT integration to be in the intron 2 of
NMDA receptor gene. Calcium imaging in the NMDAR
mutant
revealed
calcium
mishandling.
In-situ
hybridization confirmed that the gene is expressed in the
adult zebrafish heart. RNA sequencing of adult NMDAR
mutant heart revealed the transcript structure of
Objectives: The human genome sequence will underpin
human biology and medicine in the next century,
providing a single, essential reference to all genetic
information. The international project “Genetic
architecture of Kazakh population” to determine the
complete DNA sequence of Kazakh individuals is well
underway. We aimed to introduce first data on whole
genome sequences of 6 Kazakh individuals.
Methods: We sequenced 6 genomes of healthy Kazakh
individuals for the first time at high coverage using the
Illumina HiSeq2000 platform. All generated *.bcl files
were simultaneously converted and demultiplexed using
bcl2fasta application. Alignment of sequence reads
performed using bwa-mem against human b19 reference
genome. Sorting, removing of intermediate files, *.bam
files assembling, and marking duplicates were performed
using PicardTools package. GATK haplotype caller tool
was used for variant calling. ClinVar, SNPedia and Cosmic
databases were processed to identify clinical genomic
variants in 6 Kazakh whole genomes. To perform raw
data processing and running program scripts Java
Runtime Environment and R Bioconductor package were
installed.
Results: The sequence alignment and mapping
procedures on reference genome hg19 of each 6 healthy
Kazakh individual were completed. From 87,308,581,400
to 107,526,741,301 total base pairs were sequenced with
average coverage x29.85. From 98.85 to 99.58 % base
pairs were totally mapped with properly paired 96.07%
in average. Het/Hom and Ti/Tv ratios for each whole
genome ranged from 1.35 to 1.52 and from 2.07 to 2.08,
54
respectively. We compared and analyzed each genome
with on existing clinical databases ClinVar, SNPedia,
Cosmic and found from 20 to 25, from 269 to 288, from 7
to 12 SNP records, respectively. The availability of a
reference Kazakh genome sequences provides the basis
for studying the nature of sequence variation,
particularly single nucleotide polymorphisms. Potential
medical phenotypes were annotated for nonsynonymous SNPs, coding domain indels, and structural
variants.
Conclusion: Whole genome sequencing of 6 Kazakh
individuals was performed for the first time. The results
expand our knowledge of the genetic architecture of the
Kazakh
population,
which
will
benefit
the
implementation of personalized medicine for the
Kazakhstani population.
overrepresented in HAPE-c. These genes regulate
expression of hypoxia inducible transcription factor,
which regulates erythropoiesis, glycolysis, cell survival,
angiogenesis and acute hypoxia ventilatory response
under hypoxic conditions. Gene Ontology terms of 88
significant CNVs included A2A adenosine and C5a
anaphylatoxin chemotactic receptor binding, sodiumexporting and bile acid-exporting ATPase activity and
phosphatidylinositol-3,4,5-trisphosphate3 phosphatase
activity.
Conclusion: This is the first study to report CNVs
associating with HAPE. The study reveals that duplication
CNVs in IKZF3 and MEX3D convey protection against
HAPE. Our findings suggest that genomic structural
changes are important contributors to variable human
acclimatization tendencies at HA.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
O13
IN A GENOME-WIDE SEARCH, CNVS CONVEY
PROTECTION AGAINST HAPE
1 2,*
1
12
12
S. Kohli , R. Koshy , Y. Singh , M. Q. Pasha
1
CSIR-Institute of Genomics and Integrative Biology (CSIR2
IGIB), Delhi, Academy of Scientific and Innovative
Research (AcSIR), New Delhi, India
O14
PHARMCOGENETIC VARIATION OF CLOPIDOGREL DRUG
IN SOUTH INDIAN POPULATION SUGGESTS DISTINCT
INTERPOPULATION
DIFFERENCES
IN
ALLELE
FREQUENCIES
1,*
1
1
1
A. K. Patnam , A. Acharya , S. Kumar , R. K. Raman , S.
1
1
P. Kiran , S. Kumar and Mapmygenome
1
Research & Development, Mapmygenome, Hyderabad,
India
Objectives:
High-altitude
(HA)
(1500-3500m),
characterized by hypobaric hypoxic environment, is the
major cause of stress in terms of mountain diseases. High
altitude pulmonary edema (HAPE) is one such rare lifethreatening disorder that affects susceptible lowland
sojourners. It is characterized by rise in pulmonary
arterial pressure, fall in arterial oxygen saturation and
remodelling of the pulmonary vascular bed. Previous
studies have reported significant associations of SNPs
with HAPE. However, the role of common nucleotide
variations (CNVs) in HAPE susceptibility remains
untouched. Deciphering the contribution of CNVs to
clinical phenotypes is emerging as one of the fascinating
research areas of genomics. The present study attempts
to decipher CNVs associating with HAPE.
Methods: We conducted a genome wide genotyping
using Illumina Human1M omni beadchip on age, gender
and ethnicity matched 91 HAPE-patients (HAPE-p) and 85
HAPE-controls (HAPE-c). High-confidence CNV calls were
generated using PennCNV. Association analysis was
performed using Fischer's exact test as applied by
CNVRuler. QuantiSNP validated the significant CNV
regions. CNVs were scanned for overlapping genes and
molecular functions.
Results: PennCNV identified an average of 399±89 CNVs
in HAPE-p and 379±80 CNVs in HAPE-c. Association
analysis revealed 88 CNVs (79.5% duplication and 20.5%
deletion CNVs) significantly associating with HAPE (Pvalue<0.05). The most significant CNV (Chr17:3799154138021652) spanned across IKZF3 (IKAROS Family Zinc
Finger 3) (P-value=6.7E-06; OR=0.01), while the second
most significant CNV (Chr19:1550650-1580334) spanned
across MEX3D (Mex-3 homolog D) (P-value=1.3E-05;
OR=0.07). Both these duplication CNVs were
Objectives: Clopidogrel, a widely used antiplatelet drug,
exhibits high interindividual variability of more than 80%
which could be explained by genetic polymorphisms. We
calculated allele frequency of variants which majorly
affect clopidogrel response in south Indians.
Methods: We performed SNP genotyping using
sequenom platform for 650 individuals for CY2C19*1,
CYP2C19*2 & CYP2C19*3 in south indian population for
presence
of
risk
variants
associated
with
pharmacogenetics of clopidogreldrug response.
Results: Our analysis reveals significant differences in
population-scale allele frequencies between south
Indians and the global population. SOuth Indians had a
higher allele frequency for variants in the CYP2C19*2,
CYP2C19*3 genes compared with the global population.
Furthermore, from our study we proposed a model to
explain the higher prevalence of clopidogrel nonmetabolizers in south Indians.
Conclusion: This a population-scale genetic epidemiology
study that provides a high-resolution picture of risk
variants associated with clopidogrel response that could
be potentially valuable to clinicians to rationally plan
appropriate dosage for therapy in resource poor
conditions based on population level allele frequencies.
References:
1) Pharmacogenetic landscape of
clopidogrel in north Indians suggest distinct
interpopulation
differences
in
allele
frequencies.Pharmacogenomics. 2014 Apr;15(5):643-53.
2) The influence of genetic polymorphism of Cyp2c19
isoenzyme on the pharmacokinetics of clopidogrel and its
55
metabolites in patients with cardiovascular diseases.J
Clin Pharmacol. 2014 Aug;54(8):874-80.
on tacrolimus pharmacokinetics in South Indian renal
transplant recipients and also shows that majority of our
patients carry mutant allele A6986G in CYP3A5*3 gene.
Identification of CYP3A5 polymorphism prior to
transplantation could contribute to evaluate the
appropriate initial dosage of tacrolimus for each patient.
References: · Bowman LI, Brennan DC. The role of
tacrolimus in renal transplantation.
Expert Opin Pharmacother 2008, 9:635-643
Disclosure of Interest: A. K. Patnam Employee of:
Mapmygenome, A. Acharya: None Declared, S. Kumar:
None Declared, R. Raman: None Declared, S. Kiran: None
Declared, S. Kumar: None Declared
O15
IMPACT OF CYP3A5 POLYMORPHISM ON TACROLIMUS
TO
PREDICT
THE
OPTIMAL
INITIAL
DOSE
REQUIREMENTS IN SOUTH INDIAN RENAL TRANSPLANT
RECIPIENTS.
Disclosure of Interest: None Declared
R. N. Radhakrishnan
, G. Noble
, S. S
, P.
12
Radhakrishna
1
Laboratory of Molecular Medicine and Diagnostics,
RAJIV GANDHI CENTRE FOR BIOTECHNOLOGY,
2
TRIVANDRUM 695014,KERALA,INDIA, Department of
Nephrology, Govt.Medical College,, Trivandrum, India
O16
INITIAL EXPERIENCE IN IMPLEMENTATION OF A CANCER
GENE PANEL TEST TO DETERMINE THE AETIOLOGY OF
BREAST CANCER IN A DEVELOPING COUNTRY
1,*
2
1
N. D. Sirisena , G. Abeysekara , V. H. W. Dissanayake
1
Human Genetics Unit, Faculty of Medicine, University of
2
Colombo, Colombo 08, Credence Genomics, Colombo 05,
Sri Lanka
Objectives: Tacrolimus is a potent immunosuppressant
clinically used for the long term treatment of
antirejection of transplanted organs in liver and kidney
transplant recipients though dose optimization is poorly
managed. However, So far no study has been carried out
on the South Indian kidney transplant patients. The
objective of this study is to evaluate the potential
influence of a functional polymorphism in CYP3A5*3
gene on tacrolimus physiological availability/dose ratio in
South Indian renal transplant patients.
Methods: Twenty five renal transplant recipients
receiving tacrolimus were enrolled in this study. Their
body weight, drug dosage, and therapeutic
concentration of Tacrolimus were observed. All patients
were on standard immunosuppressive regime of
Tacrolimus-Mycophenolate mofetil along with steroids
on a starting dose of Tac 0.1 mg/kg/day. CYP3A5
genotyping was performed by PCR followed with RFLP.
Conformation of RFLP analysis and variation in the
nucleotide sequence of CYP3A5*3 gene were determined
by direct sequencing using a validated automated
generic analyzer.
Results: The CYP3A5 *1/*1, *1/*3 and *3/*3 genotypes
were detected in 5 (20 %), 5 (20 %) and 15 (60 %) of the
25 graft recipients, respectively.CYP3A5*3 genotypes
were found to be a good predictor of tacrolimus
Concentration/Dose ratio in kidney transplant recipients.
Significantly higher L/D was observed among nonexpressors 9.483 ng/mL(4.5- 14.1) as compared with the
expressors 5.154 ng/mL (4.42-6.5 ) of CYP3A5. Acute
rejection episodes were significantly higher for CYP3A5*1
homozygotes compared to patients with CYP3A5*1/*3
and CYP3A5*3/*3 genotypes (40 % versus 20 % and 13
%, respectively ). The dose normalized TAC concentration
(ng/ml/mg/kg) was significantly lower in patients having
CYP3A5*1/*3 polymorphism.
Conclusion: This is the first study to extensively
determine the effect of CYP3A5*3 genetic polymorphism
Objectives: Traditionally in most parts of the world,
families with inherited breast cancer are tested for
mutations in the BRCA1 and/or BRCA2 genes. Mutation
testing for other breast cancer predisposition genes is
not widely available, and when available is often
expensive and time consuming. When mutations are not
found in these genes, extending testing to other
susceptibility genes is not usually possible due to non
availability of tests, and cost considerations. The ability
to perform cancer gene panel tests on a next generation
sequencing platform makes it possible to overcome
these limitations. This report aims to describe our initial
experience in implementation of a cancer gene panel
test to determine the aetiology of hereditary breast
cancer in a developing country.
Methods: We implemented a gene panel test using a
breast cancer panel that tests for 18 cancer genes [ATM,
BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A,
MUTYH, NBN, NF1, PALB2, PTEN, RAD50, RAD51C,
RAD51D, STK11 and TP53] on the Ion Torrent PGM
platform. Sequencing is followed by bioinformatics
analysis that includes filtering of common variants and
searching the ClinVar (http://www.clinvar.com) and
locus-specific databases to determine whether the
variants identified have been reported previously in
patients with cancer. In the case of novel variants, in
silico analysis is performed to determine their
pathogencity. The putative variant is further validated by
Sanger sequencing. In addition, Sanger sequencing is
performed on other affected and non affected members
of the family for further confirmation.
Results: So far, we have tested 6 families with inherited
breast cancer with full informed consent and found 2
families with confirmed mutations. They are: A family
with breast cancer, colorectal cancer and acute
lymphoblastic leukaemia due to a missense mutation in
exon 6 of the TP53 gene (c.626G>A: p.Arg209Gln)
confirming the diagnosis of Li-Fraumeni syndrome. The
1 2
1 2
1 2,*
56
second was a family with breast, ovarian and spinal cord
cancer due to a 21 base pair non-frame shift deletion in
exon 4 of the BRCA1-associated RING domain-1 protein
(BARD1)
gene
(c.1075_1095delTTGCCTGAATGTTCTTCACCA;p.Leu359_P
ro365del).
Conclusion: The implementation of this cancer gene
panel test has enabled us to determine the aetiology of
cancer in a cost effective and timely manner leading to
better cancer management in the context of a
developing country.
eGFR loci: UMOD/PDILT (1 SNP, 1bp), GCKR (3 SNPs,
11.7kb), RGS14 (3 SNPs, 6.8kb), MPPED2 (3 SNPs,
19.6kb), BCAS3 (4 SNPs, 16.1kb), SHROOM3 (6 SNPs,
28.2kb), and UNCX (6 SNPs, 5.8kb). At GCKR, the credible
set covers three SNPs including GCKR P446L, a predicted
functional variant at this locus. Potential causal variants
at the remaining six loci, map to introns or overlap
regulatory elements from ENCODE, thereby highlighting
potentials mechanism for the action of these loci on
eGFR.
Conclusion: Our findings provide evidence that transethnic GWAS can be used for discovery of novel loci and
to fine-map potentially causal variants that can be taken
forward for experimental validation and could help to
further our understanding of the biological mechanisms
underlying disease.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
O17
FINE-MAPPING EGFR SUSCEPTIBILITY LOCI THROUGH
TRANS-ETHNIC META-ANALYSIS
1,*
2
3
4
A. Mahajan , J. Haessler , Y. Okada , A. Stilp , C. Laurie
4
5
16
, N. Franceschini , A. Morris
1
Wellcome Trust Centre for Human Genetics, University
2
of Oxford, Oxford, United Kingdom, Public Health
Sciences Division, Fred Hutchinson Cancer Research
3
Center, Seattle, United States, Graduate School of
Medical and Dental Sciences, Tokyo Medical and Dental
4
University, Tokyo, Japan, Department of Biostatistics,
5
University of Washington, Seattle, University of North
6
Carolina, Chapel Hill, United States, Department of
Biostatistics, University of Liverpool, Liverpool, United
Kingdom
O18
SPECTRUM OF HEREDITARY SPASTIC PARAPLEGIA AND
MUSCLE DISEASES IN QATAR
1,*
A. Aleem
and Mahmoud fawzy, Khalid Ibrahim,
Hussein Kamel
1
WEILL CORNELL MEDICAL COLLEGE IN QATAR, Doha,
Qatar
Objectives: Studying the clinical spectrum of hereditary
spastic parplegia in Qatar and Arab population.
Identifying the underlying gene mutations in families
enrolled in the study appying the whole genome
sequencing. Promoting the capacity of the stakeholder
and health provider in Qatar.
Methods: Review of patients' medical files and direct
interviews of patients. Collecting the demographic data
of patients and drawing the pedigrees emphasizing the
disease history in the family and consaguinity status.
Performing whole genome sequencing applying illumina
platform and alignment pipelines. Bioinformatics analysis
using the general available and commericial tools.
Candidate variants were checked againest the published
databases and the unpublished 108 Qatari genome
database. Standared and in-vito expression experiments
were used to validate the mutation pathogenicity.
Results: Herediatry spastic paraplegia of pure and
complex phenotypes were identified in our cohort. The
complex nature of HSP, the predominant phenotype in
our patients, has shown various body systems
involvements including the brain malformation.
Demographic data (gender, age group, ethnicity, disease
severity and course) and the genomic candidate genes'
variants will be shown in the presentation. There are
several known and also newly recognized genes'
mutations were identified in our families.
Conclusion: The study has identified the presence of
different modes of Mendelian inheritance in patients
ascertained under the neurodegenrative HSP disorders
with more than 90% of cases were of autosomal
recessive inheritance. Sporadic cases were also
identified. The study was able to provide well defind and
Objectives: Genome-wide association studies (GWAS)
have been successful in identifying loci for estimated
glomerular filtration rate (eGFR). However, these loci are
typically characterised by common lead SNPs with
association signals extending over large genomic
intervals containing multiple transcripts. As a result,
limited progress has been made in identifying causal
variants and understanding the downstream disease
pathogenesis. To address these drawbacks, we
performed trans-ethnic meta-analysis to: (i) discover
novel eGFR loci; and (ii) fine-map known eGFR loci by
leveraging differences in linkage disequilibrium between
diverse populations.
Methods: We considered eight GWAS comprising of
59,880 individuals of European, African American,
Hispanic, and East Asian ancestry, each supplemented by
imputation up to the 1000 Genomes Project reference
panel (March 2012 release). Within each study,
association with eGFR (MDRD equation) was tested
under an additive model. We then combined association
summary statistics across studies: (i) using trans-ethnic
fixed effects meta-analysis, for discovery; and (ii) with
MANTRA, 1Mb up and down of the lead SNP at eGFR loci,
and constructed “credible sets” of SNPs that encompass
99% of the posterior probability of being causal.
Results: We identified six novel eGFR loci at genome-8
wide significance (p<5.0x10 ), the strongest association
-9
signals mapping near LRP2 (p=8.8x10 ) and NFATC1
-8
(p=1.3x10 ). We resolved fine-mapping of potential
causal variants to less than ten variants at seven known
57
validated gene information for a quite number of
families, which enabled some of them having prenatal
diagnosis and preimplantaion genetic diagnosis. Study
outcomes have ensured accurate gene diagnosis, proper
genetic counselling and better choices for family
planning which is of particular importance for those
families of the highest rate of consanguineous
marriages.
Malays, although the latter have some indigenous
ancestry that is as deep as that of the Semang and Senoi
in Peninsular Malaysia.
Conclusion: In common with the rest of Eurasia and
Australasia, all extant Southeast Asian mtDNA lineages
have a shared ancestry in a single dispersal from Africa
~50–60 ka, and because mainstream groups have
retained greater diversity than the isolated relict groups
we are likely to learn a great deal more about the early
settlements and subsequent demographic processes by
comparing both the Orang Asli groups and the other
populations from the region in similar detail.
Disclosure of Interest: None Declared
ORAL PRESENTATIONS II
O19
COMPLETE
MITOCHONDRIAL
DNA
SEQUENCE
VARIATION IN ORANG ASLI OF PENINSULAR MALAYSIA
1,*
2
3
S. K. K. Eng , P. A. D. Soares , Z. Zafarina , S. M. S. Chia
1
1
4
5
, S. Mohd Mokhtar , S. Oppenheimer , M. B. Richards
1
Center for Global Archaeological Research, Universiti
2
Sains Malaysia, Georgetown, Malaysia, Centre of
Molecular and Environmental Biology, University of
3
Minho, Braga , Portugal, School Of Health Sciences,
Universiti Sains Malaysia, Kubang Kerian, Malaysia,
4
School of Anthropology, University of Oxford, Oxford,
5
School of Applied Sciences, University of Huddersfield,
Huddersfield, United Kingdom
Disclosure of Interest: None Declared
O20
POPULATION GENETICS OF X-LINKED SNPS IN NORTH
EURASIA AND ITS IMPLICATIONS FOR HUMAN DNA
IDENTIFICATION
1
1 2,*
1
K. Vagaitseva , V. Stepanov , V. Kharkov , E. Trifonova
1
1
INSTITUTE FOR MEDICAL GENETICS,
Univeraity, Tomsk, Russian Federation
2
Tomsk State
Objectives: X-chromosome markers are informative tool
for studying a genetic diversity in human populations and
have become a useful in DNA identification when certain
complex kinship cases need to be unraveled. In this work
we present population genetic data on X-chromosomewide SNPs in North Eurasian populations and report
XSNP multiplex system for forensic genetics.
Methods: 2867 X-chromosomal SNPs were genotyped in
12 populations using Illumina microarray platform.
Twelve populations under study (Komi, Mordva,
Russians, Kirghiz, Kazakh, Uzbek, Buryat, Yakut, Evenk,
Tuva, Khanty, Ket) represent various geographic regions
of North Eurasia (Eastern Europe, Central Asia, Siberia
and North Asia) and language families.
Results: North Eurasian populations are highly
genetically differentiated with respect to XSNPs allele
frequencies. Average level of genetic differentiation (Gst)
for 12 populations is 6.03% and ranged from 1.05% to
30.05% per individual SNP. Principal component analysis
of allele frequencies demonstrated geographic pattern of
population clustering, as well as longitudinal gradient in
genetic diversity. 66 XSNPs characterized by high
expected heterozygosity and linkage equilibrium in
populations under study were selected for constructing a
panel for forensic genetic applications. Average
heterozygosity of selected SNPs varied from 0.4925 to
0.4958. Overall values of power of discrimination for
males and females (PDm and PDf) obtained with this
XSNPs set are several magnitude higher than those for
standard forensic STR panels. Protocol for multiplex
amplification of 66 XSNPs in 2 separate multiplex PCR
reactions and MALDI-TOF mass spectrometry genotyping
was developed.
Conclusion: North Eurasian populations demonstrate
high level of genetic diversity and differentiation for X-
Objectives: To characterise the whole-mitochondrial
DNA (mtDNA) genome variation of the Orang Asli of
Peninsular Malaysia, in order to provide much greater
genealogical and therefore phylogeographic resolution,
and also much greater chronological precision, to
population-genetic analyses. To compare the Orang Asli
mtDNA genomes with the Peninsular Malays and
Southeast Asians’ variation in general, in order to trace
patterns of maternal ancestry and help to elucidate past
dispersals and admixture on the female line of descent.
Methods: We have expanded the number of Orang Asli
populations (from Semang, Senoi and Aboriginal Malay)
examined for HVS-I and analysed about 40 lineages at
the level of whole-mtDNA genomes covering most of the
extant Orang Asli mtDNA diversity. We aligned the
sequences against the revised Cambridge Reference
Sequence (rCRS) using the Sequencher 5.0 software, and
recorded variants from the rCRS. We then used the
weighted reduced-median algorithm of the Network 4.6
package to build the most parsimonious phylogeny, and
estimated time depths using maximum likelihood with
the PAML software.
Results: We use these data to help us reassess and
extend some of the suggestions about the prehistory of
the region, put forward on the basis of the earlier, more
limited datasets. Our work has confirmed that the Orang
Asli populations indeed experienced high genetic drift,
likely due to their extremely small group sizes and
population subdivision. All three Orang Asli groups have
local roots that trace back to ~50 ka, and all have been
affected to a greater or lesser extent by subsequent
migrations to Peninsular Malaysia. The Semang and
Senoi show less haplogroup diversity than the Aboriginal
58
chromosome-wide SNPs. Based on obtained population
genetic data, highly informative multiplex XSNPs panel
for forensic genetics was developed.
This work was supported by the Federal target program
“Research and development on the priority directions of
Russian scientific-technological complex development”
(Agreement #14.604.21.0019).
prediction of protein interactions by network
embedding. Bioinformatics 29, i199–209 (2013).
3) Cannistraci, C. V., Ravasi, T., Montevecchi, F. M.,
Ideker, T. & Alessio, M. Nonlinear dimension reduction
and clustering by Minimum Curvilinearity unfold
neuropathic pain and tissue embryological classes.
Bioinformatics 26, i531–9 (2010).
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
POPULATION GENETICS & STATISTICS
O21
HIGHLIGHTING NONLINEAR PATTERNS IN POPULATION
GENETICS DATASETS
1,*
T. Ravasi
1
Division of Applied Mathematics and Computer Sciences,
KING ABDULLAH UNIVERSITY OF SCIENCE &
TECHNOLOGY, THUWAL, Saudi Arabia
O22
GENES REGULATED BY VITAMIN D IN BONE CELLS ARE
POSITIVELY SELECTED IN EAST ASIANS.
1,*
1
2
1
1
Q. Ayub , E. Arciero , S. A. Biagini , Y. Chen , Y. Xue ,
2
3
1
D. Luiselli , L. Pagani , C. Tyler-Smith
1
Human Evolution, THE WELLCOME TRUST SANGER
2
INSTITUTE, Hinxton, United Kingdom, Department of
Biological, Geological and Environmental Sciences,
3
University of Bologna, Bologna, Italy, Division of
Biological Anthropology, University of Cambridge,
Cambridge, United Kingdom
Objectives: Detecting structure in population genetics
and case-control studies is important, as it exposes
phenomena such as ecoclines, admixture and
stratification. Principal Component Analysis (PCA) is a
linear dimension-reduction technique commonly used
for this purpose, but it struggles to reveal complex,
nonlinear data patterns. In this paper we introduce noncentred Minimum Curvilinear Embedding (ncMCE), a
nonlinear method to overcome this problem.
Methods: The principle behind ncMCE, suggests that
curvilinear distances between samples (here the
population individuals) may be estimated as pairwise
distances over their Minimum Spanning Tree (MST),
constructed according to a selected norm (Euclidean,
correlation, etc.) in a high-dimensional feature space
(here the genotype frequency space). The collection of
all nonlinear pairwise distances forms a distance matrix
called the MC-distance matrix or the MC-kernel, which
can be used as an input in algorithms for dimensionality
reduction, clustering, classification and more generally in
machine learning.
Results: Here we show that ncMCE can separate
individuals into ethnic groups in cases in which PCA fails
to reveal any clear structure. This increased
discrimination power arises from ncMCE’s ability to
better capture the phylogenetic signal in the samples,
whereas PCA better reflects their geographic relation.
We also demonstrate how ncMCE can discover
interesting patterns, even when the data has been poorly
pre-processed.
Conclusion: The juxtaposition of PCA and ncMCE
visualizations provides a new standard of analysis with
utility for discovering and validating significant
linear/nonlinear complementary patterns in population
genetic data.
References: 1) Alanis-Lobato G, Cannistraci CV, Ravasi T.
Exploitation of genetic interaction network topology for
the prediction of epistatic behavior. Genomics. 2013
Oct;102(4):202-8.
2) Cannistraci, C. V., Alanis-Lobato, G. & Ravasi, T.
Minimum curvilinearity to enhance topological
Objectives: Fat soluble vitamin D is activated by
ultraviolet (uv) radiation and regulates many genes that
play a major role in human development and physiology.
Our aim was to determine whether gene sets regulated
by vitamin D show signals of positive selection as humans
expanded from tropical Africa into northern hemisphere
and higher latitudes, with seasonal variation in uv
radiation, in the last 50-60,000 years.
Methods: We investigated signals of positive selection in
gene sets related to physiological function of vitamin D
using re-sequencing data from worldwide populations
generated by the 1000 Genomes Project and an
algorithm that we had developed earlier to test for
evolutionary adaption by comparing site-frequency
spectrum based summary statistics between the 9
chosen gene sets and matched controls [1,2].
Results: We detect a strong signal for positive selection
in East Asians for genes regulated by vitamin D in bone
tissue. Three genes (CXXC1, LRP5 and RUNX2) were
responsible for this signal. Gene haplotype networks
support these results and indicate the same pattern in a
smaller proportion of Europeans, albeit below the
stringent threshold used in this study, suggesting a
common adaptation signal in non-Africans to regulate
bone modelling. Using differences in derived allele
frequencies, haplotype diversity and linkage patterns we
identify several candidate regulatory variants in each
gene that may be driving this signal.
Conclusion: This study highlights positive selection in
three genes regulating vitamin D mediated bone
remodelling and shows how mechanisms other than
lighter skin pigmentation could offer protection against
infections and skeletal deformities that are associated
with reduced levels of vitamin D at higher latitudes.
References:
1. Ayub Q, B Yngvadottir, Y Chen, Y Xue,
M Hu, SC Vernes, SE Fisher and C Tyler-Smith. FOXP2
59
targets show evidence of positive selection in European
populations. Am J Hum Genet 92:696-706 (2013).
2. 1000 Genomes Project Consortium. An integrated
map of genetic variation from 1,092 human genomes.
Nature 491:56-65 (2012).
Oceania, there are additional refinements and insights to
be gained from genome-wide data.
Disclosure of Interest: None Declared
O24
SPATIALLY EXPLICIT MODELS TO RECONSTRUCT THE
COLONISATION OF ASIA
1 2,*
A. Eriksson
and PAPGI
1
Zoology, Cambridge University, Cambridge, United
2
Kingdom, Integrative Systems Biology Lab, King Abdullah
University of Science and Technology, Thuwal, Saudi
Arabia
Disclosure of Interest: None Declared
O23
INSIGHTS FROM GENOME-WIDE DATA INTO THE
PEOPLING OF NEAR AND REMOTE OCEANIA:
EXTENDING AND REFINING THE “DUAL-WAVE” MODEL
1,*
M. Stoneking
1
MPI-EVA, Leipzig, Germany
Objectives: The availability of next-generation
sequencing data offers the possibility of asking
sophisticated questions about the colonisation history of
Asia. But the wealth of information available from
complete genomes needs to be matched with clear,
hypothesis driven approaches that allow us to distinguish
among the sometimes subtly different scenarios that
have been proposed by anthropologists.
Methods: In this talk, I will present a new climate-driven
spatially explicit framework for describing the
colonisation of Asia. Simpler versions of this framework
has been used successfully to look at the out of Africa
expansion of anatomically modern humans and their
possibly hybridisation with Neanderthal, and thus offer
great promise in helping us unravel the details of the
colonisation of the Asian continent.
Results: Testing of the framework using simulated data
reveals that it has high power to detect multiple waves
into the same area using combinations of genetic
differences between populations (such as f4 statistics). I
will also present results using a global panel of highquality genomes from the Pan-Asian Population
Genomics Initiative (PAPGI) to test the hypothesis of
separate waves of colonisation of Eurasia and the extent
of gene flow between the waves.
Conclusion: The combination of next-generation
sequencing data and climate-informed spatially explicit
models of past demography allows for disentangling
subtle patterns of shared genetic variation. In addition,
the best-fitting models generate explicit predictions for
key demographic events such as first arrival time and
areas of common ancestry between populations, which
can be compared to other lines of evidence such as
archaeology.
Objectives: Previous studies of the genetic history of
Near and Remote Oceania have largely relied on data
from uniparental markers, e.g. mtDNA and the Y
chromosome (NRY). These studies have largely
supported the “Dual-Wave” model of population
settlement of Oceania, in which there was an early
migration that colonized Near Oceania some 40,00050,000 years ago. This was followed by a migration of
Austronesian-speakers from southeast Asia that began
some 4,000-5,000 years ago, moved through coastal and
island New Guinea, and eventually colonized the furthest
reaches of Remote Oceania by about 1,000 years ago.
The mtDNA/NRY studies have also revealed a strong sexbiased dichotomy in the settlement of Remote Oceania,
with a high frequency of mtDNAs of presumed
Austronesian origin and Y chromosomes of presumed
Near Oceanian origin, which may reflect a largely
matrilocal residence structure of the incoming
Austronesians.
Methods: While the studies of uniparental markers have
been quite informative, they are limited in their ability to
make inferences regarding demographic history.
Genome-wide data is ideally suited for such purposes,
but to date there have been only limited studies of
genome-wide data in Near and Remote Oceania. Here
we report the results of analyzing a dataset consisting of
256 individuals from 30 populations from southeast Asia
and Near and Remote Oceania, all genotyped on the
Affymetrix Human Origins Array for ~600,000 SNPs.
Results: These analyses reveal: unexpected genetic
structure in Near Oceania; strong support for an Out-ofTaiwan origin for the Austronesian expansion; a probable
initial colonization of Santa Cruz (in westernmost Remote
Oceania) directly from the Bismarck Archipelago that
bypassed the intervening Solomon Islands; and
subsequent bidirectional settlement of the Solomon
Islands from both the west and the east. The results of
ongoing analyses to date the admixture signals and other
demographic events revealed by the genome-wide data
will be reported at the meeting.
Conclusion: Overall, our results suggest that while the
“Dual-Wave” model is a useful framework for
understanding the settlement of Near and Remote
Disclosure of Interest: None Declared
60
CANCER GENOMICS
ORAL PRESENTATION II
O25
SMART SCREENING FOR CANCER DRUG DISCOVERY
1,*
S. Yoon
1
Biological science, Sookmyung Women's University,
Seoul, Korea, Republic Of
O29
LEVERAGING GALAX-C, A NOVEL ASIAN GENOMIC
VARIANT DATABASE TO ENHANCE DIAGNOSTIC YIELD
FOR PAEDIATRIC DEVELOPMENTAL DELAY
1,*
A. Anwar
1
Director, Sengenics, KL, Malaysia
Objectives: Discovery studies on clinically relevant drug
applications and their mode of actions are accelerated by
integrating multi-level omics data with chemical or siRNA
screening data on diverse biological samples. We have
addressed this challenge by constructing a smart
screening platform that combines technologies on big
data mining and experimental high throughput siRNA
screening for targeted cancer drug discovery.
Methods: For new target identification in mutationspecific cancer regulation, the association study of
gene/protein expression and drug response was carried
out on a wide variety of cancer cell lines. Drug response
(GI50) and omics data generated on well-characterized
cancer cell line panels were obtained from public
databases such as NCI60 (National Cancer Institute),
CCLE (Cancer Cell Line Encyclopedia), and GSK
(GlaxoSmithKline). We also used the whole exome and
RNA sequencing data from patient cancer samples,
available from TCGA (The Cancer Genome Atlas). As a
complementary system of omics profile and drug
screening data, we carried out gene perturbation assays
using the high-throughput loss-of-function screening for
a siRNA library covering 4,800 drug target genes.
Results: We have identified many unique mutationspecific gene expression markers and chemical/siRNA
response using the smart screening platform. Here we
present several achievements of data mining and
experimental validation including animal study. The
overexpression of PDE4D gene was found to be specific
to SKT11-mutated lung cancers. Knockdown or inhibition
of PDE4D gene selectively decreased the growth of
STK11 mutant lung cancer cell lines. From the combined
analysis of drug screening and siRNA library screening
data, we also identified that the inhibition of some ion
channels were specifically effective on STK11 mutant
cancer samples. in vivo animal studies confirmed the
efficacy of these targeted therapies on mutation-specific
background. In addition, siRNA library screening on cell
lines in 3D and 2D culcure conditions, revealed selected
role of genes in metabolic pathways for the sphere
formation of cancer cells.
Conclusion: The efficient, combined smart screening
platform can lead to system-level analyses for the
prediction and characterization of selective drug
response on target diseases. We now provide this
platform service to academic and industrial
organizations.
Objectives: Clinical interpretation of data from Whole
Exome Sequencing (WES) in very challenging given the
large number of variants identified. A critical impediment
relating to diagnosis of Arab and Asian individuals is the
shortage of genetic data relating to these ethnicities.
Methods: Mean allele frequency for many variants
identified by WES in these individuals is unknown. This
further complicates clinical interpretation, and can result
in false negative or false positive diagnoses. A new
database called Galax-C comprising WES data from over
4,500 normal and paediatric developmental delay
individuals from Arab and Asian ethnicities has been
constructed.
Results: Following detailed cross-analysis with data from
dbSNP, ClinVAR and the 1000 Genomes project, more
than 6.5 million non-redundant, novel variants were
identified. All known and novel variants were filtered and
prioritised using the Galax-C interface that integrates
data from Galax-C with dbSNP, ClinVAR and PharmGKB
alongside regional variant specific information. Further
filtering using empirical rules based on effect on protein
structure/function, blocks of loss of heterozygosity and
parental segregation were used to identify potential
pathogenic mutations.
Conclusion: Detailed clinical case studies of how Galax-C
allele frequencies were used to rule out benign high
frequency variants and rule in pathogenic low frequency
mutations will be presented.
Disclosure of Interest: None Declared
O30
MINING DNA: AN INVESTIGATION ON FEATURE-BASED
CLASSIFICATION IN GENOME SCALE MINING OF
ENHANCERS
1,*
1
2
1
S. Nazeri , S. N. K. Lee , N. Mustapha , M. B. Hossein
1
cognitive science, universiti malaysia sarawak, kuching,
2
FSKTM, UPM, Kuala Lumpur, Malaysia
Objectives: This paper demonstrates the categorization
of discriminative feature for Genome wide identification
of enhancers by using feature-based classification;
Feature-based classification is a pragmatic paradigm
which enables to predict the location of binding sites (i.e.
motif) including enhancers through massive data from
experimental techniques like ChIP-Seq.
This paper also attempts to present general framework
for supervised motif prediction (i.e. feature-based
classification). The framework compromises 4 steps data preparation, feature selection, classification and
Disclosure of Interest: None Declared
61
validation- for mining genome scale location of motifs.
Since distinguishing discriminative feature is crucial step
for
proposing
feature-based
models,
we
introduce general feature guidance for enhancer signal
discrimination purposes.
Methods: Documentary analysis on relevant featurebased methods which are currently being conducted.
This compromises all features they utilized for
identification of the binding sites (e.g. enhancers). We
also investigate through their goals, methods and
evaluations.
Results: We propose a new feature categorization which
includes generic features and motif specific features.
Accordingly, Features applicable for identification of all
types of motifs categorized as generic features and those
for specific motif as a motif specific features.
General features refer to general property of DNA
regions knows as CRMs (cis-regulatory regions) where
harbour sets of networks of correlated regulatory
elements. Motif specific features represent unique
property of distinct motif.
Each category of features includes own subclasses.
Generic features can be divided into three major
subclasses including K-mers, motif scores and epigenetic
features. Motif specific encompasses the sequence
information of specific binding sites. In many cases those
classes of features overlap each other.
Conclusion: Enhancers are cell specific regulatory binding
sites that regulate genes regardless of their location and
this makes the identification of enhancer notoriously
challenging.
Our review shows that combination of features which
belong to one single type (e.g. epigenetic features) gives
a clue of general binding preference. Also, association of
different types of features is vital to motif specific
extraction. In general, it is necessary to consider unique
property of specific binding sites alongside general
structure of CRMs for prediction of specific motifs.
our study is to identify additional genes with rare
variants of large effect that contribute to AD.
Methods: To identify novel genes we have applied threestage study design. First we performed exome
sequencing in 16 families with 4 or more affected cases
that include at least one distant relative (cousin). For
each family we have performed frequency filtering to
identify private functional variants that most closely cosegregate with the disease. We defined private variants
as not present in 1000 Genomes, ESP6500 and
dbSNP132. Second, for identified candidate genes we
performed a two-stage gene-mutation burden casecontrol study with Caucasian subjects. For 21 candidate
genes we performed Molecular Inversion Probes (MIP)
capture and targeted sequencing of 839 familial AD cases
from NCRAD and NIMH collections and 466 cognitively
normal elderly controls from ACT study. For 11 genes
that showed positive evidence for association in this
sample we have analyzed additional 1047 cases (NCRAD,
NACC and WashU) and 1243 controls (NCRAD, NACC,
WashU, NIMH). Lastly, for two genes that have shown
nominally significant evidence for association in the
combined sample (1886 cases and 1709 controls) we are
in the process of genotyping additional 4000 cases and
controls from Washington University.
Results: Exome sequencing in 16 families has identified
21 novel candidate genes. The mutation-burden case
control study in 839 cases and 466 controls have found
evidence for association in 11 genes and combined
analysis of 1886 cases and 1709 controls provided the
nominally significant evidence for association for two
novel genes. For two genes with nominally significant
gene-burden association the replication study in 4000
cases and controls is ongoing and will be reported.
Conclusion: Family based exome sequencing coupled
with targeted gene burden case-control analysis is a
powerful way for gene identification in complex genetic
disorders such as AD.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
MENDELIAN & COMPLEX DISEASES
O33
GENOMEWIDE ASSOCIATION STUDY OF CANNABIS
DEPENDENCE SEVERITY REVEALS NOVEL RISK VARIANTS
AND SHARED RISK WITH MAJOR DEPRESSIVE DISORDER
1
2
3
2
R. Sherva , Q. Wang , H. R. Kranzler , H. Zhao , R.
1
4
1
5,*
Koesterer , A. Herman , L. A. Farrer , J. Gelernter
1
Department of Medicine (Biomedical Genetics), BU
2
School of Medicine, Boston, Genetics, YALE UNIV.
3
SCHOOL OF MEDICINE, New Haven, Psychiatry, Univ.
Pennsylvania School of Medicine, Philadelphia,
4
Psychiatry, YALE UNIV. SCHOOL OF MEDICINE, New
5
Haven, Psychiatry and Genetics, YALE UNIV. SCHOOL OF
MEDICINE, West Haven, United States
O31
NOVEL GENE IDENTIFICATION IN ALZHEIMER DISEASE
1,*
2
2
3
3
Z. Brkanac , J. Rehker , R. Nesbitt , Q. Yi , B. Martin ,
3
4
3
5
D. Nickerson , W. Raskind , J. Shendure , C. Cruchaga
1
Department of Psychiatry, University of Washington,
2
Seatle, WA 98195-6560, Department of Psychiatry,
3
4
Department of Genome Scinences, Department of
5
Medicine, University of Washington, Seatle, Department
of Psychiatry, Washington University, St. Louis, United
States
Objectives: Late onset Alzheimer's disease (AD) is a most
common cause of dementia. The genetics of AD is
complex with contribution from rare and common
variants. In addition to PSEN1, PSEN2 and APP rare
variants with large effects that contribute to AD were
recently identified in TREM2 and PLD3. The objective of
Objectives: Cannabis dependence (CnD) is a serious and
worsening problem worldwide, of growing importance in
the US as cannabis becomes legally available amidst
uninformed perceptions of its potential harmfulness.
62
Specific risk variants have not been firmly identified
previously.
Methods: GWAS for DSM-IV CnD criteria count in two
cohorts genotyped on Illumina microarrays (5,774
African American and 6,569 European American (EA)
subjects). We also examined overlap in genetic risk
between CnD and five other psychiatric traits, using our
GWAS results together with Psychiatric Genomics
Consortium data.
Results: We identified four independent regions with
genome-wide significant single-nucleotide polymorphism
-8
associations: rs80071044 (p=1.37x10 ) on chromosome
-8
7, rs186825689 (p=1.99x10 ) near S100 calcium binding
-8
protein (S100B), rs143244591 (p=2.30x10 ), on
-8
chromosome 3, and rs77378271 (p=2.80x10 ) in cub and
sushi multiple domains 1 (CSMD1). We additionally
identified exome-wide significant association with two
-7
missense mutations: rs150054920 (p=1.43x10 ) in
ubiquitin specific protease 12 (USP12) and rs571655
-6
(p=1.10x10 ) in nephrocystin 4 (NPHP4). The GPA
method (Chung D et al 2014) was used to test
significance of pleiotropy between CnD and five major
psychiatric disorders, using Psychiatric Genomics
Consortium data and our CnD GWAS data. For each
disease pair, we estimated percentage of SNPs shared by
two traits and tested the significance of pleiotropy. In
EAs, there was significant CnD-major depressive disorder
-5
(MDD) pleiotropy (p=2.39x10 ), and genome-wide, 1.7%
of all imputed SNPs were estimated to be associated
with both CaD and MDD.
Conclusion: Several of the genes identified have
functions related to neuronal calcium homeostasis or
CNS development, pathways associated with risk for
other substance dependence phenotypes. These
analyses also showed evidence for association with SNPs
in several genes associated with schizophrenia risk, and
significant evidence for pleiotropy with MDD, raising
questions regarding the genetic overlap and suggesting
that the increased risk of schizophrenia and depression
among heavy cannabis users is partially genetic.
References: Chung D, Yang C, Li C, Gelernter J, Zhao
H: PLoS Genet. 2014 Nov 13;10(11):e1004787
(Exome variants) influencing the disease has not been
studied well. Identification of such functional variants
may reveal the biology of the disease and help to
understand the intricacy of disease. Exome wide
association study is one of the cost effective ways to
identify functional variants of diseases. Here, we present
an exome wide association study for childhood obesity in
Indian urban children of Indo-European ethnicity. The
study aims in the identification of functional variants for
childhood obesity. This study also aims to reveal the
contribution of such rare variants in precipitation of
childhood obesity.
Methods: The whole exome genotyping was performed
using Affymetrix Axiom Exome Genotyping Array in 3000
children of Indo-European ethnicity. Genotype quality
controls (sample disc quality control, plate call rate) were
performed as per the protocols given by Affymetrix.
Association of quality control-passed SNPs with
childhood obesity (dichotomous) was tested by logistic
regression analysis under a log-additive model adjusting
for age, sex, and potential population stratification using
PLINK v1.07. Monomorphic markers were removed from
the study. Burden test was performed using SNP-set
Kernel Association Test (SKAT) package in R to identify
collective contribution of all the variants in a given gene.
Results: The analysis of the data revealed two novel
variants significantly associated with obesity in Indian
children. These variants were found to be previously
associated with cholesterol level indicating the likelihood
of identifying true signals in our analysis. SKAT analysis
showed that the identified novel gene is associated with
higher burden. Further, SKAT analysis helped us to
identify relevant genes that have higher occurrence of
both rare and common variants associated with
childhood obesity. In addition, we also replicated some
known obesity associated variants thereby adding
confidence to our study.
Conclusion: Our results identified novel functional
variants that play a pivotal role in genetic predisposition
to childhood obesity in Indian children. This study gives
new insight in identifying the role of coding variants in
the etiology of childhood obesity.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
NON-CODING & RNA BIOLOGY
O34
EXOME WIDE ASSOCIATION STUDY FOR CHILDHOOD
OBESITY- AN ATTEMPT TO IDENTIFY CODING VARIANTS
1,*
1
1
2
D. bharadwaj , A. K. Giri , R. K. G , N. Tandon , B.
1
Consortium
1
Genomics and Molecular Medicine, CSIR-Institute of
2
Genomics and Integrative Biology, Department of
Endocrinology, All India Institute of Medical Sciences,
Delhi, India
O35
RECONSTRUCTION OF SYNTHESIS PROTEIN THROUGH
CODON UNIQUE REVISION (RESCUER) FOR DMD GENE
MUTATION CORRECTION IN MALAYSIAN PATIENTS
WITH DUCHENNE MUSCULAR DYSTROPHY
1 2,*
12
1
3
A. Q. Rani
, S. H. Teguh , S. Sarina , A. R. Salmi , B.
3
23
A. Zilfalil , Z. Zabidi–Hussin
1
2
Human Genome Centre, Center for Neuroscience
3
Service and Research, Paediatrics Department, School of
Medical Sciences, Universiti Sains Malaysia, USM Health
Campus, 16150 Kubang Kerian, Kelantan, Malaysia
Objectives: Childhood obesity has been related with
manifestation of metabolic disorders in later life. Genetic
composition of individuals has been found to affect
childhood obesity. The contribution of coding variants
63
Objectives: Studies in various populations have shown
that about 90% of mutations that created premature
stop codons in the reading frame (out-of-frame
mutation) of Dystrophin result in a severe Duchenne
Muscular Dystrophy (DMD) phenotype. This report aims
to investigate the ability of an approach coined
reconstruction of synthesis protein through codon
unique revision (RESCUER) to correct translation error
due to out-of-frame mutation. RESCUER is basically a
molecular approach to manipulate (artificially delete or
insert) codon’s nucleotides for restoration of aberrant
reading frame. Our study showed that the most
frequently deleted exon in our DMD patient cohort is
exon 50. Based on this, we designed a codon correction
approach within exon 51 to restore the reading frame of
dystrophin. In this study, we employed a dystrophin
deletion scenario from one of our patients having
deletion of the entire exon 50.
Methods:
Three Minigenes were created using overlapping
extension PCR to carry out this study; the Patient
Minigene consisting of exons 49,51 and 52, the
Corrected Minigene consisting of exons 49, 51 (with
artificial deletion of 2 nucleotides) and exon 52 and the
Wildtype Minigene containing exons 49,50,51 and 52.
Specific primers were used to generate these minigenes
including their specific cis-acting elements.
Results: This presentation will show preliminary data on
the effects of RESCUER approach on restoration of
aberrant Dystrophin reading frame caused by deletion of
exon 50, using a cell-based reporter assay.
Conclusion: RESCUER is a potential approach to rescue
patients with out-of-frame mutation by restoration the
open reading frame. This approach may provide the
opportunity to transform the severe DMD phenotype
into the milder Becker muscular dystrophy (BMD).
Disclosure of Interest: None Declared
Objectives: Coronary artery disease (CAD), one of the
leading causes of death globally, is influenced by both
environmental and genetic risk factors. Gene-centric
genome-wide association studies (GWAS) involving cases
and controls have been remarkably successful in
identifying genetic loci contributing to CAD. Modern in
silico platforms, such as candidate gene prediction tools,
permit a systematic analysis of GWAS data to identify
candidate genes for complex diseases like CAD.
Subsequent integration of drug-target data from drug
databases with the predicted candidate genes can
potentially identify novel therapeutics suitable for
repositioning towards treatment of CAD.
Methods: Previously, we were able to predict 264
candidate genes and 104 potential therapeutic targets
for CAD using Gentrepid (www.gentrepid.org), a
candidate gene prediction platform with two
bioinformatic modules to reanlyze Wellcome Trust CaseControl Consortium GWAS data. In an expanded study,
using five bioinformatic modules on the same data,
Gentrepid predicted 647 candidate genes and
successfully replicated 55% of the candidate genes
identified by the more powerful CARDIoGRAMplusC4D
consortium meta-analysis (Figure 1). Hence, Gentrepid
was capable of enhancing lower quality genotypephenotype data, using an independent knowledgebase of
existing biological data. Here, we used our methodology
to integrate drug data from three drug databases: the
Therapeutic Target Database, PharmGKB and Drug Bank,
with the 647 candidate gene predictions from Gentrepid.
We utilized known CAD targets, the scientific literature,
existing drug data and the CARDIoGRAMplusC4D metaanalysis study as benchmarks to validate Gentrepid
predictions for CAD.
Results: Our analysis identified a total of 184 predicted
candidate genes as novel therapeutic targets for CAD,
and 981 novel therapeutics feasible for repositioning in
clinical trials towards treatment of CAD (Figure 1). The
benchmarks based on known CAD targets and the
scientific literature showed that our results were
significant (p < 0.05).
Conclusion: We have demonstrated that available drugs
may potentially be repositioned as novel therapeutics for
the treatment of CAD. Drug repositioning can save
valuable time and money spent on preclinical and phase I
clinical studies.Disclosure of Interest: None Declared
O36
NOVEL THERAPEUTICS FOR CORONARY ARTERY DISEASE
FROM GENOME-WIDE ASSOCIATION STUDY DATA
1,*
2
1
3
M. Grover , S. Ballouz , T. Crowley , R. George , C.
1
1
Sherman , M. Wouters
1
2
Deakin University, Geelong, Australia, Cold Spring
3
Harbor Laboratory, NewYork, United States, Victor
Chang Cardiac Research Institute, Sydney, Australia
64
Picture/graph (O36)
Results: Across all species, remarkably, we observed
definitive evidence that on each lineage, specific genomic
"words" have been rapidly removed from the genome, at
rates highly inconsistent with neutral mutation changes.
It seemed possible that they might have been past
binding targets of PRDM9, with rapid evolution of the
PRDM9 zinc finger array explaining their lineagespecificity, and differences in PRDM9 binding explaining
the stronger signals in specific genomic regions. As
predicted by BGC, we saw an overwhelming support for
bias towards acceleration of motif loss rather than motif
gain. In human lineage, it is shown that the method
almost successfully identifies the current human hotspot
motif, CCNCCNTNNCCNC.
Conclusion: It is suggestive that we are able to see
positions of ancient hotspots, and could even make maps
of ancient hotspot positions, by looking at the
distribution of motif losses along the genomes. The
findings could further shed light on the dynamic turnover
of PRDM9 binding sites, and help understand the details
of how recombination has shaped over genomes.
POSTERS
BIOINFORMATICS
P001
SIGNATURES OF RAPID CHANGE IN PRDM9 BINDING
TARGETS ARE EVIDENT IN ARCHAIC HUMANS
1,*
2
3
A. Tumian , R. Davies , S. Myers
1
International Islamic University Malaysia, Kuala Lumpur,
2
Malaysia, Wellcome Trust Centre for Human Genetics,
3
Department of Statistics, University of Oxford, Oxford,
United Kingdom
Objectives: Multiple lines of evidence suggest that the
rapidly evolving zinc-finger (ZF) protein, PRDM9, is
responsible for initiating much or all of recombination in
human. PRDM9 shows extreme variation in both the
number and sequence of its ZFs, between species and
amongst individuals, across mammals. The rapid
evolution of the PRDM9 ZF array may be a response to
escape a self-destructive drive called biased gene
conversion (BGC), which can cause preferential
transmission of hotspot disrupting alleles, and leading to
erosion of vital recombination sites in the genome
through time. Using the recent available Neanderthal
and Denisovan high quality genomes, we developed
statistical methods that identify the locations where
meiotic recombination could have occurred in the past.
This is achieved by looking for short words that have
undergone rapid losses or gains in each lineage.
Methods: In particular, the statistical framework involves
an enumerative approach that scans genomewide
archaic human genomes which have been mapped to a
6-way primate alignment, exhaustively catalogues all
short exact motifs, and identifies statistically highly
evolved words.
Disclosure of Interest: None Declared
P002
USING THE SEQUENCE CHROMATOGRAPHY TO ANALYZE
THE QUANTITY OF COPY NUMBER VARIATION
1,*
2
C.-L. Tsai , Y.-S. Lee
1
Genomic Medicine Research Core Laboratory, Chang
2
Gung Memorial Hospital, Department of Biotechnology,
Ming-Chuan University, Kwei-Shan, Taiwan, Province of
China
Objectives: Copy number variations (CNVs) means
amplified or deleted a region of DNA sequence in
65
genome, which sometimes associates with some
diseases; such as cancer, autism or inherited diseases.
The aim of this study was to reveal the CNVs of target
genes through analyzing heterozygous chromatography
trace of PCR direct sequencing.
Methods: Among the methods used to detect CNVs, the
Paralogue ratio test (PRT) used a pair of fluorescentlabeled primer to amplify the target sequence and
paralogous DNA sequences. After comparing two PCR
products signal, the copy number of target sequence can
be estimated by PRT method. According this algorism,
the log ratio of intensity (LRi) of the heterozygous DNA
sequence chromatogram from two PCR products also
could be estimate the copy number of target genes by
Mixed
Sequence
Reader
(MSR)
method
1
(http://msr.cs.nthu.edu.tw/) . Both PRT and MSR
required for designing at least 20 bp paralogous DNA
sequence; however, it is not easy to design 20 basepair
(bp) paralogous sequence primers which suitable for all
of CNV regions
Results: To test this hypothesis, we tried to design the
shorter primers that contain only 18, 12 or 10 bp
paralogous sequence primers to detect the target genes.
Here, we choose the PGK1 and ARAF gene that located
on the X chromosome, which could be 2 copies in female
and one copy in male. Our results show that only 12 bp
paralogous DNA sequence primers can be successfully
used to detect CNVs by MSR method. In addition, the
similar methods could be applied to detect CNVs of
DEFB4 and AMY1A in our study.
Conclusion: Our results show that only 12 bp paralogous
DNA sequence primers can be successfully used to detect
CNVs by MSR method.
References: Chang CT#, Tsai CN#, Tang CY, Chen CH, Lian
JH, Hu CY, Tsai CL, Chao A, Lai CH, Wang TH* and Lee YS*.
Mixed Sequence Reader (MSR) for Analyzing DNA
sequences
with
heterozygous
base
calling
chromatography to detect genomic variations with a
reference database. 2012, The Scientific World Journal,
2012:365104.
the proteins in snake venom have very specific effects on
various biological functions including blood coagulation,
blood pressure regulation, and transmission of the
nervous or muscular impulse and have been developed
for use as pharmacological or diagnostic tools or even
useful drugs. [2].
Methods: we will adopted methodology and by using A
MySQL and PHP which and for designing VISIO 2007.
Results: This report focuses on the processes and
Development of database .Although snake venom can be
fatal for humans, but it has also gained tremendous
prospects for the use in pharmaceutical field.. Besides
the obvious benefits to produce antivenom, there are
many exciting discoveries in various studies that gives
promise on many medical fronts.
Conclusion: We provide an intuitive, well organized and
user friendly web interface that allows users to explore
the detail information of snake and venom proteins. It
includes common name, scientific name, entry id, entry
name, protein name and length of the protein sequence.
The information was incorporated from UniProt. Clicking
links leads to more detailed information. The utility of
this database is that it can provide a user-friendly
interface for users to retrieve the information about
snakes , venom and venom protein of different snake
species. A MySQL and PHP which and for designing VISIO
2007.
References:
1-Grant,G.A., Frazier,M.W.and chiappinelli, V.A.(1988)
Amino acid sequence kappa- flavitoxin : establishment of
a new family of snake venom neurotoxins. Biochemistry,
72, 3794-3798.
2.Mehdi Achour
Friedhelm Betz,AntonyDovgal
Nuno Lopes2014-05-2,Mysql,PHP Program.
3- Havey,A.L. and Anderson,A.J.(1991) Dendrotoxins :
snake toxins that block potassium channels and faciliate
neurotransmitter releasee. In Harvey,A.L. (ed), Snake
Toxins . pergamon press, New York,pp. 131-164.
4 - Wag staff Sc, Sanz L, Juarez P, Harrison RA, Calvete JJ.
(2009) , Combined snake venomics and venom gland
transcriptomic analysis of the ocellated carpet viper,
Echis ocellatus. J Proteomics, issue6 ,Page 609-623.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P003
WIDE-RANGING SNAKE VENOM DATABASE
1,*
1
1
I. A. Tayubi , A. S. A. Tawalah , F. J. Alzahrani , T. Khan
P004
BIOINFORMATIC APPROACH TO ANALYSE THE
FUNCTIONAL
EFFECT
OF
SNPS
IN
THE
OLIGOMERISATION DOMAIN "COILED-COIL"
1,*
1
2
K. Mohanasundaram , M. GROVER , A. GOSCINSKI , T.
13
1
CROWLEY , M. WOUTERS
1
2
School of medicine, SCHOOL OF INFORMATION
3
TECHNOLOGY, DEAKIN UNIVERSITY,
AUSTRALIAN
ANIMAL HEALTH LABORATORY, CSIRO BIOSECURITY
FLAGSHIP, GEELONG, Australia
1
1
Computer science, Kingabdulaziz university , jeddah
Saudi Arabia, rabigh, Saudi Arabia
Objectives: Snakes belongs to reptilia phylum of animal
kingdom. They produce a special kind of substance which
is mostly poisonous but not all snakes are poisonous.
This special kind of substance is called venom. Snake bite
causes number deaths or in some came physical or
physiological abnormalities. Venom is composition of
many types of protein, which differs from species to
species [1]. Venoms contain more than 20 different
compounds, mostly proteins and polypeptides. Some of
Objectives: With the advent of exome sequencing, the
need to identify pathogenic mutations at the amino acid
level has become urgent. While several tools have been
66
developed to distinguish pathogenic mutations from
harmless genetic variations, many of these knowledgebased systems are predicated on data from Mendelian
diseases, which may not translate well to interpretation
of disease-associated variants in complex diseases. We
posit that the context of the mutation (such as the
functional domain) is an important entity in determining
the phenotype. In this work, we adopted a bioinformatic
approach to distinguish harmless polymorphisms from
those likely to be pertinent to the phenotype in question
in a specific context. We studied the genotypephenotype relationship based on patterns of disease
mutations and polymorphisms observed in a common
structural unit, the coiled-coil domain. We chose coiledcoil domains because, like disordered regions, they are
involved in important protein-protein interactions.
Methods: We mined Uniprot for proteins with coiled-coil
domains. We extracted mutations from the online
databases - Uniprot and The Human Gene Mutation
Database. To compare differences between the stability
of the wild-type and varaint protein sequences, two
popular coiled-coil prediction methods were used:
multicoil and marcoil.
Results: Proline, lysine and valine were the most
overrepresented introduced mutations, with almost 36%
of the DM and 16% of all PV. Disease mutations were
majorly distributed in major registers a, d, e & g, whereas
polymorphisms were more in case of minor registers
such as b, c & f. We examined the difference between
oligomerisation scores of wild type and mutated
sequences, defined as ∆os = os(WT residue)-os(mutated).
The mean difference in case of disease mutants and their
wild types was .1676440, while for polymorphic variants
it was .0616565. We observed that 30% of the DM in
coiled-coil regions result in a Coil->Non-Coil transition,
compared to only 12.3% in the PV. Dimers were more
affected in DM.
Conclusion: DM in coiled-coil regions are more likely to
cause a significant structural perturbation and possibly
disrupt functions that necessitate the oligomerisation
formation and other vital functions of the coiled-coil
domain required for normal functioning of the protein.
Objectives: The widespread availability of nextgeneration sequencing technologies holds a promise for
widespread application of these technologies in
pathogen identification, and characterization in clinical
settings. Though a number of clinical isolates of
Mycobacterium tuberculosis complex (MTBC), the
causative organism for human tuberculosis has been
sequenced,
the
widespread
adaptation
and
implementation of this in clinical settings is largely
limited by the availability of a comprehensive pipeline
and annotation engine for automated analysis and
interpretation of data. To bridge the gap, we aim to
create a comprehensive database and annotation
resource for interpretation of variations from clinical resequencing
datasets of Mycobacterium tuberculosis complex.
Methods: Alignment and variation discovery was carried
out for over 4900 resequencing datasets of clinical
isolates that were publicly available in public domain and
deposited at the sequence read archive (SRA). Stringent
quality control analysis was done on sequencing data and
variations. We have used an in-house pipeline to
systematically analyze and curate single nucleotide
variations (SNV) as well as structural variations (SV) in
the form of insertions and deletions (indels). Annotations
and functional consequences prediction of the variations
was performed using ANNOVAR and SIFT tools
respectively. Apart from this, the data was also derived
from TBDreamDB database and from in-house literature
curation for annotating drug resistant variations.
Results: The update to TBvar currently provides
annotation for over 600,000 genomic variations, which
forms the largest and most comprehensive compendium
of genomic variations in MTBC. The resource apart from
providing annotations for the variations, also provides
information on the functional consequence and
frequency information. This forms the baseline to
annotate and interpret variations from clinical
resequencing of MTBC through a user friendly web
interface. The complete resource is accessible as a web resource.
Conclusion: We present an update to the largest
resource on single nucleotide variations and structural
variations for Mycobacterium tuberculosis complex with
a view to extending the knowledge related to the
variome of the pathogen for clinical applications.
Disclosure of Interest: None Declared
P005
TBVAR 2.0: A COMPREHENSIVE DATABASE AND
ANNOTATION
RESOURCE
FOR
ANALYSIS
OF
CLINICAL
RESEQUENCING
DATASETS
OF
MYCOBACTERIUM TUBERCULOSIS
1 2,*
3
4
K. Joshi , H. Dhiman , V. Scaria
1
2
CSIROpen Source Drug Discovery Unit, Academy of
Scientific
and
Innovative
Research
(AcSIR),
3
Department of Biotechnology, Delhi Technological
4
University, GN Ramachandran Knowledge Center for
Genome Informatics, CSIR INSTITUTE OF GENOMICS AND
INTEGRATIVE BIOLOGY (CSIR-IGIB), DELHI, India
Disclosure of Interest: None Declared
P006
FIRST TRIMESTER MATERNAL SERUM GLYCINE PREDICTS
THE RISK OF GESTATIONAL DIABETES IN OBESE
WOMEN.
1,*
2
1
M. Ryynanen , M. Gissler , M. Vaarasmaki , T.
3
4
Vaskivuo , S. Timonen
1
Department of Obstetrics and Gynecology, OULU
2
UNIVERSITY HOSPITAL, Oulu, National Institute for
Health and Welfare, National Institute for Health and
3
Welfare, Helsinki, Laboratories, OULU UNIVERSITY
67
4
HOSPITAL, Oulu, Department of Obstetrics and
Gynecology, Turku University Hospital, Turku, Finland
following a holistic perspective and see if biological
knowledge could be validated and, better yet, generated.
Methods: We represented autoimmune disease data
from the GWAS Catalogue1 as a Disease Network where
genes are linked by weighted edges indicating the
number of common diseases they are associated with2
(see the generated network below). We then performed
network analysis, link prediction, and bioinformatic
analysis over this network.
Results: Many real networks are known to have the small
world property and heavy-tailed node degree
distributions. To make sure that the topology of the
constructed network was not just random but was forced
by the biological properties of its nodes, we compared its
properties against those of random graphs with the same
number of nodes and edges (840 and 49,485
respectively). As it is clear from the table below, the
constructed disease network is far from being random.
After the application of a community detection
algorithm, based on Modularity Optimization, we found
that genes associated with the same disease or with
related diseases clustered together based only on
network topological features (e.g. see the community
grouping genes associated with Multiple Sclerosis or the
community grouping genes associated with inflammatory
diseases).
Conclusion: We are proposing a new means to study
GWAS data based on a systems perspective that allows
for the analysis of autoimmune disease genes not as
isolated entities but as important parts of a whole. The
preliminary results presented on this poster suggest that
systems biology and network science are two tools that
could help us untangle the intricate relationships
between genotype and phenotype.
Objectives: To evaluate the association between
gestational diabetes (GDM) and first trimester maternal
serum glycine concentration.
Methods: The original group comprised 31 146 women
who participated voluntarily to first trimester combined
Down screening at Oulu University Hospital during
1.1.2008-31.12.2011. Data concerning diabetes was
obtained from the National Research and Development
Centre for Welfare and Health, which records the
outcome of the pregnancy of all women in the country.
We chose in the study group 69 women with gestational
diabetes and 305 women without diabetes before or
after pregnancy. Women were divided in three
categories after their BMI: normal weight (BMI > 18.5 –
24.9) (N=12 GDM, 131 controls), overweight (BMI 25 –
29.9) (N= 28 GDM, 73 controls) and obesity (BMI > 30)
(N= 29 GDM, 75 controls). Glycine concentrations were
analyzed retrospectively by PerkinElmer from frozen first
trimester Down screening samples.
Results: The mean maternal age was 31.1 years and the
median weight 79.0 kg in GDM women. In controls the
corresponding figures were 29.4 years and 70.5 kg.
Overall, the risk of GDM was 6 %. The overall median
glycine concentration in GDM women was 0.93 MoM and
in controls 1.0 MoM.
In normal weight women there were no significant
difference of glycine concentrations between the groups
(0.99 GDM vs. 1.0 control) (Figure 1). In overweight and
obese women in the GDM group maternal serum glycine
concentration were significantly lower compared with
the control group. In the overweight women the median
glycine concentration was 0.95 MoM in GDM group vs
1.0 MoM in controls. In obese women the equivalent
figure was 0.88 vs 0.99, 1.03 MoMs.
Conclusion: Lower glycine levels in the first trimester
maternal serum are associated with GDM in overweight
and obese women. Glycine might be a reasonable marker
for GDM in obese women.
References: -
Disclosure of Interest: None Declared
COMPLEX GENETICS
P008
FUNCTIONAL STUDY OF PEPTIDYLARGININE DEIMINASE
TYPE 4 AS A GENETIC RISK FACTOR FOR RHEUMATOID
ARTHRITIS
1,*
1
2
3
A. Suzuki , Y. Kochi , R. Yamada , K. Yamamoto
1
2
RIKEN, Yokohama, Center for Genomic Medicine, Kyoto,
3
Department of Allergy and Rheumatology, Graduate
School of Medicine, The University of Tokyo, Tokyo, Japan
Disclosure of Interest: None Declared
P007
LEARNING NEW BIOLOGY FROM GWAS BY MEANS OF
NETWORK ANALYSIS AND LINK PREDICTION
1,*
T. Ravasi
1
Division of Applied Mathematics and Computer Sciences,
KAUST, THUWAL, Saudi Arabia
Objectives: Previously, peptidylarginine deiminase type 4
(PADI4) was identified as a susceptibility gene for
rheumatoid arthritis (RA) by genome-wide association
studies (ref1). PADI4 is highly expressed in bone marrow,
macrophages, neutrophils, and monocytes. Peptidyl
citrulline is an interesting molecule in RA because it is a
target antigen of anti-citrullinated peptide antibodies
(ACPAs), and only PADs (translated protein from PADI
genes) can provide peptidyl citrulline via modification of
protein substrates. The aim of this study was to evaluate
the importance of the PADI4 gene in the progression of
RA.
Objectives: Ever since the first Genome Wide Association
Study (GWAS) was carried out we have seen many
biological discoveries. However, an important amount of
scientists consider that these research outcomes and
their utility is far from what was expected from GWASs.
The objective of this work was to represent GWAS data
68
Methods: We generated Padi4 knockout (Padi4−/−)
DBA1J mice. Padi4−/− DBA1J and wild-type mice were
immunized with bovine type II collagen (CII) to develop
collagen-induced arthritis (CIA). Expression of various
inflammatory cytokines and Padi genes in immune cells
was detected by real-time TaqMan assay. Cytokine
concentrations in sera were measured by enzyme-linked
immunosorbent assay. Localization of PAD4 and PAD2
protein was indicated by immunohistochemistry.
Results: We demonstrated that the clinical disease score
was significantly decreased in Padi4−/− mice and Padi4
expression was induced by CII immunization. In Padi4−/−
mice, serum anti-type II collagen (CII) IgM, IgG, and
inflammatory cytokine levels were significantly
decreased compared with those in wild-type mice.
Interestingly, Padi2 expression was induced in immune
cells of Padi4-/- mice in compensation for the defect in
Padi4.
Conclusion: Padi4 affected on severity of CIA mice and is
involoved in the enhancement of collagen-initiated
inflammatory responses.
References: 1) Suzuki, A. et al Nat. Genet.34, 395-402
(2003)
across studies by meta-analysis (fixed-effect method for
single variants and Fisher’s method for gene-based
tests). We conducted pathway analysis on the basis of
single variant meta-analysis summary statistics using the
most up to date curated pathway gene-sets from the
molecular signatures database with MAGENTA.
Results: No individual coding variants achieved exome-7
wide significant evidence of association (p<5x10 ,
Bonferroni correction for 100,000 variants). The
strongest signals include deleterious missense variants in
-5
TAF1L (D141N, p=1.5x10 , MAF=0.077%) and BMP3
-5
(Y67N, p=3.2x10 , MAF=2.7%). We observed exome-6
wide significant evidence of association (p<2.5x10 ,
Bonferroni correction for 20,000 genes) with
burden/over-dispersion of loss of function variants in
-6
C16orf89 (p=1.1x10 ) and rare non-synonymous changes
-7
-6
in NECAB3 (p=1.7x10 ), ZNF485 (p=1.1x10 ), and RSAD2
-6
(p=2.1x10 ). MAGENTA analyses highlighted potential
involvement of cell adhesion/structure, immune function
and cancer-related pathways in endometriosis.
Conclusion: Our study provides preliminary novel insight
into the contribution of coding variation to the genetic
component of endometriosis. None of the identified
genes from these analyses map to established
endometriosis loci, providing no support for the
hypothesis that rare coding variation can explain
common SNP association signals.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P009
LARGE-SCALE EXOME CHIP GENOTYPING REVEALS
NOVEL CODING VARIATION ASSOCIATED WITH
ENDOMETRIOSIS
1 2 3,*
1
3
3
A. P. Morris
, R. Magi , N. Rahmioglu , A. Mahajan ,
4
5 6
3
N. Robertson , A. Salumets , K. Zondervan and UK
Exome Chip Consortium
1
Estonian Genome Center, University of Tartu, Tartu,
2
Estonia, Department of Biostatistics, University of
3
Liverpool, Liverpool, Wellcome Trust Centre for Human
4
Genetics, University of Oxford, Oxford, Wellcome Trust
Centre for Human Genetics, University of Oxford,
5
Liverpool, United Kingdom, Department of Obstetrics
6
and Gynaecology, Institute of Bio- and Translational
Medicine, University of Tartu, Tartu, Estonia
P010
ASSOCIATION OF HHEX GENE POLYMORPHISM WITH
TYPE 2 DIABETES MELLITUS AMONG THE MALAYS
1,*
2
3
F. Hayati , A. Hazim , W. M. I. Wan Mohamad , J. Daud
4
2
1
3
, N. S. Yaacob , G. Siew Hua , W. M. Wan Bebakar
1
2
Human Genome Centre, Department of Chemical
3
4
Pathology, Department of Medicine, Family Medicine
Clinic, Universiti Sains Malaysia, Kota Bharu, Malaysia
Objectives: To investigate the association of HHEX(A/G)
polymorphism with type 2 diabetes mellitus (T2DM) in
Malaysian Malay population.
Methods: T2DM patients (n=180) aged 18 years and
above as well as healthy subjects (n=180) were recruited
following institutional ethical approval. All patients
signed written informed consents. Genomic DNA was
extracted from whole blood using a commercial kit.
Flanking sequences of target single nucleotide
polymorphism were amplified using polymerase chain
reaction. Single base extension (minisequencing) was
used for genotyping due to its ability to multiplex and
allowance for automation.
Results: : The GG genotype of HHEX gene was overrepresented in T2DM cases when compared with
controls (15 % vs 7.7 %, p = 0.031). HHEX (GG genotype)
was significantly associated with increased risk of for
T2DM (p = 0.046, RR 1.35 (1.04 - 1.77).
Conclusion: HHEX variant is associated with T2DM in
Malaysian Malay population
Disclosure of Interest: None Declared
Objectives: To investigate the contribution of coding
variation to endometriosis pathogenesis, we undertook
genotyping with the Illumina Exome Chip of two studies
of European ancestry: (i) 910 cases from the Oxford
Endometriosis Gene (OXEGENE) study and 13,334
population controls (6,828 females) from the UK Exome
Chip Consortium; and (ii) 326 cases and 711 population
controls (363 females) from the Estonian Biobank.
Methods: Within each study, we evaluated the
association of endometriosis with: (i) individual coding
variants; and (ii) burden/over-dispersion of loss of
function (all frequencies) and rare non-synonymous
(minor allele frequency [MAF] less than 1%) variants
within genes using SKAT-O. Analyses were adjusted for
principal components to account for population
structure and restricted to females for X chromosome
variants. Association summary statistics were combined
69
3
P011
IL-6 GENE PROMOTER POLYMORPHISM IS ASSOCIATED
WITH SUSCEPTIBILITY OF
RHEUMATOID ARTHRITIS
IN DRAVIDIAN POPULATION.
1,*
2
2
3
1
K. Priya , S. Sathyan , L. Sreenivas , R. , S. Kesavarao ,
2
M. Banerjee
1
Human Genetics Laboratory, Bharathiar university,
2
Coimbatore, Human Molecular Genetics Laboratory,
3
Rajiv Gandhi Center for Biotechnology, Rheumatology,
KIMS Hospital, Trivandrum, India
University, Taipei, Department of Nursing, Cardinal Tien
College of Healthcare & Management, I-Lan, Taiwan,
Province of China
Objectives: Genome-wide association (GWA) studies can
efficiently search for disease associated loci, especially
for complex traits. However, the majority of identified
loci from previous GWA studies did not map to known
genes and are lack of functional interpretation. Recent
advances in knowledge about non-coding regions open a
window for understanding potential roles of significant
single nucleotide polymorphisms (SNPs) underlying the
trait of interest.
Methods: The current study utilized a large GWA dataset
of bipolar disorder (BPD), which is a complex and severe
psychiatric disorder. We aimed to first identify
susceptible loci for BPD, and then map these loci with
available non-coding RNAs, in particular long non-coding
RNAs (lncRNAs) database in the hope of providing new
insights about the lncRNAs regulation in the
pathogenesis of BPD. The GWA data is obtained from
National Institute of Mental Health with more than 7000
cases and 7000 controls, with more than 4 million of
imputed SNPs. Human lncRNAs release 37 data from the
Ensembl genome browser are used. A 10 kb up and
down-stream of the lncRNAs regions are considered as
transcription factor binding site. The lncRNAs data were
manually annotated on the case-by-case basis of the
HAVANA project, and 11038 autosomal lncRNAs were
selected for SNP mapping. The SNPfold website was also
used to predict whether the associated SNPs affect the
secondary structure of mapped lncRNAs.
Results: In about two-fifth of testing samples, we found
that 79 unique BPD-associated SNPs mapped to 85
unique lncRNAs. Less than 10% of intergenic lncRNAs
were mapped to multiple associated SNPs. Similarly,
roughly 10% of the SNPs mapped to multiple lncRNAs.
The lncRNA, ENSG00000233005 was the most significant
result, which was mapped by four SNPs: rs17397220,
rs10199484, rs219548 and rs721064.
Conclusion: However, the four SNPs had no significant
effect on its secondary structure. Interestingly, this
lncRNA has two transcripts and is found to express both
in brain and blood tissues. Experimental validation is
necessary in a human sample to further confirm its role
in BPD.
Objectives: Rheumatoid arthritis (RA) is a multigenic
inflammatory disease characterized by persistent
synovitis, chronic inflammation and extra-articular
manifestations. The occurrence rate of RA is 1%
worldwide
and
0.75%
in
adult
Indian
population. Inflammatory cytokines plays an extensive
role in the pathogenesis of rheumatoid arthritis. IL-6
cytokine is a pleiotropic and pro-inflammatory cytokine
involved in the biological process like activation of T cells,
induction of acute phase response, stimulation and
differentiation of hematopoietic cells. Although, etiology
of RA is unknown it has been demonstrated that
overproduction of IL-6 plays a crucial role in the
inflammatory pathways of RA. The objective of the
present study was to elucidate possible association of
variants in promoter regions rs1800795, rs1800797 and
rs1800796 of IL-6 gene and its susceptibility to RA
patients in Dravidian population.
Methods: Our study population includes 180 RA patients
and 244 age and ethnically matched healthy controls.
The targeted promoter regions of IL-6 were genotyped
by polymer chain reaction followed by restriction
fragment length polymorphism. The chi square test was
performed to detect the potential association of our
cases-control samples, odds ratio and 95% confidence
intervals were also calculated.
Results: Interestingly, the promoter region rs 1800796
show significant association with rheumatoid arthritis in
our population. None of the other SNPs shows an
association with susceptibility to rheumatoid arthritis.
Conclusion: The present study concludes that in
rs1800796 C allele show risk allele and CC genotype of
rs1800796 was more susceptible to RA in our population.
Our findings also provide the strong evidence that the
functional polymorphism of interleukin genes can
provide precious insight into disease onset and possibly a
predictive marker for RA in Dravidian population.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P013
LARGE SCALE GENOME-WIDE ASSOCIATION STUDY FOR
BIRTH WEIGHT FINDS EIGHT NOVEL LOCI EXTENDING
THE GENETIC LINK BETWEEN EARLY GROWTH AND TYPE
2 DIABETES
1,*
12
M. Horikoshi , A. P. Morris and EGG Consortium
1
Wellcome Trust Centre for Human Genetics, University of
2
Oxford, Oxford, University of Liverpool, Liverpool, United
Kingdom
P012
LINKING LNCRNAS WITH ASSOCIATED LOCI IN GENOMEWIDE ASSOCIATION STUDIES
1 2,*
2
2
3
K. Po-Hsiu , L. Ya-Chin , K. Chung-Feng , C. Li-Chung
1
Research Center for Genes, Environment and Human
2
Health, National Taiwan University, Department of
Public Health & Institute of Epidemiology and Preventive
Medicine, College of Public Health, National Taiwan
70
4
Objectives: Lower birth weight (BW) is associated with
increased risk of future type 2 diabetes (T2D) and
cardiovascular disease. Based on HapMap 2 imputed
European genome-wide association (GWA) studies, we
previously reported 7 loci associated with BW, of which
two (ADCY5, CDKAL1) have been implicated in T2D and
one (ADRB1) in hypertension. Here we report analyses
based on an increased sample size (55,729 full term
singletons) from multiethnic groups (22 European and 6
non-European of African-Americans (AA), Philippines,
Moroccan, Surinamese, Turkish and Chinese descent)
and imputation up to 20.8M SNPs from the more dense
1000 Genomes Project reference panel.
Methods: Using inverse-variance fixed-effects metaanalysis, GWA summary statistics between standardized
sex-specific Z-scores of BW (gestational week adjusted)
and each SNP were combined across studies in sexcombined and sex-stratified manner.
Results: We detected five novel loci at genome-wide
-9
-8
significance: near EPAS1 (p=2.4x10 ), YKT6 (p=1.2x10 ),
-8
-8
SREBF2/CENPM (p=3.5x10 ) and MAFB (p=4.1x10 ) from
sex-combined meta-analysis and KIAA0907 (pmale=0.22,
-8
pfemale=2.8x10 , pheterogeneity=0.0023) from sex-stratified
meta-analysis. There was no heterogeneity between
ethnicities at any of the novel loci (Cochran’s Q p > 0.05).
All loci were common variant loci except for YKT6 (MAF
EUR:1%, AA:0.2%). Other variants in the MAFB locus
have been implicated in hyperlipidemia. We then finemapped established and novel loci by constructing
credible sets of variants with 99% overall posterior
probability of being causal. The 99% credible sets
included fewer than 20 SNPs at 7 loci. At ADRB1, the
credible set consisted of just 5 variants, including
missense G389R (posterior probability 0.13, r2 with index
SNP
in
EUR:0.85,
AA:0.47
and
East
Asian:0.95). Approximate conditional analysis showed
that ADRB1 signal could be explained by G389R (ADRB1
-10
index SNP punconditional=6.1x10 , pconditional on G389R = 0.22).
Conclusion: Collectively, we have extended the number
of BW associated signals from 7 to 12 at both common
and low-frequency loci, of which 4 loci provide genetic
links between BW and T2D, hypertension and
hyperlipidemia,
highlighting
complex
non-linear
relationships between genetic variation, early growth
and later metabolic disease.
Pathology Department, CHU Ibn Rochd, Casablanca,
Morocco
Objectives: Inflammatory bowel disease (IBD) comprises
Crohn's disease (CD) and ulcerative colitis (UC). The exact
cause of IBD remains unknown. Available evidence
suggests combined effects of susceptibility genes and
environmental factors. Polymorphisms in genes
regulating inflammation may explain part of the genetic
heritage. The purpose of this study was to investigate
whether common variants in inflammatory and immune
response genes influence IBD risk in Moroccan patients.
Methods: Using a candidate gene approach, 19 single
nucleotide polymorphisms (SNPs) in 11 genes were
assessed in 308 controls and 199 IBD patients.
Genotyping was performed with the TaqMan® allelic
discrimination technology. The results were analysed
using PLINK software.
Results: Among the 11 studied genes, we found a
significant association for the TNFα_rs1800629
polymorphism (OR= 2.15; 95% confidence interval 1.393.32; p = 0.0005), a trend of association was observed for
PTPN22_rs2476601 without reaching the significance
level. No significant association was observed for the
remaining SNPs in the following genes: MIF_rs755622,
NFKB1_rs28362491,
HIF1-α_rs11549467,
IL6_rs2069840,
IL-6R_rs2228145,
IL6ST_rs2228044,
TYK2_(rs2304856,
rs12720356,
rs34536443,
rs35018800),
STAT3_(rs2293152,
rs744166),
IL17A_(rs2275913, rs4711998, rs7747909, rs8193036,
rs3819024).
Conclusion: The observed association suggest the
important role of genetically determined high
inflammatory response in the pathogenesis of IBD in the
Moroccan population.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P015
CAN INSULIN LIKE FACTOR-3 (INSL3) BE A POTENTIAL
CANDIDATE GENE FOR POLYCYSTIC OVARY SYNDROME
(PCOS) PATHOPHYSIOLOGY?
1,*
2
1
N. Shaikh , N. Shah , S. Mukherjee
1
Molecular Endocrinology, National Institute for Research
2
in Reproductive Health (ICMR), Endocrinology, GS
Medical College and KEM Hospital, Mumbai, India
P014
GENETIC DETERMINANTS OF SUSCEPTIBILITY TO
INFLAMMATORY BOWEL DISEASE IN A MOROCCAN
COHORT
1,*
2
3
1
N. Senhaji , W. Badre , A. Serrano , N. Serbati , M.
4
1
3
Karkouri , S. Nadifi , J. Martin
1
Laboratory of Genetics and Molecular pathologies,
Faculty of Medecine and Pharmacy of Casablanca,
2
Gastroenterology Department, CHU Ibn Rochd,
3
Casablanca, Morocco, Instituto de Parasitología y
Biomedicina López-Neyra, CSIC, Granada, Spain,
Objectives: PCOS is a heterogeneous, complex genetic
disorder seen in women of reproductive age. INSL3,
secreted by the ovarian theca and corpora luteal cells is
involved in androgen production, follicular growth and
oocyte maturation. Serum INSL3 levels are reported to
be
elevated
in
women
with
PCOS.
As
hyperandrogenemia plays a central pathogenic role in
PCOS, our aim was to investigate whether INSL3
polymorphisms are also involved in PCOS susceptibility
and its related traits.
Methods: A case-control association study with a total of
292 women with PCOS diagnosed according to
71
Rotterdam consensus criteria and 204 healthy regularly
menstruating women as controls were recruited from
India. Study subjects were phenotypically well
characterized in terms of clinical, hormonal and
biochemical parameters. Screening of both known and
novel polymorphisms in INSL3 and subsequent
genotyping was carried out by direct sequencing.
Results: Of all polymorphisms investigated, only rs6523
polymorphism showed significant association with
increased risk for PCOS (O.R. 1.84, p=0.002). Haplotype
association revealed that GAAG (p=0.0008) and AGAG
(p=0.008) haplotypes were significantly different
between controls and women with PCOS. In control
subjects, the polymorphic genotype carriers of rs6523
polymorphism had decreased fasting blood sugar
(p=0.011), apolipoprotein-A1 (p=0.03), bioavailable
testosterone (p=0.04) and increased SHBG levels
(p=0.02), while in the PCOS group the polymorphic
carriers had increased cholesterol levels (p=0.006). The
other rs1003887 polymorphism showed significant
association with obesity (p=0.001) in both controls and
women with PCOS. This polymorphism further was
significantly associated with metabolic related traits
(fasting insulin, HOMA, QUICKI and HDL-C levels) in
controls and improved androgen related parameters
(decreased testosterone and bioavailable testosterone
levels) in women with PCOS.
Conclusion: We provide the first evidence that INSL3 is a
predisposing genetic factor involved in manifestation of
PCOS. Polymorphisms of this gene also influence
hyperandrogenemia and hyperinsulinemia related
phenotypes of PCOS. Replication of INSL3 association is
warranted in other populations.
References: Szydlarska D, Grzesiuk W, Trybuch A,
Kondracka A, Kowalik I, Bar-Andziak E. Insulin-like factor
3 -- a new hormone related to polycystic ovary
syndrome? Endokrynol Pol 2012;63: 356-361.
Results: The questionnaires on food preferences were
filled by 291 “parent-offspring” pairs (including 19
“father-son” pairs, 54 “mother-son” pairs, 34 “fatherdaughter” pairs and 184 “mother-daughter” pairs), 84
sibling pairs (including 7 male sibling pairs, 36 female
sibling pairs and 41 opposite sex sibling pairs) and 70
marital couples. All the participants of the study were the
residents of Ukraine, predominantly of Kharkov
population. Genetic analysis was performed taking into
account the correlation coefficients for the parentoffspring pairs, sibling pairs and husband-wife pairs. Not
high, but significant correlation coefficients are observed
for preferences for meat (0.28), fruit (0.17), salty food
(0.19) and the first vegetable courses (0.25). In pairs
“mother-son” a significant correlation coefficient was
observed only for fruit (0.39), and in pairs “fatherdaughter” – only by salty food (0.36). The significant
correlation coefficients for five food preferences for
siblings were approximately similar – 0.33-0.37.
Conclusion: The moderate heritability coefficient was
obtained for preferences for first vegetable courses
(50%). High heritability coefficients were recorded for
food preferences for meat (88%), salty food (76%) and
fruit (88%). Two preferences (for sweet and fast food)
presented the maximum possible heritability coefficients
(100%).
References: Breen F.M. Heritability of food preferences
in young children / F.M. Breen, R. Plomin, J. Wardle //
Physiology & Behavior. – 2006. – Vol.88, Is.5. – P.443447.
Wardle J. One man's meat is another man's poison / J.
Wardle, L.J. Cooke // EMBO Rep. – 2010. – Vol.11, No.11.
– P.816-821.
Disclosure of Interest: None Declared
P017
GENE-GENE AND GENE-ENVIRONMENT INTERACTIONS
IN THE ETIOLOGY OF TYPE 2 DIABETES MELLITUS IN THE
POPULATION OF HYDERABAD, INDIA
1,*
2
U. J. Kommoju , B. Mohan Reddy
1
Senior Research Fellow, Biological Anthropology Unit,
2
Biological Anthropology Unit, Indian Statistical Institute,
Hyderabad, India, Hyderabad, India
Disclosure of Interest: None Declared
P016
HERITABILITY OF FOOD PREFERENCES AMONG
UKRAINIANS
1,*
1
2
O. V. Filiptsova , I. A. Timoshyna , M. N. Kobets , I. S.
1
1
1
Burlaka , P. V. Rakeev , I. A. Gurko
1
2
Biology Department, Department of Pharmaceutical
Marketing and Management, NATIONAL UNIVERSITY OF
PHARMACY, Kharkiv, Ukraine
Objectives: Genetic and Environment factors and their
interactions play a crucial role in the etiology of Type 2
Diabetes Mellitus (T2DM). We attempt to analyze the
role of gene-gene and gene-environment interactions in
the manifestation of T2DM in the population of
Hyderabad, India.
Methods: A sample of 1379 individuals, 758 T2DM cases
and 621 controls were genotyped for fifteen SNPs from
nine different genes i.e TCF7L2, IGF2BP2, SLC30A8,
CDKAL1, HHEX, CDKN2A/B, CAPN10, IRS-1 and PPARG on
Sequenom Massarray platform. Multivariate logistic
regression analysis, gene-gene, gene-environment and
cumulative effect of risk alleles analysis were carried out
inorder to assess the possible interactions.
Objectives: Aim. Genetic influence on eating behavior
and food preferences are intensively studied worldwide.
The majority of these studies have been carried out on
twins and other relatives and family members.
Methods: In the current study we evaluated the
heritability of several food preferences among the
residents of Ukraine on the basis of the correlation
analysis in pairs “parent-child”, in siblings pairs and in
married couples.
72
Results:
The
multivariate
analysis
suggests
TCF7L2,CDKAL1, IGF2BP2, HHEX and PPARG genes as
significantly associated with T2DM, albeit only the first
two of the above 5 were associated in the univariate
analysis. Significant gene-gene and gene-environment
interactions were also observed in which TCF7L2,
CAPN10 and CDKAL1 emerge as prominent genes,
highlighting their importance in the pathophysiology of
T2DM. In the analysis for cumulative effect of risk alleles,
SLC30A8 steps in as significant contributor to the disease
by its presence in all combinations of risk alleles. A
striking difference between risk allele categories, 1-4 and
5-6, was evident in showing protective and susceptible
roles, respectively, the latter being characterized by the
presence of TCF7L2 and CDKAL1 variants.
Conclusion: Our study fills the lacunae in understanding
the complex interplay of genes and environment in the
etiology of T2DM in the population of Hyderabad, which
has not been explored hitherto. Overall, the two genes
TCF7L2 and CDKAL1 showed strong association with
T2DM, either individually or in interaction with the other
genes. Our study also brought out IGF2BP2, SLC30A8,
HHEX, CDKN2A/B, PPARG as significantly interacting
among them as well as the environmental factors such
as BMI, Alcohol and Smoking with TCF1,CDK2,CAP1
genes, providing support for gene-gene and geneenvironment interactions in the manifestation of T2DM
in this population. Further studies with relatively larger
samples are needed on gene-gene and geneenvironment interactions among heterogeneous Indian
populations to obtain more unequivocal conclusions on
the genetic etiology of T2DM.
on the X chromosome, statistical analyses were
conducted in a sex-specific manner.
Results: SNP rs2235306 was significantly associated with
asthma. Compared with the TT genotype, the TC/CC
genotypes had an OR of 2.07 (95% CI: 1.23, 3.49) for
female patients (P = 0.006) and an OR of 2.29 (95% CI:
1.25, 4.19) for male patients (P = 0.007). In asthma
patients who carried the TC/CC genotypes of rs2235306,
APLN messenger RNA levels were higher than in those
with TT genotype.
Conclusion: Our findings indicated the association
between the APLN rs2235306 polymorphism, mRNA
expression and asthma. Our studies suggested that allele
C or TC/CC genotypes of APLN polymorphism were
associated with overexpression of APLN and risks of
asthma phenotypes.
References: This study was supported by Basic Research
grant from Qingdao Municipal Science and Technology
program 2012-5-022-YY.
Disclosure of Interest: None Declared
EPIGENETICS
P019
INTEGRATING SEQUENCING ERRORS AND NONCONVERSION RATES INTO METHYLATION CALLING
1,*
A. Salim
1
Mathematics and Statistics, La Trobe University,
Melbourne, Australia
Objectives: DNA Methylation is an epigenetic mechanism
that plays important roles in regulating gene expression
and has been shown to be involved in carcinogenesis.
Over the last 4-5 years, Bisulfite sequencing technology
has allowed genome-wide interrogations of methylation
profiles Despite the advance of the Bisulfite sequencing
technology, it is still not perfect. There are various
potential errors from the stage of samples extraction,
cytosine conversion and sequencing error. For example,
it is known that not 100% of unmethylated cytosine (C)
will be converted to uracil (U) Sample extraction is also a
potential source of bias, as in many cases the extracted
samples will contain a mixture of normal, unmethylated
and cancerous, methylated cells. Hence, contrary to the
principle behind current practice of calling CpG as either
‘methylated’ or ‘unmethylated’, methylation levels is
better expressed as a fraction of methylated cells.
Objective: To develop an integrated methylation calling
algorithm that takes into account the sequencing errors
and non-conversion rates.
Methods: Methods: We use generalized linear mixed
model (GLMM) with iterative weighted least squares
(IWLS) algorithm to estimate methylation levels at a
particular locus. The called methylation levels takes into
account the uncertainty in non-conversion rates
estimated from spiked-in unmethylated Lambda Phage
genome. Methylation levels of neighbouring loci are
allowed to be correlated, thus improving the precision of
Disclosure of Interest: None Declared
P018
APLN POLYMORPHISM INFLUENCES ITS EXPRESSION
AND ASTHMA PHENOTYPES IN CHINESE
1,*
1
1
1
1
1
X. Ji , W. Zhang , S. Jia , R. Xu , J. Gao , W. Zhang
1
qingdao municipal hospital, qingdao, China
Objectives: Apelin (APLN), which is a newly identified
adipokine, is related to obesity and insulin resistance. A
positive
correlation
between
plasma
APLN
concentrations and obesity traits was reported. The
rs2235306 of APLN polymorphism has been shown to be
associated with fasting plasma glucose levels and
obesity. The present study aimed to investigate the
impact of the APLN rs2235306 gene polymorphism on
the risk of asthma in a sample of the Chinese population.
We tested associations between APLN gene
polymorphism, APLN expression levels in different
genotypes and asthma phenotypes.
Methods: This population-based cross-sectional study
was performed on 566 subjects with Asthma and 523
without Asthma. One promoter region single nucleotide
polymorphism (SNP) of APLN (rs2235306) was detected
using the tetra amplification refractory mutation system–
polymerase chain reaction. Because the APLN is located
73
methylation level estimates for regions with low
coverage.
Results: Using two publicly-available whole-genome
bisulfite sequencing datasets, we showed that our calling
achieves better sensitivity and markedly lower false
dicovery rates when compared to popular methylation
caller software, Bismark.
Conclusion: Taking into account non-conversion rates
and sequencing errors increase sensitivity and reduce
false discovery rates when performing methylation
calling
methylation. Since the pri-miR-208b transcript
coordinates the regulatory actions of transcription
factors at the bidirectional promoter of the MHC gene,
we show sex differences for coregulator binding directed
by RNA methylation and gene function in the heart.
Conclusion: Our results are particularly novel for several
reasons that provide novel insights to lncRNA-mediated
chromatin modification in the heart. We show epigenetic
modification of ncRNAs serve to regulate chromatin
structure and gene function coordinated by the actions
of coregulatory complexes. We show epigenetic
modification regulates cardiac gene expression is subject
to sex differences.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P020
SEX DISTINGUISHES EPIGENETIC REGULATION BY NONCODING RNA IN THE HEART
1
1
2
1
P. Mathiyalagan , H. KN , W. A. Gold , J. Okabe , J.
2
1
1 3 4,*
Christodoulou , X.-J. Du , A. El-Osta
1
Epigenetics in Human Health and Disease, BakerIDI
2
Heart & Diabetes Institute, Melbourne, NSW Centre for
Rett Syndrome Research, Children’s Hospital at
3
Westmead, Sydney, Faculty of Medicine, Monash
4
University, Department of Pathology, The University of
Melbourne, Melbourne, Australia
P021
HISTONE DEACETYLASE INHIBITORS INCREASE SMN2
EXPRESSION THROUGH METHYLATION
1,*
2
1
J. Mohseni , Z.-H. ZAMH , T. H. Sasongko
1
2
Human Genome Centre, Department of Pediatrics,
School of Medical Sciences, Universiti Sains Malaysia,
Kota Bharu, Malaysia
Objectives: Increasing Survival motor neuron 2 (SMN2)
expression is a promising strategy for Spinal Muscular
Atrophy (SMA).
Histone deacetylase inhibitors are able to increase SMN2
gene expression by modulating acetylation and
methylation activity.
we investigated the level of SMN2 promoter methylation
in human SMA-affected fibroblast cells after exposure to
SAHA, Dacinostat and SRT1720 as compared to
unexposed cells.
Methods: Using high resolution melting (HRM).
Results: Our preliminary data suggested that Dacinostat
and SRT1720 showed demethylation effect on SMN2
promoter. Meythlation level of promoter region of SMN2
significantly changed from 74.02±5.01% in Mock to
51.31±1.69, 54.74±0.07, and 51.06±3.35 after 48 h
exposure to 10 µM SAHA, 30 nM Dacinostat and 1.6µM
SRT1720, respectively.
Conclusion: This effect links with these compounds
ability to increase SMN2 gene expression.
Objectives: The year 1993 was the first glimpse into
miRNAs with back-to-back articles describing timed
developmental control in C. elegans. More than 20 years
on, and with the discoveries of pervasive transcription
and increasing complexity of the epigenome, we have
gained considerable insight into gene regulation.
However a fundamental question remains, are ncRNA
transcripts under the control of the epigenome to
regulate gene expression? If so, then what are the true
physiological targets of ncRNAs? In this article we explore
the mechanisms coordinating gene expression in the
heart and ask the question; does sex distinguish
epigenetic regulation by precisely controlling ncRNA
actions?
Methods: Assays examining long ncRNAs (lncRNAs) were
performed from heart tissue derived from the left
ventricles (LV) in male and female C57BL/6 mice. RNAchromatin immunoprecipitation (RNA-ChIP) techniques
examine lncRNA-protein and lncRNA-DNA interactions.
Chromatin isolation by RNA purification (ChIRP)
strategies were specifically developed for heart tissue.
Bisulfite-based deamination procedures were used to
define DNA and RNA methylation.
Results: Strand-specific analyses show increased myosin
heavy chain expression in the female heart when
compared to male mice. Transcript analysis identified sex
differences for the lncRNA, pri-miR-208b. ChIP
experiments reveal unique RE1-Silencing Transcription
Factor (REST) and methyl CpG binding protein 2 (MeCP2)
co-repressor complexes regulating ncRNA transcription.
ChIRP assays demonstrate specific binding of the 5’
domain of AS β-MHC transcript to microRNA-208b
promoter in a mechanism that is dependent on RNA
Disclosure of Interest: None Declared
P022
A NOVEL 19Q13.4 MICRODELETION INCLUDING THE
IMPRINTED GENE PEG3 IS ASSOCIATED WITH SHORT
STATURE, DEVELOPMENTAL DELAY, CLEFT LIP AND
PALATE, AND DYSMORPHIC FEATURES
1 2,*
12
12
L. Badalato , A. C. Smith , G. E. Graham
1
Department of Genetics, Children's Hospital of Eastern
2
Ontario, Faculty of Medicine, University of Ottawa,
Ottawa, Canada
74
Objectives: Imprinted genes often play important roles in
growth and development, and their disruption can entail
significant clinical consequences. Here we present a
patient with a novel microdeletion of chromosome
19q13.42q13.43, which includes imprinted gene PEG3
(paternally expressed gene 3). This gene has not
previously been reported as disease causing in humans.
Methods: Our patient is a 6-year-old boy who presented
with growth failure (height -3.7SD, weight -3.58SD, OFC 2SD), right unilateral cleft lip and palate, global
developmental
delay,
right
esotropia,
and
dysmorphism. A chromosomal microarray revealed a
deletion on chromosome 19q, which includes part of the
PEG3 imprinted domain. We assessed the methylation
status of the CpG islands in the 5'UTR of PEG3 using
methylation sensitive restriction enzyme digest with HhaI
followed by PCR amplification.
Results: Our patient’s deletion at chr19:5603941557566332 is 1.5Mb in size and includes 40 genes, most of
which encode zinc finger or NLR family proteins, none of
which are known disease-causing genes. This deletion
has not been reported in the database of genomic
variants. Parental samples were not available to
determine inheritance. Several genes in the PEG3
imprinted domain, including PEG3 and its isoform ZIM2,
were encompassed by the deletion. Preliminary
methylation studies suggested that the remaining copy
of PEG3 is methylated in our patient. Alterations in
expression of PEG3 have been described in some human
cancers, but phenotypes resulting from germline
mutations or deletions have not been previously
reported in humans. In the mouse model, disruption of
PEG3 has been associated with growth impairment and
neurobehavioural abnormalities, which correlates with
our patient’s phenotype.
Conclusion: We present a novel microdeletion at
19q13.4 that includes part of an imprinted domain. Given
that this is a rare deletion involving a large number of
genes, we are highly suspicious that it is responsible for
his phenotype. We feel that PEG3 is an excellent
candidate to explain many of our patient’s features,
given its imprinted status, known expression in the brain,
and its effects on growth and neurodevelopment in the
mouse model. Further methylation studies are ongoing
to confirm the imprinting status at this locus.
Objectives: Studies have shown the methylation of
NR3C1 is a common candidate mechanism for the major
depressive disorder (MDD). Also, environmental factor
may influence the epigenetic changes on certain genes.
Childhood maltreatment is most widely studied toward
MDD and also the most significant factor. Recent studies
indicated that the long-term effect of early life stress
might influence the combination of intestinal
microbiome in adult. One possible hypothesis indicated
that early life stress might induce phenomena of leaky
gut and consequent bacterial translocation, and then
associated with MDD.
Methods: We recruited 37 cases and 33 controls, and
designed a retrospective case-control study to determine
possible gene-environment interaction of the
methylation of NR3C1 for MDD. The Childhood Trauma
Questionnaire (CTQ), a self-report questionnaire, was
used to present the frequency of each dimension of
childhood maltreatment. The primer was designed using
the PyroMark Assay Design software (Qiagen) for a 162bp region on the promoter of NR3C1 gene. The
methylation levels for the ten CpG sites were generated
by PyroMark Q96 ID instrument (Qiagen). Detection of
16S rDNA, a conservative area of ribosomal DNA in
bacteria, will used to examine the micro-expression of
bacteria in the peripheral blood sample of subjects.
Results: The experience of childhood maltreatment were
associated with an decreased pattern of both
methylation of CpG sites 1 and 5 of NR3C1 showing odds
ratios (ORs) with95% confidence intervals (CI) of 0.4 (0.11.1). Our analysis shown a significant finding for the
association between methylation of CpG sites 6 and
gastrointestinal disorder of the study participants (pvalue of chi-square test =0.023). After adjusted the
methylation of the 3 certain CpG sites, both the
experience
of
childhood
maltreatment
and
gastrointestinal disorder were associated with an
increased risk of the MDD showing multivariate ORs (95%
CIs) of 4.7 (1.4-15.6) and 4.1 (1.1-15.9), respectively.
Experimental validation is underway for the microexpression of bacteria in the peripheral blood sample to
evaluate the possible hypothesis of leaky gut.
Conclusion: The methylation levels of different CpG sites
in NR3C1 were associated with different important
genetic and environmental risk factors for MDD in
Taiwanese population.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P023
THE PILOT STUDY FOR ASSOCIATION ASSAY OF
METHYLATION
OF
NR3C1
AND
CHILDHOOD
MALTREATMENT WITH MAJOR DEPRESSIVE DISORDER
IN TAIWAN
1,*
2
2
2
L.-C. Chuang , J.-H. Shen , Y.-C. Chung , P.-H. Kuo
1
Department of Nursing, Cardinal Tien Junior College of
2
Healthcare & Management, Yilan County, Institute of
Epidemiology and Preventive Medicine, College of Public
Health, National Taiwan University, Taipei, Taiwan,
Province of China
P024
A GENOME-SCALE MAP OF THE EPIGENETIC PROGRAM
IN EARLY ZEBRAFISH DEVELOPMENT
1,*
1
1
1
S. Kapoor , S. Ghosh , C. Sachidanandan , V. Scaria
1
CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE
BIOLOGY (CSIR-IGIB), DELHI, India
Objectives: Embryonic development requires a highly
regulated and specific gene expression, maintained by
the dynamicity of chromatin structure which at its heart
75
is governed by DNA and histone modifications. Recent
advancements in technology has enabled the genomewide mapping of epigenetic marks across a wide variety
of organisms including humans. A variety of human
diseases including developmental disorders are known to
be caused by altered epigenetic programs which raises
the necessity to understand and model the epigenetic
dynamics during development. Zebrafish, being a popular
model system for human diseases, we aim to understand
the epigenetic program during early development by
establishing an epigenetic landscape of early zebrafish
development by integrating genome-wide datasets from
a number of sources available in public domain.
Methods: We have made an attempt to construct the
epigenetic program by understanding the expression and
regulation of histone modifiers and integrating temporal
profiles of histone modification marks across promoters.
We have performed orthologous mapping of histone
modifiers for human and zebrafish. We assembled a total
of 151 human epigenetic modifier orthologs in zebrafish
and mapped their temporal expression profiles in early
development across 7 developmental stages using RNA
seq data sets . We integrated and mapped ChIP seq data
sets for histone modification marks from various studies
across 7 zebrafish developmental stages to the zebrafish
reference genome using MAQ followed by peak calling
using MACS. Genome wide analysis of the signals for
histone marks was further performed across the
promoters.
Results: We found all the 151 human orthologs in
zebrafish defining their conservation across the
vertebrates. Expression analysis revealed specific
patterns of temporal regulation of histone modifier
genes during early development. Analysis of the histone
modification marks encompassing both activatory and
inhibitory marks provided a systematic map of the
epigenetic program during development. We further
integrate these marks towards understanding their
contribution to gene expression and regulation.
Conclusion: Our analysis would provide the first glimpse
of the epigenetic program during early zebrafish
development. We further aim to establish a complete
epigenetic profile for the early embryogenesis and build
up a model so as to predict the effect of presence or
absence of an epigenetic mark over transcript
expression.
the JAK-STAT pathway in acute myeloid leukemia (AML)
cells carrying a FLT3-ITD mutation.
Methods: AML cell line, MV4-11 treated with TSA, 5-AZA
and combination of TSA and 5-AZA at two different
concentrations, 0.5 µM and at IC50 concentrations. Cell
viability assay was performed by trypan blue exclusion
(TBEA). One-Color Microarray-based expression analysis
(Agilent SurePrint Technology) was utilized, analyzed by
Genespring 12.6 software. These datasets were imported
to online DAVID tool (http://david.abcc.ncifcrf.gov/) for
regulated pathways analysis using KEGG pathway
database.
Results: We report 1291 genes related with drug to drug
interaction. 10 genes were evolved in the JAK-STAT
pathway (DAVID analysis)-CLCF 1 and G-CSF 3, CRLF 2,
IL11 ra, IL2 rg, IL5 ra, LEPR, STAT 6, SOS 2 and SOCS-3
genes. TSA at IC50 concentration showed elevated level of
SOCS-3, G-CSF 3, CRLF 2 and IL11 ra; 147.43, 52.35, 9.78
and 48.93 folds, respectively, higher expression
compared with AZA; 66.23, 1.27, 3.04, 12.59 folds
(Genespring analysis, Benjamini Hochberg, p<0.05),
respectively. While STAT 6 (-8.57 and -2.28), CLCF 1 (9.66 and -1.39), IL2 rg (-11.19 and -2.85), IL5 ra (-4.96
and -5.06), LEPR (-1.51 and-1.49) and SOS 2 (-3.13 and 1.26) genes were down-regulated. Overexpression of
SOCS-3 was associated with reduced activity of STAT 6,
which greater expression was seen in TSA rather than 5AZA. Combined drugs of TSA + 5-AZA did not cause
significant changes in the fold change in gene expression
compared with single drug action.
Conclusion: SOCS-3 remains the prominent target gene
in the JAK-STAT signalling in acute myeloid leukemia.
However, it is still unclear whether the deactivation of
JAK-STAT signalling that leads to growth arrest would
also deregulate FLT3-ITD transcription activity and its
involvement with epigenetic mechanism. Further study
in the interaction of FLT3-ITD mutation with epigenetic
activity associated with cellular signalling is essential.
References:
1. Williams J.J.L., Munro K.M.A. and
Palmer T.M. Role of Ubiquitylation in Controlling
Suppressor of Cytokine Signalling 3 (SOCS3) Function and
Expression. Cells 2014, 3, 546-562.
2. Wang Y.G, Wang N, Li G.M, Fang W.L, Wei J, Ma
J.L et al: Mechanisms of trichostatin A inhibiting AGS
proliferation and identification of lysine-acetylated
proteins. World Journal of Gastroenterology : WJG. 2013;
19:3226-40.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P025
TRICHOSTATIN A ENHANCES SOCS-3 AND REDUCES
STAT 6 EXPRESSION IN FLT3-ITD ACUTE MYELOID
LEUKEMIC CELLS
1,*
1
S. A. Mat Jusoh , M. F. Johan
1
Hematology department, Universiti Sains Malaysia, Kota
Bharu, Malaysia
ETHICS AND GENOMICS
P026
OPINIONS OF HEARING PARENTS ABOUT THE CAUSES
OF HEARING LOSS IN THEIR DEAF CHILDREN COMPARED
WITH GJB2 (CX26) GENETIC TESTING RESULTS IN RUSSIA
12
3
45
N. A. Barashkov , L. U. Dzhemileva , O. L. Posukh , A.
1,*
46
12
V. Solovyev , M. S. Bady-Khoo , V. G. Pshennikova ,
1 2
3
7
F. M. Teryutin , S. L. Lobov , A. B. Neustroeva , K. A.
Objectives: To study the mechanism of Trichostatin A
(TSA) action in regulating gene expression specifically in
76
2
1
8
Kurtanov , L. A. Klarov , L. M. Vasilyeva , E. E. Fedotova
8
1
12
12
, A. M. Rafailov , N. A. Solovyeva , S. K. Kononova , A.
9
1
3 10
N. Alekseev , S. A. Fedorova , E. K. Khusnutdinova
1
Institute of Natural Sciences, Laboratory of Molecular
Biology, M.K. Ammosov North-Eastern Federal University,
2
Laboratory of Molecular Genetics, Yakut Scientific Centre
of Complex Medical Problems, Siberian Branch of the
Russian Academy of Medical Sciences, Yakutsk,
3
Laboratory of Human Molecular Genetics, Institute of
Biochemistry and Genetics, Ufa Scientific Centre, Russian
4
Academy of Sciences, Ufa, Laboratory of Human
Molecular Genetics, Institute of Cytology and Genetics,
Siberian Branch of the Russian Academy of Science,
5
Department of Cytology and Genetics, Novosibirsk
National Research State University, Novosibirsk,
6
7
Republican Hospital №3, Kyzyl, Center of Social
Problems of Labour, Academy of Sciences of the Sakha
8
Republic, Audiology-Logopaedic Center, Republican
Hospital No. 1, National Medical Centre, Ministry of
9
Public Health of the Sakha Republic, Institute of
Humanitarian Research and Indigenous People of the
North, Siberian Branch of the Russian Academy of
10
Sciences, Yakutsk,
Department of Genetics and
Fundamental Medicine, Bashkir State University, Ufa,
Russian Federation
Educational Foundation for Young Scientists of Republic
of Sakha».
Disclosure of Interest: None Declared
P027
EXPERIENTIAL PROCESS OF SECURING FREE PRIOR
INFORMED CONSENT FOR GENETICS RESEARCH FROM
AN INDIGENOUS POPULATION IN THE PHILIPPINES
1,*
1
2
1
C. D. Padilla , A. L. Sur , M. T. G. Padilla , M. Baluyot ,
1
2
E. M. Cutiongco-de la Paz , S. Padilla
1
Institute of Human Genetics - National Institutes of
Health, University of the Philippines Manila, Manila,
2
Antro Watch Philippines, Quezon City, Philippines
Objectives: Of the 110 ethno-linguistic groups in the
Philippines, 35 are Negritos, known by various names.
i.e., Agta, Atta, Aeta, Ayta, Alta, Arta, Dumagats, Ati, Ata,
Abiyan, Batak, Mamanwa, Ata Manobo, Iraya Mangya,
and Remontado. The conduct of genomic research needs
approval from the National Commission on Indigenous
Populations (NCIP), a government agency mandated to
protect the interest of the indigenous peoples (IPs).
Methods: 1) consultation with NCIP; 2) identification of a
social development organization and other major players
that deal directly with IPs; 3) development of culturally
sensitive modules in securing FPIC; 4) pilot testing of
modules among lay and IPs; and 5) use of the protocol in
orienting major players.
Results: After consultations with NCIP, IPs and NGOs
dealing with IPs, the protocol was finalized. The 2-hour
module utilized picture analysis, lecture and an
interactive orientation. The module included: 1)
introduction of participants; 2) warm-up exercise:
Binukid “body parts” song which aims to arouse their
curiosity on the topic; 3) What are the parts of the body?
where participants are asked on their concepts of
different parts of the bodies; 4) Guessing game, an
interactive activity demonstrating that important body
parts are not always visible to the eyes,
i.e., chromosomes, genes and DNA. The signing of FPIC
by the Tribal Council and the IP participants
(signature/thumb mark) ends the module.
Conclusion: Genomic research on IPs require a special
process for FPIC. Although a tedious process, the
presented protocol is a model procedure that can be
used by researchers involving genomic research.
References: Beskow LM, Burke W, Merz JF et. Al. (2001).
JAMA. 286(18):2315-21.
Boga M, Davies A, Kamuya D. (2011). PLoS Med.
8(9):e1001089. Epub 2011 Sep 13.
Brannigan MC. (2008). Camb Q Healthc Ethics.
17(2):173-84.
Greely HT. (2001). Annu Rev Genet. 35:785-800.
Marshall PA. (2008). Camb Q Healthc Ethics. 17(2):20615.
National Indigenous Peoples Commission (NCIP). (2012).
Administrative Order No. 1, Series of 2012: The
Indigenous Knowledge Systems and Practices (IKSPs) and
Objectives: Hereditary hearing impairment (HI) caused
by GJB2 mutations is frequent sensory disorder. The
results of research on molecular basis of HI are widely
used in practice as various genetic test systems.
However, primary subjective opinions of parents about
causes of HI in their children should be taken in to
account at the interpretation of genetic testing results
especially in regions where genetic testing has not yet
been widely used in public health.
Methods: We conducted the first sociological research
based on surveys of hearing parents of deaf children in
three national Republics of Russia: Sakha (n=101), Tuva
(n=61), and Bashkortostan (n=21) for analysis of
subjective opinions of parents about causes of HI in their
children followed by comparison with results of genetic
testing of GJB2 gene.
Results: Most of respondents (73.8%>86.1%) chose
answer “non-hereditary” for question about presumptive
causes of HI of children and their opinions are more likely
based on the absence of deaf relatives.
Conclusion: Subjective opinions of parents are
inconsistent with genetic testing results, despite
different contributions of GJB2 mutations (16%>71%) in
studied regions, and in many cases the announcement of
testing results may have severe psycho-emotional
influence on parents.
References: Study was supported by Project №
6.656.2014/К of Ministry of Education and Science of
Russia, RFBR (#14-04-01741_A, 14-04-9010_Bel_A), RHRF
(15-36-01262_a2), SBRAS Integration project #92, the
Sakha Republic President grant for Young Researchers for
2015, RAS Program «Fundamental Sciences for
Medicine» (#30 for 2013-2015), and «Scientific and
77
Customary Laws (CLs) Research and Documentation
Guidelines of 2012. Retrieved 24 October 2012,
Padilla Jr., SG. (2000). The Journal of History. XLVI(14):35-53. Retrieved 30 May 2012
Perrault, A. (2004). F Sustainable Development Law and
Policy. 21-26.
can be used in service of the public good and not to cure,
protect and enrich the most privileged.
References: Hvistendahl, M. 2012 Unnatural Selection.
Public Affairs
Disclosure of Interest: None Declared
P029
BIOETHICS AND GOVERNANCE OVER HUMAN GENOME
RESEARCH IN SOUTH KOREA
1 2 3,*
123
S.-H. Kim
, S. Y. Kim
1
Centre for ELSI Research, Korea Health Industry
2
Development Institute (KHIDI), Asian Institute for
Bioethics and Health Law (AIBHL), WHO Collaborating
3
Centre for Health Law and Bioethics, Health Law and
Bioethics, Yonsei University College of Medicine, Seoul,
Korea, Republic Of
Disclosure of Interest: None Declared
P028
EDUCATING
FOR
THE
POTENTIAL
GLOBAL
CONSEQUENCES OF THE HUMAN GENOME PROJECT
1,*
J. Garrett
1
Biology, Hamilton College, Clinton, United States
Objectives: The rapid expansion of technologies to
analyze, manipulate and synthesize genomes has
resulted in an extraordinary expansion of the potential
for the human-directed creation of modified, or even
novel, organisms. Scientists and developers of genomic
technologies need to be cognizant of the potential uses
of their developments and be cautious about the
commercialization of their products many of which have
precipitated serious unease in the public. I will consider
the mechanisms by which the next generation of
bioscientists should be prepared for this challenge.
Methods: I surveyed undergraduate professors of
genetics in US colleges and universities to investigate the
mechanisms by which ELSI issues (ethical, legal, social
and social consequences) are taught to biology majors.
Results: Overall, a very small percentage of institutions
ensure that their science students have any preparation
to confront ELSI issues arising form their work. Most
departments do not require ethics courses of their
science majors and few instructors include significant
ELSI content in their science courses.
I will discuss one example: embryo trait selection. Some
fertility clinics are already advancing limited trait
selection (e.g. eye, hair, skin color - Fertility Institutes,
CA). These developments should be a cause for serious
concern as technologies developed for one culture and
market can have very different impact when adopted
elsewhere. Consider the impact that ultrasound fetal
screening has had on the gender balance of countries
where there is pressure to control population and/or a
cultural bias for males. These severe gender
imbalances have serious social implications (Hvistendahl,
2010). If gender selection can have such drastic
consequences it is important to consider how other types
of selection could result in unintended and undesirable
consequences.
Conclusion: In the US, we are not preparing students
adequately to address the dramatic advances in genomic
technologies and play a balanced role in regulating these
advances. It is imperative that future scientists
understand both the potential, and the potential
consequences, of human genomics so that this science
Objectives: For the last two decades, the emerging field
of biotechnology in South Korea has advanced
drastically. In particular, the government perceived
human genome research as promising future industry for
country development, and started to support it actively
since early 2000s. Yet, mere promotion of research in the
beginning raised several important ethical issues, as it
was not ready to protect human subjects sufficiently.
Therefore, the need of bioethics and governance over
scientific research became indeed crucial.
This paper aims to address and overview the historical
development of bioethics and governance over human
genome research in South Korea, what were the issues it
had to confront with and what were the influences of the
international community over the country through the
works of the International Bioethics Committee of
UNESCO (IBC). It will include the legislation of ‘Bioethics
and Safety Act’ (2005) as a legal instrument that provides
the basis of bioethical consideration and governance
over human research. And it will also briefly describe the
government’s recent activity, the initiation of Center for
Ethical, Legal, and Social Implication (ELSI) Research in
2011, which has been studied human genome research
in South Korea at national level.
Disclosure of Interest: None Declared
P030
PROTECTING PRIVACY THROUGH CONTROLLED ACCESS
IN LARGE SCALE CANCER GENOMIC RESEARCH
1,*
2
Y. Joly , E. de Vries-Seguin
1
2
Centre of Genomics and Policy, Public Population
Project in Genomics and Society (P3G), Montreal, Canada
Objectives: This communication will use empirical data
to refute the widespread negative perception of
controlled access and show that it is possible to
efficiently use this strategy to protect the genomic and
clinical data of a large scale research consortium in the
field of cancer genomics.
78
Methods: Our data comes from statistical analysis of
over 270 access requests made over the four last years of
operation of the Data access compliance office (DACO) of
the International Cancer Genome Consortium (ICGC)
complemented by operational data associated to the
administration of DACO.
Results: The data obtained shows that DACO has been a
highly cost-efficient infrastructure and that it has
successfully fulfilled its mission of adding a protection
and oversight layer to the more sensitive data of the
ICGC. One potential area for improvement would be that
of developing more efficient compliance framework to
ensure post approval ethical data usage.
Conclusion: It is possible to provide additional protection
to sensitive genomic data at little cost to the scientific
community by using a controlled approach to data
access. The required infrastructure can be designed to
run on a limited budget while addressing access requests
and queries from users in a very short timeframe. This
approach to the protection of genomic data is also highly
flexible and can be used in combination with a variety of
other consent, privacy and security strategies including
the more recent ones involving substantial information
technology components.
Disclosure of Interest: None Declared
mosaic mutation were also detected in three of our
patients (p.Gln446*, p.Asn1476Lys, p.Leu1550Arg) which
could contribute to the epileptic encephalopathy.
Pathogenicity prediction of the 28 novel mutations were
carried out using Mutation Taster showed that they
could affect protein function.
Conclusion: These findings widely expand the SCN1A
mutation
spectrum
identified
in
epileptic
encephalopathies children. Molecular diagnosis of SCN1A
gene is important for clinician in deciding appropriate
treatment as well as for genetic counselling.
References: 1. The spectrum of SCN1A-related infantile
epileptic encephalopathies. Louise A.Harkin. Brain
(2007), 130,843-852.
2. Spectrum of SCN1A gene mutations associated with
Dravet Syndrome: analysis of 333 patients. C.Depienne.
J.Med Genet (2009), 46:183-191.
3.Cryptogenic Epileptic Syndromes Related to SCN1A.
Claudio Zucca. Arch Neurol (2008), 65: 489-492.
4. SCN1A mutational analysis in Korean patients with
Dravet Syndrome. Byung Chan Lim. Seizure (2011),
20:789-794.
Disclosure of Interest: None Declared
P032
CHARACTERIZATION
OF
MYCOBACTERIUM
TUBERCULOSIS CLINICAL ISOLATES FROM KAZAKHSTAN
BY SPOLIGOTYPING
1
1
1
U. Kozhamkulov , A. Akhmetova , Z. Zhumadilov , A.
1,*
Akilzhanova
1
Department of Genomic and Personalized Medicine,
Center for Life Sciences, Nazarbayev University, Astana,
Kazakhstan
GENERAL GENETICS & GENOMICS
P031
MOLECULAR CHARACTERIZATION OF SCN1A GENE IN
EPILEPTIC ENCEPHALOPATHIES CHILDREN IN MALAYSIA
1,*
1
A. W. Siti Aishah , Y. Yusnita
1
Unit Molecular Diagnostics & Protein, Institute for
Medical Research, Kuala Lumpur, Malaysia
Objectives: SCN1A gene encodes for sodium channel
alpha 1 subunit was found to be the the most common
mutated gene in epilepsy patients. To date over 700
mutations have been found, majority of which nonsense
and missense mutations. The objective of this study is to
characterize the SCN1A mutations in epileptic
encephalopathy children in Malaysia.
Methods: A total of 194 epileptic encephalopathy
children referred from hospitals all over Malaysia were
included in the study. PCR and bidirectional sequencing
were used to identify SCN1A mutations.
Results: Forty nine heterozygous mutations have been
detected, 28 (57.1%) of which were novel mutations.
Nonsense mutations theoretically leading to truncated
protein were the most common mutation type,
encountered in 19 (38.8%) patients. Other mutation
types were missense mutations (18, 36.7%), splices sites
mutations (4, 8.2%), and small deletions or insertions
leading to a frameshift (8, 16.3%). These mutations were
spread throughout the gene with most of missense
mutations (14, 77.8%) localized to the transmembrane
region of the protein, in particular the S5-S6 loop of
domain that function as channel ion pore. In contrast,
truncation mutations (16, 59.3%) were positioned in
intracellular loops of the protein. Typical appearance of
Objectives: In Kazakhstan, the incidence of tuberculosis
in 2013 was 73.4 cases per 100,000 people, and the
mortality rate was 5.6 per 100,000 people. At the
moment in many countries around the world noted the
spread of Beijing family strains of M.tuberculosis which
associated with a high risk of drug resistance. The aim of
this study is characterization of Mycobacterium
tuberculosis clinical isolates collected in Kazakhstan by
spoligotyping.
Methods: The structure of the DR-region by
spoligotyping was determined for 270 M. tuberculosis
isolated from new diagnosed TB patients in three regions
of Kazakhstan. A loopful of culture was suspended in trisethylenediamine tetra-acetic acid (EDTA) TE buffer and
inactivated at 80ºC for 60 min. The pellet was
resuspended in the same TE buffer, stored at -20ºC.
Spoligotyping was performed on DNA by using the
standard method (Kamerbeek et al. 1997) using a reverse
dot-blot spoligotyping commercially available kit
(Ocimum Biosolutions Inc) with positive controls (M.
tuberculosis strain H37Ra and M. bovis BCG ) and
negative control without DNA. Hybridization procedure
of PCR fragments on the membrane with
chemiluminescent detection and further analysis was
79
carried out by protocol of Mycobacteriology laboratory
in Wadsworth center (NY, USA).
Results: Comparative analysis of the obtained data with
the international SpolDB4, SITVIT data bases divided the
investigated strains into 49 genotypes belonging to the
eight genetic families. Twenty-one clinical isolates (7.7%)
from this collection are not represented in the database
of Mycobacteriology laboratory of Wadsworth center
(NY, USA), but were found in SpolDB4 and SITVITweb
data bases. Thirty-five (12.9%) clinical isolates had
unique spoligopatterns. The largest cluster of 163
(60.3%) clinical isolates was formed by strains belonging
to the W-Beijing family. Another big group of strains
included in the following three clades: Haarlem - 47
(17.4%), T - 35 (12.9%) and LAM - 13 (4.8%). Other
families and genotypes are presented in smaller numbers
and each constitutes less than 2% MANU, U, Orphan,
M.bovis. In one case clinical isolate was identified as
M.abscessus.
Conclusion: The genotyping results of M.tuberculosis
strains by spoligotyping showed the prevalence of WBeijing family (60.3%) among clinical isolates collected in
Kazakhstan and possible associated with drug resistance.
susceptibility to PTB among participants in TaqI-C/C
genotype (OR=1.27; 95%, CI: 0.93-1.74, p=0,054), BsmIC/T (OR=1.46; 95%, CI: 1.07-1.98, p=0,049) of VDR gene,
and A/A genotype of IF-γ gene (OR=1.95; 95%, CI: 1.073.55, p=0,029) among females. Analysis inside “Ethnicity”
showed strong correlation with susceptibility (OR=2.11;
95%, CI: 1.04-4.27, p=0,039) to PTB among Caucasians of
research participants. Genotyping results inside Cases
revealed very strong association with susceptibility to
PTB among Caucasians by 4 polymorphisms. Caucasian
population of Kazakhstan are more susceptible in
compare to Asians more than 2.5-fold.
Conclusion: Analysis of genetic and epidemiological data
revealed susceptibility to PTB among women of
Kazakhstan. Results showed strong correlation among
Caucasian ethnic group of participants. Results can be
used as prerequisites for personalized approaches in PTB
treatment.
Disclosure of Interest: None Declared
P034
INTERACTION BETWEEN FTO AND DRD2 GENE
VARIANTS AND FOOD ENERGY DENSITY IN HUMAN
BRAIN REWARD SYSTEM RESPONSES TO FOOD
PICTURES
1,*
2
3
A. M. Yiorkas , C. G. Prechtl , M. L. Sleeth , A. D. Miras
2
2
3
4
, S. Scholtz , N. M. Daud , G. Durighel , S. F. M. Alberts
2
3
2
1
, G. S. Frost , J. D. Bell , A. I. F. Blakemore , A. P.
25
Goldstone
1
Section of Investigative Medicine, Division of Diabetes,
2
Endocrinology and Metabolism,
Metabolic and
Molecular Imaging Group, MRC Clinical Sciences Centre,
3
Nutrition and Dietetic Research Group, Division of
4
Diabetes, Endocrinology and Metabolism, Robert Steiner
5
MRI Unit, MRC Clinical Sciences Centre, Computational,
Cognitive and Clinical Neuroimaging Laboratory and
Centre for Neuropsychopharmacology, Division of Brain
Sciences, Imperial College London, Hammersmith
Hospital, London, United Kingdom
Disclosure of Interest: None Declared
P033
ASSOCIATION OF VITAMIN D RECEPTOR (FOKI, TAQI,
APAI & BSMI) AND IFG GENES’ POLYMORPHISMS WITH
RISK OF DEVELOPING PULMONARY TB (PTB) AMONG
KAZAKHSTANI POPULATION
1
1
1
1
D. Yerezhepov , M. Zhabagin , Z. Abilova , A. Askapuli ,
1
1
1
A. Abilmazhinova , S. Rakhimova , U. Kairov , A.
1
1
1
Molkenov , U. Kozhamkulov , A. Akhmetova , A.
1,*
Akilzhanova
1
Center for Life Sciences, Nazarbayev University, Astana,
Kazakhstan
Objectives: Our aim is to investigate an association of
Vitamin D receptor (FokI, TaqI, ApaI & BsmI) and IF-γ
genes’ polymorphisms with risk of developing pulmonary
TB (PTB) among Kazakhstani population.
Methods: Patients and healthy volunteers recruitment
from three regions of Kazakhstan. Data collection by
medical cards, interviews and questionnaires.
Genotyping for specific SNPs. Analysis of genotyping data
for correlation with PTB susceptibility.
Results: All required epidemiological data from 560
cases, 489 samples of familial contorol, and 520 samples
of external control is collected. 46,6% of all participants
were males. Kazakhs were major nationality in group
nd
(75,65%). Russians (15,3%) were 2 , Uighurs (2,93%)
rd
were 3
major nationality. Employed/unemployed
participants’ ratio was approximately equal but 65% of
all cases were unemployed. Main risk factor was tobacco
smoking (14,5%). Genotyping of all group did not showed
significant association with PTB (p>0,05) possibly due to
heterogeneity of participants. However grouping by
covariate
“Gender”
showed
association
with
Objectives: The function of the Fat mass and obesityassociated (FTO) gene is unclear. Rodent studies have
suggested that Fto influences dopaminergic neuronal
function. We hypothesised that a functional single
nucleotide polymorphism (SNP) associated with altered
dopaminergic signalling would interact with an FTO
obesity-associated SNP to alter human anticipatory food
reward, and furthermore that this would depend on the
energy density of the presented food cues.
Methods: 45 European Caucasian adults (age 19-55
2
years, BMI 19.1-53.1 kg/m ) underwent functional MRI to
measure blood oxygen level dependent (BOLD) signal in
brain regions involved in reward processing, including
nucleus accumbens, caudate, anterior insula, amygdala
and orbitofrontal cortex, during evaluation of high- or
low-energy dense food pictures after an overnight fast.
DNA genotyping assessed carrier status of FTO
rs9939609 A and dopamine receptor D2 (DRD2) Taq1A
80
effect alleles by restriction fragment length
polymorphism (RFLP) analysis of genomic DNA.
Results: In European Caucasians, DRD2 A1 carrier status
alone, but not FTO A carrier status, increased reward
system BOLD signal to low-energy foods, particularly in
the caudate nucleus. The FTO A allele increased reward
system BOLD signal to high-energy foods, but this was
attenuated or reversed by the presence of the DRD2 A1
allele and/or vice versa (independent of age, gender and
percentage body fat). Similar FTO x DRD2 x energy
density interactions were seen in an expanded mixed
ethnicity cohort comprising 75 adults.
Conclusion: These results support a mechanism by which
this FTO obesity-associated SNP influences body weight
by alteration of human food reward processing through
influences on dopaminergic neuronal function.
Disclosure of Interest: None Declared
described (causal) in the UMD. Information about
personal and family history was recorded for the
analyzed patients.
Conclusion: A) The novel variants detected are of high
utility for the local clinicians and genetists in the
interpretation of the results. B) The results reinforces the
necessity in our country for the full sequencing of both
genes and remarks the unfeasibility of any panel of
mutations in a genetic study for our population. C) The
importance of the availability for the knowledge of all the
variants is crucial in the clinical application of the local
genetic testing in hereditary cancer (and extensive to
whoever is interested). We are highly involved in this
mission and soon will be continuing with other genes for
hereditary cancers.
P035
GERMLINE MUTATIONS IN BRCA1/2 IN PATIENTS FROM
CEMIC AND THE UNIVERSITY OF BUENOS AIRES
REVEALS HIGH HETEROGENEITY AND NOVEL VARIANTS:
CONSTRUCTING THE INSTITUTIONAL GENETIC VARIANT
BASE AND THE FIRST IN THE COUNTRY
1 2,*
1
3
1
A. R. Solano , F. C. Cardoso , F. Poletta , V. Romano ,
1
3
4
S. Quiroga , J. Lopez Camelo , O. Mando
1
2
DAC, CEMIC, INBIOMED-CONICET, Departamento de
Bioquimica, Fac. de Medicina, Univ. de Buenos Aires,
3
4
Departmento de Investigacion, Direccion de Asistencia
Medica, CEMIC, CABA, Argentina
P036
RESISTIN RS1862513 [-420 C/G] POLYMORPHISM IN
PSORIASIS IN SOUTH INDIAN POPULATION
1,*
1
1
2
A. Sudhesan , M. Rajappa , A. PH , D. M. Thappa , S.
3
4
Satheesh , A. C
1
2
3
4
Biochemistry,
Dermatology,
Cardiology,
Clinical
pharmacology, Jawaharlal Institute of Postgraduate
Medical Education and Research, Puducherry, India
Disclosure of Interest: None Declared
Objectives: Psoriasis is a multi-factorial heritable
prototypical
T-helper
(Th)-1/Th-17
mediated
inflammatory
disease,
characterized
by
hyperproliferation of keratinocytes in the affected skin.
Psoriasis is associated with co-morbidities such as
diabetes and cardiovascular disease. Resistin is a proinflammatory adipokine, with important role in the
pathogenesis of chronic inflammatory diseases, including
psoriasis. There are no studies till date, to the best of our
knowledge, about the association of resistin single
nucleotide polymorphism (SNP), with susceptibility to the
disease in South Indian patients with psoriasis.
Objectives: Genetic databases are mostly generated
in the first world and reflect the population analyzed.
Since 1996 we studied patients with family history of
cancer; this data is the first in Argentina and in South
America. We found novel variants, clinically: benign,
uncertain or deleterious, surprisingly, even after more
than 1700 causal mutations listed in the Breast Cancer
Information Core (BIC). Our purpose is to present a
summary of our results in germline mutations and the in
silico analysis.
Methods: Massive parallel sequencing (Ion Torrent) and
Sanger confirmation in a DNA sample from blood.
Analyzed full coding sequence and 30bp of introns on the
BRCA1/2 genes.
Results: Mutations in BRCA1/2 have few data in South
America. We analyzed the full sequence in 524 patients
(including 144 healthy). Recurrent mutations in the 148
mutated patients are: c.181T>G and c.211A>G in BRCA1
and c.2808_2811delACAA in BRCA2. Novel mutations
(23) are: fifteen (6 in BRCA1 and 9 in BRCA2) are
deleterious; eight variants c.4484+3A>G and p.S114C in
BRCA1 and p.G173C, c.7426_7428delGAA (in frame
deletion), p.D2680N, p.K426T, p.S1106G and p.A2387P in
BRCA2 resulted in either putative altered splicing (the
intronic +3 variant and the base change at the last base
of the exon c.517 C>T at the G173C), or the in silico
analysis is probably/possibly damaging. None variant are
listed in the BIC/LOVD databases and six of them are
The main objective of the study was to examine the
relationship between single nucleotide polymorphism
(SNP) of resistin gene (RETN) rs1862513 (-420C/G) and
susceptibility to psoriasis in South Indian ethnic
population.
Methods: 100 cases with psoriasis and 100 healthy
controls were enrolled in the present study. Severity
grading was done in patients with psoriasis, according to
psoriasis area severity index (PASI) scoring. Genotyping
of resistin gene (RETN) rs1862513 (-420C/G) was done by
polymerase chain reaction restriction fragment length
polymorphism (PCR-RFLP). Plasma resistin levels were
assayed using commercially available ELISA kit.
Results: In our study, we observed that the plasma
resistin levels and cardiovascular risk, as estimated by
Framingham risk score, were significantly elevated in
patients with psoriasis, compared with controls.
However, we did not observe any significant statistical
81
significance between resistin gene (RETN) rs1862513 (420C/G) single nucleotide polymorphism and psoriasis
risk in South Indian Tamil population
Conclusion: Our results suggest that cardiovascular risk is
more in the psoriatic cases, as compared with controls
and that the resistin gene (RETN) rs1862513 (-420C/G)
single nucleotide polymorphism is not associated with
susceptibility to psoriasis in our ethnic South Indian
population.
Disclosure of Interest: None Declared
variant genotype and neonatal hyperbilirubinemia risk in
the females were observed (OR=0.44; 95% CI=0.20−0.95,
p = 0.034).
Conclusion: In conclusion, the homozygous variant
genotype of NR1I3 MPJ6_1I3008 polymorphism could
decrease the risk of neonatal hyperbilirubinemia in the
Malay females.
Disclosure of Interest: None Declared
P038
NON-INVASIVE PRENATAL SCREENING PLUS (NIPS+):
DETECTION OF FETAL 22Q11.2 MICRODELETION AND
MICRODUPLICATION SYNDROMES.
1 2,*
1
C.-C. Hung , Y.-N. Su
1
2
Sofiva Genomics Co., Ltd, Graduate Institute of Medical
Genomics and Proteomics, National Taiwan University
College of Medicine, Taipei, Taiwan
P037
INVERSE ASSOCIATION BETWEEN MPJ6_1I3008 OF THE
NR1I3 GENE AND NEONATAL HYPERBILIRUBINEMIA IN
THE MALAY FEMALES
1,*
1
1
1
C. Tian Pei , S. Yusoff , R. Ismail , N. N. Nawawi , N. A.
1
1
1
1
Abdullah , N. Ramli , N. R. Ibrahim , N. Hj. Abd Majid ,
2
3
1
N. M. Yusoff , H. Nishio , H. Van Rostenberghe
1
Pediatrics, Universiti Sains Malaysia, Kubang Kerian,
2
Advanced Medical and Dental Institute (AMDI),
3
Universiti Sains Malaysia, Bertam, Malaysia, Graduate
School of Medicine, Kobe University, Hyogo Prefecture,
Japan
Objectives: Non-invasive prenatal screening (NIPS) by
next-generation sequencing (NGS) of cell-free DNA
(cfDNA) from maternal plasma has been demonstrated
to be a powerful method for the detection of fetal
aneuploidies including trisomies 21, 18, and 13. Non+
invasive prenatal screening plus (NIPS ) have
extended these analyses to screen for 20 common
microdeletion syndromes. Here we describe two health
pregnant women, each carrying a fetus to be affected by
22q11.2 microdeletion and microduplication syndromes
+
by NIPS testing
Methods: We sequenced cfDNA isolated from
maternal plasma obtained at 14 and 21 weeks of
gestation from two health pregnant woman with a
singleton pregnancy. NGS data were aligned to the Homo
sapiens (human) as provided by UCSC (hg19). We
removed repetitive regions and normalized for GC
content. Finally, z scores were calculated for the targeted
region.
Results: We detected a statistically significant loss and
gain of chromosome 22q11.2 in these two cases, and the
Z score values are -3.67 and 7.30, respectively. The
positive results of 3.15 Mb-microdeletion at 22q11.21
and 4.14 Mb-microduplication at 22q11.1-q11.21 were
confirmed by array comparative genomic hybridization
(aCGH) diagnostic genetic tests in amniotic fluid.
+
Conclusion: NIPS can detect 22q11 microdeletion and
microduplication which are compatible with DiGeorge
syndrome and Cat-eye syndrome. Non-invasive prenatal
screening for microdeletion syndromes is feasible and
should be considered for pregnant women.
Disclosure of Interest: None Declared
Objectives: Neonatal hyperbilirubinemia is a common
clinical manifestation encountered in newborns.
However, newborns with severe hyperbilirubinemia are
at an elevated risk for kernicterus or even death.
Constitutive androstane receptor (CAR), encoded by
nuclear receptor subfamily 1, group I, member 3 (NR1I3)
gene, has been implicated in the regulation of bilirubin
excretion. Therefore, NR1I3 genetic variants may
modulate bilirubin metabolism and lead to neonatal
hyperbilirubinemia. To date, the association between
NR1I3 variants and neonatal hyperbilirubinemia has not
been investigated in any population. We aimed to
determine the association between MPJ6_1I3008
(rs10157822) polymorphism in the NR1I3 gene and
neonatal hyperbilirubinemia development in Malay
population.
Methods: A total of 509 newborns comprising 232
hyperbilirubinemia and 277 non-hyperbilirubinemia
newborns admitted to and/or born in Hospital Universiti
Sains
Malaysia
(HUSM)
were
recruited.
Hyperbilirubinemia group constituted those who
developed total serum bilirubin levels ≥250 µmol/L
within the first week after birth while nonhyperbilirubinemia subjects were healthy newborns
without significant hyperbilirubinemia. MPJ6_1I3008 was
genotyped using high resolution melting analysis of the
DNA samples that were isolated from buccal swab
specimens. Binary logistic regression was used to assess
the association between polymorphic genotypes of
MPJ6_1I3008 and risk of neonatal hyperbilirubinemia.
Results: The genotypic and allelic frequencies of
MPJ6_1I3008 were not significantly different between
hyperbilirubinemia and non-hyperbilirubinemia groups.
However, when the results were stratified by gender, a
significant inverse association between homozygous
P039
TARGETED NEXT-GENERATION SEQUENCING PANEL FOR
DETECTION OF MUTATIONS IN HEARING IMPAIRMENT
1 2 3,*
12
C.-C. Hung
, Y.-N. Su
1
2
Phoebus Genetics Co., Ltd., Sofiva Genomics Co., Ltd.,
3
Graduate Institute of Medical Genomics and Proteomics,
82
National Taiwan University College of Medicine, Taipei,
Taiwan, Province of China
members were extracted from peripheral blood
leukocytes and exome sequencing was performed by Ion
Torrent Amplicon Sequencing platform.
Results: There were 6 T1D cases in the two core families
with more than one member affected. The autoantibody
was not consistent with the members of the same family
on both anti-GAD and IA2 antibodies. Exome sequencing
was performed on DNA samples obtained from the two
core families after PST analysis. An average of 300010000 nonsynonymous / splice acceptor and donor site /
insertions or deletions (NS/SS/Indel) variants were
detected in each of the T1D family members sequenced.
After serial filters, we generated an average of 180 -700
variants from each family. Changes that were predicted
as non-significant were identified and excluded from the
variant list using POLYPHEN (BENIGN) and SIFT
(TOLERATED) software. In comparison with NCBI
database and DISEASES text mining, the nonsynonymous
variants were fine-mapping to the FLJ22184 genes after
confirmation of direct PCR and Sanger sequencing.
Conclusion: FLJ22184 gene variant was identified from
the family of more than two members of T1D in Taiwan.
The roles of FLJ22184 played in the pathogenesis of T1D
warrant further investigation.
Disclosure of Interest: None Declared
Objectives: Next-generation sequencing (NGS) allows for
high-throughput sequencing analysis of large regions of
the human genome. We explored the use of
targeted NGS for simultaneous genetic testing for
multiple genes in hearing impairment.
Methods: We designed a custom panel to capture and
enrich 103
hearing
impairment-related
genes.
Additionally, NGS was performed to jointly sequence
captured DNA individually for 3 cases with nonsyndromic
phenotype, including 2 cases with known family history.
Results: Using targeted sequencing, we achieved an
average sequence depth of ~200× per base. We analyzed
DNA from 3 unrelated hearing impairment patients and
identified a c.920G>T (p.G370V) mutation of the KCNQ4
gene in case 1, a compound heterozygous mutation
c.5375G>A/c.7068T>G (p.G1792E/ p.N2356K) of the
USH2A gene in case 2, and a novel +15 A>G mutation in
the seed region of the miR-96 gene for case 3,
respectively.
Conclusion: The hearing impairment NGS panel allows
simultaneous testing for multiple genes with high
accuracy. Using this approach can fast identification of
mutations in hearing impairment.
Disclosure of Interest: None Declared
P041
FOK1 AND TAQ1 POLYMORPHISMS OF VDR GENE AND
STUNTED GROWTH IN TRANSFUSION DEPENDENT
THALASSEMIA PATIENT: A PRELIMINARY STUDY
1,*
2
1
1
D. Rashid , W.-Z. Abdullah , A. Nasir , P. Yahya , N. F.
1
1
2
2
2
Azman , S. Hanafi , M. F. Johan , R. Bahar , R. Hassan ,
1
B. Zilfalil
1
2
Pediatrics, Hematology, Universiti Sains Malaysia,
Kubang Kerian, Malaysia
P040
WHOLE-EXOME SEQUENCING IDENTIFIED FLJ22184
NON-SYNONYMOUS MUTATION COMMON IN TWO
TYPE 1 DIABETES CORE FAMILIES WITH MULTIPLE CASES
1,*
2
3
1
4
C.-H. Lin , I. J. Tsai , Y.-S. Lee , Y.-Y. Huang , F.-S. Lo ,
5
5
Z.-S. Chen , C.-N. Tsai
1
Endocrinology and Metabolism, Chang-Gung Memorial
2
Hospital, Taipei, Taiwan, Biodiversity Research Center,
3
Academia Sinica, Taipei, Taiwan, Department of
Biotechnology, Ming Chuan University, Taipei, Taiwan,
4
Department of Pediatrics, Chang-Gung Memorial
5
Hospital, Taipei, Taiwan, Taipei, Graduate Institute of
Clinical
Medical
Sciences,
Chang
Gung
University,Taoyuan, Taiwan, Taoyuan, Taiwan, Province
of China
Objectives: Thalassemia patients may develop bony
complications from multiple factors including genetic
determinant such as Vitamin D receptor (VDR) gene.
Association of Fok1 and Taq1 Single Nucleotide
Polymorphisms (SNPs) of VDR gene has been reported in
low bone mineral density (BMD), osteoporosis and
sometimes stunted growth phenotype. It is hypothesized
that higher frequency of VDR gene SNPs among
physically stunted growth appearance in Thalassemia
patients. This study was done to compare the presence
of the 2 SNPs in the VDR gene among the stunted growth
and non-stunted growth transfusion dependent
Thalassemia patients.
Methods: Thirty one transfusion dependent thalassemia
patients were recruited in this study and were
categorized into 2 groups; stunted and non-stunted
growth groups based on height percentile. DNA was
extracted using QIAamp Blood Maxi Kit. Subsequently,
genomic DNA was used for the genotyping using RFLPPCR method. The VDR gene polymorphisms were
detected by the restriction enzymes Fok1 and Taq1;
where the F and T allele indicated absence of cuttable
site and wild type respectively and the f and t allele were
Objectives: Genetic linkage study in type 1 DM (T1D)
remains limited in Taiwan especially for the family of
more than one case. We carried out exome sequencing
from two core families with multiple T1D members in
Taiwan in hope to identify heritable mutations that may
be responsible in causing T1D.
Methods: The family database from the trial of PST
(parent-sibling tracing) linkage based analysis in the
family of more than two members with type 1 diabetes
in Taiwan (PATT) was used for DNA analysis. Diagnosis of
T1D was made based on the criteria of the American
Diabetes Association with a very low C-peptide level
(<0.35 ng/mL) with or without the experience of diabetic
ketoacidosis. Patients with ages of onset more than 35
years were excluded. The genomic DNA of the family
83
the presence. We then associate the genotypes to
stunted growth patients using Chi-square test analysis of
SPSS version 22.
Results: Out of 31 samples analyzed for Fok1 and Taq1
polymorphism, the following genotype frequency was
obtained; FF 59.3%, Ff 40.7% and TT 71%, Tt 29%.
Genotype distribution of FF, Ff, TT, Tt in stunted growth
were; 29.6%(8), 25.9%(7), 38.7%(12), 22.6%(7)
respectively and 29.6%(8), 14.8%(4), 32.3%(10), 6.5%(2)
in non-stunted growth group respectively. From this
preliminary study, none of the stunted growth and
normal growth patients was observed to have
homozygous mutant Fok1 and Taq1 polymorphisms.
Higher frequencies of heterozygous Fok1 and Taq1 were
observed in the stunted growth Thalassemia patients
however not statistically significant (p>0.05).
Conclusion: The presence of these 2 polymorphisms
were not associated with growth in our cohort of
patients. The inclusion of bone mineral density (BMD)
measurement, Vitamin D status assessment and bigger
sample size may produce statistically significant result.
Disclosure of Interest: None Declared
localized at cytoplasmic loops (connecting 2 nearby
homologous domains), and 3 mutations were localized at
transmembrane segments. Nine of these 14 SCN1A
mutations were novel and parental DNA analysis for the
identified mutations show that all of the mutations were
de nono. Besides well-known genotype–phenotype
correlations, our study results strongly suggests the
existence of modifying factors.
Conclusion: In our study, the proportion of SCN1A
mutations among Vietmamese Dravet patients appeared
to be consistent with other populations. Our study also
expands the spectrum of SCN1A mutations and confirms
the current understanding of genotype–phenotype
correlations.
Disclosure of Interest: None Declared
P043
ACUTE ENCEPHALOPATHY IN TWO CHILDREN WITH
DRAVET SYNDROME
1,*
2
2
D. Thi Thu Hang , H. Thi Thuy Kieu , L. Thi Khanh Van
1
School of Medicine, Vietnam National University - Ho Chi
2
Minh City, Neurology Department, Children Hospital II,
Ho Chi Minh City, Viet Nam
P042
MUTATIONS OF THE SCN1A GENE IN VIETNAMESE
CHILDREN WITH DRAVET SYNDROME
1,*
2
2
D. T. T. Hang , B. Chi Bao , V. Diem My
1
School of Medicine, Vietnam National University - Ho Chi
2
Minh City, Center of Molecular Medicine, University of
Medicine and Pharmacy, Ho Chi Minh City, Viet Nam
Objectives: Dravet syndrome is a rare and severe
infantile-onset epilepsy syndrome, mainly caused by
mutations in SCN1A gene. Acute encephalopathy
resulting in sudden and serious neurological
deterioration is an unusual complication in Dravet
syndrome and has been reported sporadically. However,
risk factors for this complication in Dravet patients are
not well-known yet and further research and discussion
on this topic is needed.
Methods: We present two cases of Dravet syndrome
with acute encephalopathy at Children Hospital II,
Vietnam. The two patient had typical characteristics of
Dravet syndrome and experienced complicated,
refractory status epilepticus at 50 months and 24
months, respectively. After the refractory status
epilepticus, in spite of the decline in their epilepsy, both
patients underwent persistent and severe cognitive and
motor deterioration over the 9-month follow-up period.
Results: Compared to other patients in our cohort of 20
patients with Dravet syndrome who were still in common
course of the disease, the two patients had much more
severe epilepsy including more seizure types (hemiclonic, tonic-clonic, myoclonic and complex partial) and
especially, more repetitive episodes of status epilepticus
(SE) before the occurrence of the refractory status
epilepticus. SCN1A mutational analysis by PCRsequencing and MLPA showed that one patient had a
nonsense mutation (R1525X) in exon 24. And for the
other patient, we surprisingly detected a homozygous
missense mutation (A1440V) in exon 22.
Conclusion: Combining with other published data, we
suggest that severe epilepsy including multiple seizure
types and frequent status epilepticus together with
serious mutations in SCN1A gene may be risk factors for
Dravet patients to develop acute encephalopathy.
Objectives: Dravet syndrome is one of the most
catastrophic types of epilepsy in infants. It is found that
up to 70 - 80% of cases, Dravet syndrome is caused by
mutations in SCN1A, the gene encoding alpha-1
subunit of the sodium channel. Mutations of the SCN1A
gene have an autosomal dominant inheritance pattern.
To date, over 800 SCN1A mutations have been reported
all over the world, however, no SCN1A mutation studies
have been performed in the Vietnamese population, and
genetic characteristics of Vietnamese Dravet patients are
not yet clear. In this study, we analyzed SCN1A gene in
18 Vietnamese patients with typical clinical
characteristics of Dravet syndrome at Children's Hospital
2, Ho Chi Minh City, Vietnam.
Methods: PCR–DNA sequencing and multiple ligationdependent probe amplication (MLPA) were performed to
screen the entire coding region as well as exon-intron
boundaries of the gene. Mutations were classified as
truncation (nonsense and frameshift) and missense
mutations.
Results: Forthteen mutations (14/18; 78%) were
identified including 13 point mutations detected by PCRSequencing and 1 large deletion mutation spanning
nearly whole exon 7 detected by MLPA. Five mutations
were classified as truncations (2 frameshift and 3
nonsense mutations) and 9 were classified as missense
mutations. There were 6 mutations were localized at
pore-forming loop (connecting S5-S6); 5 mutations were
84
1
Disclosure of Interest: None Declared
1
1
1
S. Maran , S. A. Faten , H. Hashim , N. A. Mohd Nawi ,
1
2 3
4
N. Ramli , W. P. Wan Ibrahim , A. R. Wong , M. R.
3
12
1
1,*
Mohd Zain , W. R. Wan Taib , R. Ankathil , H. L. Tan
1
Human Genome Center, Universiti Sains Malaysia,
2
Kubang Kerian, Kota Bharu, Faculty of Medicine and
Health Sciences, Universiti Sultan Zainal Abidin, Kuala
3
Terengganu, Terengganu, Department of Paediatrics,
Universiti Sains Malaysia, Kubang Kerian, Kota Bharu,
4
Department of Paediatrics, Hospital Raja Perempuan
Zainab II, Kota Bharu, Malaysia
P044
CLASSIFICATION OF HBE/BETA – THALASSAEMIA
DISEASE SEVERITY BASED ON SCORING SYSTEM AND
MOLECULAR GENOTYPE
1,*
2
2
2
2
H. Alsaleh , A. Nasir , Z. Alwi , S. Hanafi , D. Rashid ,
1
R. Hassan
1
Department of Hematology, School of Medical Sciences,
2
Department of Pediatrics, School of Medical Sciences,
Universiti Sains Malaysia, kota bharu, Malaysia
Objectives: The 22q11.2 microdeletion syndrome
(22q11.2 DS) occurs in 1/4000 births. It is a congenital
abnormality involving primarily heart defects, facial
dymorphisms, thymic hypoplasia, cleft palate and
hypocalcaemia. Patients with heart defects are generally
not tested for this syndrome and might be underrecognised. Multiplex Ligation-dependent Probe
Amplification (MLPA) is a variation of multiplex PCR
technique that enables detection of microdeletion and
microduplication using DNA extracted from blood. FISH is
a molecular cytogenetic technique that detects and
localizes microdeletions and microduplications of
chromosome on cultured peripheral blood metaphases.
This study was set out to utilize MLPA as an adjunct to
FISH in detecting 22q11.2 DS among 39 atrial septal
defects (ASD) patients and to compare the concordance
of both techniques in 22q11.2DS detection.
Methods: The analysis of microdeletion was conducted
using fluorescence in-situ hybridization (FISH) probe on
metaphase chromosomes and interphase nuclei isolated
from venous peripheral blood cultures. VCFS TUPLE 1
(Cytocell, USA), a molecular probe specific to 22q11
region was used for the hybridisation. Multiplex Ligationdependent Probe Amplification (MLPA) was conducted
using SALSA MLPA P250-A1 DiGeorge Kit (MRC Holland)
on DNA extracted from the blood samples.
Results: Both MLPA and FISH analysis showed no
microdeletion in all the ASD patients, indicating that
22q11.2 DS is not a common syndrome among the
recruited ASD patients in current study. MLPA analysis
result showed a complete concordance with FISH assay.
Conclusion: On this basis, we concluded that MLPA is an
accurate, reliable, and cost-effective method that
provides an alternative to FISH assay in the screening for
microdeletion syndromes. The advantage of MLPA in
employing DNA as starting materials will enable the
usage of other sources such as saliva and hair root
instead of peripheral blood and in turn will accelerate the
testing of 22q11.2 DS in more patients.
Disclosure of Interest: None Declared
Objectives: HbE/ β – thalassaemia (HbE/ β thal) is a
known health problem in Malaysia and Southeast Asia. In
this study our aim was to classify HbE/ β – thalassaemia
disease severity using adapted scoring system and
molecular genotype.
Methods: A total of 26 blood samples were collected
from transfusion dependent HbE/ β thalassaemia
patients. DNA was extracted for multiplex amplification
refractory mutation system (MARMS). This MARMS
detects 25 type of mutations commonly found in
Malaysia. A scoring system adapted by Orapan Sripichai
et al, (2008) is used to classify patients into mild,
moderate and severe depending on six factors; age of
presentation, age of first transfusion, haemoglobin (Hb)
level, spleen size, growth development and transfusion
frequency (Sripichai et al., 2008).
Results: Based on the scoring system, nine patients
(34.6%) were classified under severe group. Seventeen
(65.4 %) were moderate and no mild case identified.
Genotype analysis by MARMS showed that 16 (61.5%)
E 0
E +
exhibed β /β and five (19.2%) were β /β . The remaining
five patients showed only HbE with no beta thal
mutation detected. Gene sequencing will be perform on
E 0
these samples. Based on molecular genotype of β /β and
adapted scoring system only three (11.6%) patients were
consistent in the classification as severe disease. Thirteen
E 0
with β /β were moderate in their clinical manifestation.
Underlying modifying factors need to be excluded.
Conclusion: Both scoring system and molecular genotype
are important to classify HbE/ β thal disease severity.
Further analysis is required, taking into consideration
other genetic modifiers.
References: Sripichai, O., Makarasara, W., Munkongdee,
T., Kumkhaek, C., Nuchprayoon, I., Chuansumrit, A.,
Chuncharunee, S., Chantrakoon, N., Boonmongkol, P. &
Winichagoon, P. (2008). A scoring system for the
classification of β‐thalassemia/Hb E disease severity.
American journal of hematology, 83(6), 482-484.
Disclosure of Interest: None Declared
P046
FEATURES OF THE FIRST REFERENCE SEQUENCE OF
SAUDI
1,*
1
1
I. Alabdulkareem , W. Alharbi , M. Ballow , Y. Alhaidan
1
1
1
1
, A. AlAbdulrahman , Z. Rabhan , M. Aljumah , M.
1
Albalwi
1
MEDICAL GENOMICS, KAIMRC, RIYADH, Saudi Arabia
P045
COMPARISON OF MLPA WITH FISH TECHNIQUE IN
DETECTION
OF
CHROMOSOME
22Q11.2
MICRODELETION SYNDROME AMONG ATRIAL SEPTAL
DEFECTS PATIENTS
85
Objectives:
- Establishment Saudi Human Genome
Database (SHGD)
- Detection of genetics variations and biomarkers
providing a comprehensive survey of the landscape of
genetics variant compare to other populations such as:
Results: In this study, 64.5% and 40.0% patients with RA
were positive for ACPA and HLA-DRB1 SE alleles,
respectively. Our data showed a positive association
between LTA genetic variant rs2857602_G and RA, both
in the allelic model (OR: 1.19, 95% CI:1.07-1.33) and in
the genotypic model (OR: 1.29; 95% CI:1.11-1.51). In
addition, we observed a decreased risk of developing RA
with the rs1800629_ATNF genetic risk variant both in the
allelic model (OR: 0.77; 95% CI:0.62-0.97) and the
genotypic model (OR:0.77; 95% CI:0.68-0.98),
respectively. Haplotype analysis for four selected LTATNF SNPs revealed a significant association of one with
-5
susceptibility (p-value: 6.3 x 10 ) and of another with a
protective effect (p-value: 0.03). Stratification analysis by
ACPA status demonstrated significant associations of
both theLTA genetic variant rs2857602_G (OR: 1.40; 95%
CI: 1.18-1.67) and the TNF genetic variant rs1800629_A
(OR:0.72; 95% CI:1.18 – 1.67) with the ACPA-positive RA.
No statistical significant association was observed in the
ACPA-negative RA and also in the RA subsets stratified by
the HLA-DRB1 SE status.
Conclusion: Our findings suggest that the risk of
developing ACPA-positive RA is associated with the
genetic variations within the TNF-LTA gene region in the
Malaysian population.
Disclosure of Interest: None Declared
- Copy numbers variation (CNVs)
- Indels large structural rearrangements
- Single nucleotide polymorphisms
- DNA methylation database
Methods: In this summery; the first Saudi genome was
assembled from healthy volunteer using NGS technology
(5500xl Genetic Analyzer).
Results: A total of 2311051 unique variants were
detected in the reference subjects that use for
establishment of Saudi genomics reference sequence.
however; the Alignment of the genomics data of the
targeted subject was performed against human genome
(hg19) by hybrid approach. it was noticed that more than
10000 unique indels and almost 16000 structural variants
were detected the reference subjects
Our previous data showed more than 14% of the SNPs
were unique among 32 subjects was also present at our
proposed reference. A de novo assembly of 9,894 contigs
sequences was not represented in NCBI reference
genome.
Conclusion: De novo assembled and analyzed full Saudi
Arabian individual genome of showed more than 231K
polymorphisms that is sole compare to the reference
sequence.
References: Hum Mol Genet. 2013 Oct 15;22(R1):R27-31.
doi: 10.1093/hmg/ddt384. Epub 2013 Aug 19.
Databases of genomic variation and phenotypes: existing
resources and future needs.
Johnston JJ, Biesecker LG.
Disclosure of Interest: None Declared
P048
THE
NON-GENOMIC
ACTION
OF
DIHYDROTESTOSTERONE (DHT) IN SKELETAL MUSCLE
FIBRE TYPES
1,*
M. H. Mahmood
1
Department of Para-Clinical Sciences, Universiti
Malaysia Sarawak, Faculty of Medicine & Health
Sciences, Kuching, Malaysia
Objectives: Anabolic-androgenic steroids (AASs) such as
testosterone (T) and its derivative Dihydrotestosterone
(DHT) are commonly used for enhancement of skeletal
muscle mass. AASs are thought to demonstrate both
genomic action, which takes days to manifest; mediated
through the androgen receptor and non-genomic action,
occurring within minutes and affected through signalling
pathway. Although there are many studies on the
genomic action, little is known about non-genomic effect
of AASs on skeletal muscle. The objective of this study
was to investigate the non-genomic effects of T and DHT
on amino acid uptake in skeletal muscle fibre types.
Methods: This study conformed to the local ethical
requirement. All experiments were performed at room
temperature using small muscle fibre bundles isolated
from either extensor digitorum longus (fast fibre) or
soleus (slow fibre) of adult CD-1 female mice (N=20), age
average 57.43 ± 2.01days (age range 54 to 61 days). They
were treated for one hour with standard Ringer’s
14
solution plus 2mM of carbon-14 labelled isoleucine [L-U
-1
C] with either 630ρgml of DHT, testosterone or the
vehicle, ethanol. In another set of experiments, the
bundles were pre-treated for 30 minutes with inhibitors
P047
TNF-LTA GENE VARIATIONS AND THE RISK OF
DEVELOPING RHEUMATOID ARTHRITIS IN THE MYEIRA
STUDY
1,*
1
1
2
L. K. Tan , S. Sulaiman , J. S. Dhaliwal , S. Murad , C. L.
1
Too
1
Allergy and Immunology Research Center, Institute for
2
Medical Research, Ministry of Health, Kuala Lumpur,
Malaysia
Objectives: We aimed to determine the association
between the TNF-LTA genes polymorphisms and the risk
of developing RA in the Malaysian population stratified
by anti-citrullinated protein antibody (ACPA) and HLADRB1 shared epitope (SE) status.
Methods: A total of five single nucleotide polymorphisms
(SNPs) withinthe TNF-LTA genes region were genotyped
in the 1,235 RA cases and 1,625 control subjects from the
Malaysian Epidemiological Investigation of Rheumatoid
Arthritis (MyEIRA) case-control study. The risk of
developing RA was determined by a 2 x 2 association test
with 95% confidence interval (95% CI).
86
of EGFR, MEK, androgen receptor, translation and
transcription before treatment with DHT plus the
14
inhibitor and 2mM of L-U C for one hour.
Results: Results show that one hour DHT treatment
increases isoleucine incorporation in fast fibre (88.65 ±
3.74%)*; on the contrary decreases isoleucine uptake in
slow fibre (0.26 ± 1.97%)* (*p<0.05). However treatment
with testosterone does not increase uptake of isoleucine
in either fast or slow fibre bundles. Moreover this
increase was blocked by inhibitor of EGFR, MEK, and
translation but not by inhibitor of androgen and
transcription in both fast and slow fibres.
Conclusion: DHT is more potent than testosterone. This
is a non-genomic effect whereby DHT mediates its action
through the EGFR via the MAPK/ERK pathway.
Disclosure of Interest: None Declared
0.02 for the IL28B G allele. No IL28B G/G genotype was
observed between the two groups.
Conclusion: No significant differences in IL28B
rs12979860 C>T and rs8099917 T>G allelic and genotype
frequencies between normal controls and NAFLD
patients were noted. Our data showed that the allelic
frequencies of IL28B rs12979860 C>T and rs8099917 T>G
in the Filipino normal controls were significantly different
from Caucasians but similar with other Asian
populations.
References: Petta S et al. IL28B and PNPLA3
polymorphisms affect histological liver damage
in patients with non-alcoholic fatty liver disease. Journal
of Hepatology 2012;56:1356-1362.
Garrett ME et al. IL28B rs12979860 is not associated
with histologic features of NAFLD in a cohort of
Caucasian North American patients. Journal of
Hepatology 2013;58:402-403.
P049
FREQUENCY OF HUMAN INTERLEUKIN 28B RS12979860
C>T AND RS8099917 T>G VARIANTS IN FILIPINO
PATIENTS WITH NON-ALCOHOLIC FATTY LIVER DISEASE
1,*
2
M. Baclig , J. Gopez-Cervantes and St. Luke’s Liver
Diseases Study Group
1
2
Research and Biotechnology, Liver Disease and
Transplant Center, St. Luke's Medical Center, Quezon
City, Philippines
Disclosure of Interest: None Declared
P050
TRANSCRIPTIONAL PROFILING OF AGEING IN MICE
REVEALS EFFECTIVENESS OF SHORT- AND LONG-TERM
PIPER BETLE SUPPLEMENTATION
1,*
1
2
M. F. A. Shukor , W. Z. Wan Ngah , N. A. Abdul Hamid
1
Biochemistry, Universiti Kebangsaan Malaysia, Bandar
2
Tun Razak, Basic Medical Sciences, Cyberjaya University
College of Medical Sciences (CUCMS), Selangor, Malaysia
Objectives: Non-alcoholic fatty liver disease (NAFLD) is a
common cause of chronic liver disease worldwide and
may progress to cirrhosis and hepatocellular carcinoma.
Increasing though contrasting studies suggests that
genetic variation may play a role in the susceptibility to
NAFLD and in the severity of liver disease. A hospitalbased study was conducted to determine the frequency
of human interleukin 28B (IL28B) rs12979860 C>T and
rs8099917 T>G variants among Filipino patients clinically
diagnosed and histologically confirmed with NAFLD and
among normal controls. In addition, the frequency
distribution of IL28B variants was compared with various
ethnic populations.
Methods: Real-time PCR was performed using the
Taqman SNP genotyping assay for IL28B rs12979860 and
rs8099917. DNA sequencing was done to confirm the
IL28B genotypes.
Results: The allelic frequencies among normal controls
were 0.94 and 0.06 for the IL28B C and IL28B T alleles,
respectively. Calculated frequencies in Hardy Weinberg
Equilibrium (HWE) were 88% for IL28B C/C and 12% for
IL28B C/T genotype. Among patients with NAFLD, the
allelic frequencies were 0.98 for the IL28B C allele and
0.02 for the IL28B T allele. No IL28B T/T genotype was
observed between the two groups. For IL28B rs8099917,
allelic frequencies in HWE among normal controls were
0.95 for the T allele and 0.05 for the G allele. Ninety-one
percent were identified as homozygous for the wild-type
T/T genotype and 9% were identified as heterozygous for
the T/G genotype. Among patients with NAFLD, the
allelic frequencies were 0.98 for the IL28B T allele and
Objectives: To evaluate the short- (ST-PB) and long-term
Piper betle (LT-PB) effect on whole genomic changes
during normal ageing.
Methods: This study was conducted in healthy young
male mice (C57BL/6) age 5 month-old. ST-PB was
supplemented for 2 months while LT-PB was
supplemented for 13.5 months. At the end of
supplementation, mice were sacrificed by cervical
dislocation. Total RNA in the liver tissue was extracted,
hybridized and injected into Affymetrix GeneChip®
Mouse Gene 1.0 ST Arrays.
Results: Using a T-test unpaired at 1.2-fold cut-off and
false discovery rate <0.05, our results indicated that the
expression of 71 genes (37 overexpressed, 34 genes
underexpressed) and 120 genes (34 overexpressed, 86
underexpressed) was altered by ST- and LT-PB,
respectively. Analysis by GSEA and Fisher Exact test
showed
that
long-term
Piper betle
(LT-PB)
supplementation reduced apoptosis (↓Ei24, ↓C16orf5)
and response to oxidative stress (↓Vnn1, ↓Tor1a,
↓Egfr) pathways. Meanwhile, short-term Piper betle (STPB) supplementation just for 2 months was also able to
reduce response to oxidative stress pathway as well as
LT-PB.
Conclusion: LT-PB modulated more genes expression
compared to ST-PB and may showed more beneficial
effects in preventing age-related deterioration as it can
reduce oxidative stress and apoptosis.
Disclosure of Interest: None Declared
87
P051
EVIDENCE OF HAPLOTYPE ASSOCIATION OF SLC2A9
POLYMORPHISMS IN GOUTY MALAY POPULATION
1,*
1
2
N. Mohd Yunus , M. Adanan , W. S. Wan Ghazali , T.
1
3
Huay Lin , W. R. Wan Taib
1
Human Genome Center, School of Medical Sciences,
2
Department of Medicine, School of Medical Sciences,
Health Campus, Universiti Sains Malaysia, Kubang Kerian,
3
Kelantan, School of Diagnostic and Biomedical Sciences,
Faculty of Medicine and Health Sciences, Science and
Medicine Foundation Center, Universiti Sultan Zainal
Abidin, Kuala Terengganu, Terengganu, Malaysia
P052
PTPN11 GENE ANALYSIS IN TUNISIAN PATIENTS WITH
NOONAN SYNDROME
1,*
N. G. Abroug
and Nehla Ghédira1*, Natacha Fillot3,
Emna Kerkeni1, Sana Sfar1, Sofiene Bouaziz1, Rania
Sakka1.², Fatma-Zohra Chioukh², Karim Ben Ameur².,
Hayet Ben Hmida², Hélène Cavé3, Kamel Monastiri1.².
1Unité de Génétique des processus évolutifs et adaptatifs
& Etiopa
1
university of Monastir, Faculté de Médecine de
Monastir, Monastir, Tunisia
Objectives: Noonan syndrome (NS, OMIM 163950) is an
autosomal dominant disorder affecting 1/1000-2500 live
births. Although his variable clinical phenotype, this
developmental disorder is characterized by a facial
dysmorphism, congenital cardiac defects, reduced
postnatal growth and a variable degree of neurocognitif
delay. NS patients have an increased risk of developing
several types of childhood tumors. Germline missense
mutations in PTPN11 gene are the major cause of this
syndrome. These gain-of-function mutations disrupt SHP2 activity, a protein Tyrosine Kinase that plays diverse
roles in signal transduction, especially via the RASMitogen Activated Protein Kinases (MAPK) pathway.
In order to confirm the clinical diagnosis and predict
cancer risks, a complementary genetic analysis was
carried out in Tunisian patients classified as NS.
Methods: Mutations screening of PTPN11 was
performed on genomic DNA by bi-directional Sanger
sequencing of exons and their flanking intron-exon
boundaries. Furthermore, bioinformatics’ tools were
used to evaluate the impact of identified mutations on
the SHP2 protein conformation and function.
Objectives: Gout is an inflammatory arthritis that arises
from the deposition of uric acid crystals in articular
joints. Genetic and environmental factors play a pivotal
role in gout development. The evidence from genomewide association studies have confirmed genetic
contribution involving several genes (SLC2A9, ABCG2,
SLC22A12, and URATE1) in renal excretion of uric acid
and development of gout. Solute carrier family 2,
member 9 (SLC2A9), is a uric acid transporter at the renal
proximal tubule which involves in reabsorption and
excretion of uric acid, thus influencing serum urate
levels. Polymorphisms of these genes have been
observed to associate with gouty arthritis susceptibility
among Caucasians and Asian populations.
This study aimed to determine the role of SLC2A9
haplotypes in gout development among Malays.
Methods: 89 gouty patients and 100 normal subjects
were recruited and given consent. All the diagnosed gout
patients met the ACR 1977 criteria. Both cases and
controls cohort were Malays and fulfilled the inclusion
and exclusion criteria. Four SNPs of SLC2A9 were
genotyped that assigned as rs3733591, rs5028843,
rs11942223 and rs16890979 using PCR-RFLP technique.
SHEsis online software was used to measure the
association of SLC2A9 variants with gout development
for cases and controls providing odd ratios (ORs) and
95% confidence interval (95%CI). A p value of <0.05 is
considered statistically significant.
Results: Single association analysis of rs3733591,
rs5028843 and rs11942223 revealed a significant
association with p values of 0.0020, 0.009 and 0.022,
respectively with OR>3.0. Nonetheless rs16890979 did
not yield a significant value of association with p value of
0.289. Further investigation on haplotype 1/2/1/1 and
1/1/2/1 representing rs16890979, rs3733591, rs5028843
and rs11942223 revealed a positive association with
p=0.035 and p=0.047 in a susceptible manner (OR=4.642
[0.973-22.151]
and
OR=3.554
[0.942-13.409]),
respectively.
Conclusion: This study showed the minor alleles of
rs3733591 and rs5028843 might be the causal alleles for
the development of gouty arthritis. Therefore, it suggests
an evidence of haplotype association of SLC2A9 variants
(rs3733591 and rs5028843) with the susceptibility effect
in Malay gouty patients.
Results: PTPN11 gene was altered in 3/9 cases of
analysed NS patients. A novel mutation was identified in
the exon 3 of the PTPN11 gene in a new-born girl with an
Artery Valve Stenosis and a typical phenotype of NS. This
is a de novo mutation which was not detected in
patient’s parents. +
Conclusion: While PTPN11 mutations are significally
associated with NS, mutations scanning of others genes
coding effectors of the RAS MAPK pathway (KRAS, SOS1,
RAF1, SHOC1…and recently RIT1) stays essentials to
elucidate molecular causes of Noonan syndrome and
related disorders. At present, the major advantage of
mutation analysis is to predict the risk of malignant
tumors development as well as a prenatal diagnosis.
Disclosure of Interest: None Declared
P053
MUTATIONS IN ARYLSULFATASE A GENE OF MALAYSIAN
PATIENTS WITH METACHROMATIC LEUKODYSTROPHY.
1,*
2
1
N. A. B. Abdul Azize , A. B. Omar , Y. B. Yakob , Z. B.
2
Md Yunus
Disclosure of Interest: None Declared
88
1
1,*
Molecular Diagnostics & Protein Unit, Specialised
2
Diagnostics Centre, Biochemistry Unit, Institute For
Medical Research, Wilayah Persekutuan, Malaysia
2
2
N. S. Ab Rajab , M. R. Salleh , M. A. Mohd Yasin , W. S.
3
4
5
Wan Ghazali , N. Abdul Talib , W. R. Wan Taib , S.
1
Sulong
1
2
3
Human Genome Centre,
Psychiatry,
Medical,
4
UNIVERSITI SAINS MALAYSIA, KOTA BHARU, Medicine,
International Islamic University Malaysia, Kuantan,
5
Medical and Health Sciences, University Sultan Zainal
Abidin, Kuala Terengganu, Malaysia
Objectives: Metachromatic Leukodystrophy (MLD) is an
autosomal recessively inherited lysosomal storage
disease due the arylsulfatase A (ARSA) enzyme activity of
less than 10% of normal controls. Assay of the ARSA
enzyme activity alone is not sufficient for diagnosis; ARSA
pseudodeficiency, which is characterized by enzyme
activity that is 5~20% of normal controls does not cause
MLD. Mutation analysis in ARSA gene is needed to
confirm the diagnosis.
Methods: Whole blood in EDTA tube was collected from
two patients with clinical suspicion of MLD. ARSA enzyme
activity was measured using ρ-nitrocatechol sulphate
(ρNCS) as a synthetic substrate in their leukocytes. Their
DNA was extracted for mutational analysis. All the eight
exons and exon-intron boundaries of ARSA gene were
amplified by PCR using specific primers followed by
direct sequencing. DNA sequencing data were then
analyzed for mutation using SeqScape software.
Detected mutations were compared with Human Gene
Mutation Database (HGMD) to evaluate whether the
mutation has been reported by other study, whereas
Mutation Taster software was used to evaluate diseasecausing potential of sequence alterations.
Results: ARSA enzyme activity was noted to be
undetectable in these two patients. Molecular analysis
revealed mutations in both patients. Patient 1 has a
homozygous mutation detected at c.746 T>C,
p.[Phe249Ser] in exon 4. Mutation Taster analysis
predicted this is a disease- causing mutation. Patient 2
has a homozygous mutation at c.1283_1284insCC,
p.[Pro428Profs*32] in exon 8. This mutation caused a
frame-shift in the protein translation and introduces stop
codon at amino acid 32. Both mutations have been
reported previously for MLD.
Conclusion: In conclusion, diagnosis of MLD cannot be
based solely by enzyme assay and has to be confirmed by
molecular analysis, especially to confirm the proband,
carriers and prenatal diagnosis in families with MLD.
References: 1.Wang J, Zhang W, Pan H, Bao X, Wu Y, Wu
X, Jiang Y.ARSA gene mutations in five Chinese
metachromatic leukodystrophy patients. Pediatr Neurol
2007;36:397-401.
2.LindaBerna´,VolkmarGieselmann,HelenaPoupeˇtova´,M
artinHrˇebı´cˇek,1MilanElleder,1
andJanaLedvinova´.NovelMutationsAssociatedWithMeta
chromatic Leukodystrophy: Phenotype and Expression
Studies in Nine Czech and Slovak Patients. American
Journal of Medical Genetics 129A : 277 – 281 (2004)
Disclosure of Interest: None Declared
Objectives: Mutation of a TCF4 gene was previously
reported as the cause of Schizophrenia. As documented
long ago, there were inverse relationship between
Schizophrenia (SZ) and Rheumatoid Arthritis (RA). Aim of
this study is to detect genetic associations of a Single
Nucleotide Polymorphism (SNP), rs9960767 at TCF4 gene
between both patients group with controls.
Methods: A total of 3ml whole blood was obtained from
47 SZ patients, 47 RA patients and 48 controls. Genomic
DNA was extracted and PCR amplification of the exon 18
of TCF4 gene was performed. The PCR amplicon was
digested with AluI restriction enzyme for rapid
genotyping of the SNP and followed with 3% gel
electrophoresis. Single association was analyzed using
online SHEsis software based on Hardy-Weinberg
Equilibrium using Chi-square calculation with 95%
confidence interval (CI) and P value <0.05 is considered
statistically significant.
Results: The incidence of the mutation allele among the
patients were 3.2% in SZ and 2.1% in RA while compared
to controls incidence are 3.1% (p=0.98, OR=0.978; %95
CI=0.193-4.98 between SZ and controls and p=0.67,
OR=1.48; %95 CI=0.24-9.09 between RA and controls).
Genotype frequencies for SZ, RA and controls for AA
(wild type homozygous) are 93.6 %, 97.9% and 93.8%
respectively. AC genotype frequencies (mutant
heterozygous) are 6.4% for SZ, 4.3% for RA and 6.2% for
controls. However, none was found for allele CC (mutant
homozygous) in all groups.
Conclusion: The presence of SNP rs9960767 of the TCF4
gene statistically did not show association in our SZ
patients. The negative association arises when the C
allele from the SNP predispose to RA and protects from
having SZ. However, a bigger sample size is needed to
confirm this correlation.
Disclosure of Interest: None Declared
P055
GENOME WIDE ASSOCIATION STUDIES (GWAS) ON
TRANSFUSION DEPENDENT HBE/ BETA THALASSEMIA
PATIENT IN KELANTAN, A PRELIMINARY REPORT.
1,*
2
1
1
N. F. Azman , R. Hassan , S. Hanafi , D. Rashid , A.
1
1
2
2
Nasir , P. Yahya , W.-Z. Abdullah , M. F. Johan , R.
2
1
Bahar , B. Zilfalil
1
2
Pediatrics, Hematology, Universiti Sains Malaysia,
Kubang Kerian, Malaysia
P054
IDENTIFICATION OF RS9960767 AT TCF4 GENE IN
MALAYSIAN
SCHIZOPHRENIA AND RHEUMATOID
ARHTRITIS PATIENTS: A PRELIMINARY STUDY
Objectives: Hemoglobin E- beta thalassaemia (Hb E/βthalassaemia), is a type of thalassemia classified under
89
HbE syndrome. The Malaysia National Thalassemia
Registry revealed that approximately 31.6 % of
population inherited the HbE/Beta thalassemia with high
prevalence of Hb E/β-thalassemia reported among
Malays and the Orang Asli ethnic groups. We conducted
a study to detect the single nucleotide polymorphisms
(SNPs) variations in HbE/Beta thalassemia Malay
patients.
Methods: Transfusions dependent Malay HbE/beta
thalassemia patients were recruited in this study and six
ml of blood was withdrawn from each subject. DNA was
extracted and 50 ng/µl was used for SNPs genotyping
using Affymetrix microarray SNP 6. Data analysis was
carried out using Affymetrix Genotyping Console and SNP
Nexus software.
Results: Preliminary results showed that there were 6
common SNPs resided in chromosomes 11 which are
associated with HBG2 gene; rs2855039, rs2855122,
rs11036634,
rs6578603,
rs11036815
and
rs6578605. Nine SNPs have been found on chromosome
2 and most common SNPs reported are rs11886868,
rs6545816 which are related to BCL11A gene. While SNPs
rs9376092 and rs4895441 reported in chromosome 6
related to intergenic region between HBS1L and MYB.
Among all the SNPs found, rs9376092 SNPs in HBS1LMYB has been reported frequently in Indonesian Origin
o
and Thai and Thai – Chinese β - thalassemia/HbE patients
(Nuinoon et al.,2010). These SNPs is known to be
o
associated with the β - thalassemia/HbE patient.
Conclusion: In conclusion, we postulate that β – globin
gene cluster, BCL11A and HBS1L-MYB gene play an
important biomarker to predict disease severity. Further
studies are ongoing to obtain more data on these gene
and other genetic determinants in Malay HbE/beta
thalassemia patient.
genotyped using microarray Human Omni Express-12
platform. We used 2,645 Malay from Singapore Malay
Eye Study (SiMES) as controls for our analysis. Genome
studio was used and further analyzed using PLINK.
Results: Our data showed that the most significant loci
for primary open angle glaucoma are rs1620264 in
KIRREL3 (odds ratio (OR) 2.43; P=2.25×10e-7) and
rs1392912 in KALRN (OR 2.19; P=1..26×10e-6), rs1009364
in FAM110B (OR 13.06; P=1.86×10e-5) and rs1014979 in
NPAS3 (OR 32.81; P=2.29×10e-5) were found as markers
for RNFL thickness, rs347866 (OR 5.70;P=1.56×10e-5)
and rs347861 (OR 0.05; P=1.74×10e-5) of chromosome
15;SLC12A6 gene for VCDR. We identified novel genetic
markers; rs814836 (OR 15.47; P=6.58×10e-12) and
rs190254 (OR15.47; P=6.58×10e-12) that potentially
involved in IOP.
Conclusion: rs1620264 and rs1392912 as the most
potential susceptibility genetic markers for POAG in
Malay population. These genetic markers were not found
in glaucoma patients in other population. A larger sample
size is needed to verify this finding.
Disclosure of Interest: None Declared
P057
PARTIAL TRISOMY 22(PTER-Q11.23): CASE REPORT OF A
RARE SYNDROME
1,*
1
1
1
R. A. Adnan , Z. Abu Bakar , S. M. Ismail , N. Ramli , N.
1
1
1
M. Z. Mat Zin , N. A. Nawi , M. Q. Abu Bakar , H.
1
1
1
2
Hashim , R. H. Razali , N. Mohd Yunus , I. H. Ibrahim ,
3
1
M. H. Mohd Jamil , R. Ankathil
1
Human Genome Center, Universiti Sains Malaysia,
2
3
Pathology Department,
Paediatrics Department,
Hospital Raja Perempuan Zainab II, Kota Bharu, Kelantan,
Malaysia
Disclosure of Interest: None Declared
Objectives: Chromosome 22q11 region is involved in
chromosomal rearrangements that lead to altered gene
dosage, resulting in genomic disorders. Cat eye
syndrome, partial trisomy 22(pter-q11.23) or der(22)
syndrome and Velocardiofacial syndrome/DiGeorge
syndrome are genomic disorders associated with four,
three and one dose, respectively of parts of 22q11.2. The
present study aimed to detect the identity of an extra
marker chromosome observed in a 4 months old Malay
boy, the firstborn of non-consanguineous parents. He
presented with cleft palate, left preauricular pit, bilateral
clinodactyly, micropenis and ventriculoseptal defect.
Methods: Peripheral blood lymphocytes were cultured
and chromosome preparations were made as per
procedures. Karyotype analysis was carried out based on
ISCN (2013). FISH analysis was carried out using probes
for DGCR 22q11.2 and WCP 22 as per standard
procedures.
Results: Cytogenetic analysis carried out in 30 GTG
banded metaphases showed 47, XY, +22(pter-q11.23)
abnormal karyotype involving an extra derivative
chromosome 22 resulting from partial trisomy 22(pterq11.23) with an additional segment of unknown origin.
P056
IDENTIFICATION OF THE SUSCEPTIBILITY GENETIC
MARKERS FOR PRIMARY OPEN ANGLE GLAUCOMA IN
MALAYS
1,*
1
R. Thambiraja , M. Imran Bukhari , L. S. Ahmad Tajudin
1
2
3
4
, K. Chiea Chuen , Z. Bin Alwi , S. Sulong
1
Ophthalmology, Universiti Sains Malaysia, Kubang
2
Kerian, Malaysia,
Genome Institute Of Singapore,
National University Of Singapore, Singapore, Singapore,
3
4
Paediatric, Human Genome Centre, Universiti Sains
Malaysia, Kubang Kerian, Malaysia
Objectives: To identify the susceptibility genetic markers
for primary open angle glaucoma (POAG) in Malays using
microarray technique.
Methods: A total of 108 Malay patients with POAG were
recruited from eye clinic, Hospital Universiti Sains
Malaysia. Intraocular pressure (IOP), vertical cup to disc
ration (VCDR) and retinal fiber layer (RNFL) thickness
using optical coherent tomography was included.
Venesection was done. DNA was extracted and
90
Molecular cytogenetic analysis employing FISH technique
using DiGeorge probe showed presence of 3R signals
indicating 3 copies of 22q11.23 region and 2G signals
only for long arm terminal region of chromosome 22,
confirming the missing 22q13–qter region in the extra
chromosome 22. The clinical features and karyotype
results are strongly in favour of Emanuel syndrome.
However, for further confirmation, FISH study to identify
the extra segment on chromosome 22 and parental
karyotyping from the carrier parent will be carried out
and presented.
Conclusion: Der(22) is a rare syndrome and the case is
presented due to its rarity. While the true mortality rate
is unknown, longterm survival is possible if the patient
survives infancy. Early diagnosis and timely intervention
can improve the survival and quality of life.
References: 1. McDermid, Heather E., and Bernice E.
Morrow. "Genomic disorders on 22q11."The American
Journal of Human Genetics 70.5 (2002): 1077-1088.
vector pETBlue-1. To facilitate protein elongation, the
codons used were those found in highly expressed genes
of E. coli
Results:
Conclusion: In conclusion, this study demonstrates the
efficient use of synthetic G-CSF cDNA in combination
with recombinant DNA protocols for rapid and reliable
synthesis of the target genes and thus the commercial
level end product, the specific protein. Further studies
are warranted to testify the functional activity of
biotechnologically-produced G-CSF, particularly utilizing
the cell proliferation approaches.
Disclosure of Interest: None Declared
P059
MOLECULAR CHARACTERISATION AND FREQUENCY OF
GΓ XMN I POLYMORPHISM IN TRANSFUSION
DEPENDENT
HBE/Β-THALASSEMIA PATIENTS IN
KELANTAN, WEST OF MALAYSIA
1,*
2
2
2
S. Hanafi , R. Hassan , R. Bahar , M. F. Johan , W. Z.
2
1
1
1
Abdullah , N. D. Rashid , N. F. Azman , A. Nasir , N.
1
3
4
1
Mohamad , N. K. Nik Yussof , S. Salleh , B. A. Zilfalil
1
2
Pediatric, Hematology, Universiti Sains Malaysia,
3
Kubang Kerian, Pediatric, Hospital Raja Perempuan
4
Zainab II, Kota Bharu Kelantan, Kota Bharu, Medical,
Hospital Kuala Krai, Kelantan, Kuala Krai, Malaysia
Disclosure of Interest: None Declared
P058
CHEMICAL SYNTHESIS OF A RECOMBINANT HUMAN
GRANULOCYTE COLONY STIMULATING FACTOR (RHGCSF) CDNA AND ITS EXPRESSION ANALYSIS
1,*
S. A. Alrokayan
1
Departments: Biochemistry,, King Saud University,
College of Science, RIYADH, Saudi Arabia
Objectives: This study aims to determine the frequency
of the different genotypes of the Gγ Xmn I polymorphism
and to correlate its genotypes with Hb F level in
transfusion dependent HbE/β-thalassemia patients who
attended government hospital in Kelantan.
Methods: Totals of 35 transfusion dependent HbE/β
thalassemia patients were selected from government
hospital in Kelantan. They were 20 females and 15 males
with age ranged from 9 to 26 years old. 4 patients are
Chinese and the rest are Malays. Whole blood samples
were collected in EDTA bottle and subjected to
Restriction Fragment Length Polymorphism (RFLP)
Polymerase Chain Reaction by Xmn 1 digestion after DNA
amplification of a 650 bp sequence to identify the
different genotype of Xmn1 G gamma polymorphism.
Results: The most common genotype observed in the
HBE/β-thalassemia patient in Kelantan population was
heterozyosity of the Xmn I site (+/-) (54.3%) and 45.7 %
of the patients showed to have homozygosity the for
Xmn 1 site (-/-). However, homozygosity for the Xmn I
site (+/+) was absent in the all HbE/β-thalassemia
patients in this study. All the Chinese patients in this
study showed to have Xmn 1 site (-/-). No significant
correlation was observed between F value and type of
genotype, this is due to the small sample recruiting in
this study.
Conclusion: To our knowledge this is the first reported
molecular basis of Gγ Xmn I polymorphism among
transfusion dependent Hb/E β thalassemia patients in
Kelantan. Further studies on the association of the
Objectives: Recently, granulocyte colony-stimulating
factor (G-CSF) has been recognized as an important
molecule for the treatment of a wide range of complex
ailments such as cancer, AIDS, H1N1 influenza, cardiac
and neurological diseases. Such a vast therapeutic
potential of G-CSF has lured the scientists to utilize
biotechnological approaches for the synthesis of this
pharmacologically active agent. This study describes the
use of a synthetic G-CSF cDNA molecule and its efficient
utilization of producing the target protein by a simple
cloning protocol. We constructed the entire synthetic
cDNA using a DNA synthesizer with the aim to increase
its expression level by specific sequence modifications at
the 5' end of the G-CSF coding region and decreasing the
GC content without altering the predicted amino acids
sequence. The identity of the resulting protein was
confirmed by the highly specific enzyme-linked
immunosorbent assay. In conclusion, a synthetic G-CSF
cDNA in combination with the recombinant DNA
protocol offers a rapid and reliable strategy for
synthesizing the target protein. However, the
commercial utilization of this methodology requires
rigorous validation and quality control.
Methods: A cDNA was designed with the help of Vector
NT software to code for hrG-CSF and to maximize
translational initiation and protein elongation in E. coli.
To facilitate the initiation of translation, the nucleotide
sequence of the cDNA was adjusted to expose the start
codon and Shine-Dalgarno sequence of its transcript in
91
different genotypes of the Gγ Xmn I polymorphism with
clinical severity of the disease will be carried out as
clinical data of the patients is being collected.
Disclosure of Interest: None Declared
2
3
P060
MOLECULAR PHYLOGENETIC OF SELECTED ORANG ASLI
TRIBES (ABORIGINES) IN PENINSULAR MALAYSIA
INFERRED FROM BETA FIBRINOGEN GENE.
1 2,*
2
3
2
S. Mat Yasin
, N. Mohd Nasir , E. Ismail , Z. Alwi , R.
1
4
Zainudin , M. T. Abdullah
1
Department of Zoology, Faculty of Resource Science and
Technology, Universiti Malaysia Sarawak, Kota
2
Samarahan, Sarawak, Department of Paediatric,School
of Medical Sciences , Universiti Sains Malaysia, Kubang
3
Kerian, Faculty of Science & Technology , Universiti
4
Kebangsaan Malaysia, Bangi, Selangor, Center for Kenyir
Ecosystem, Kenyir Research Institute, Universiti Malaysia
Terengganu, Kuala Terengganu, Terengganu,, Malaysia
Objectives: Esophageal squamous cell carcinoma (ESCC)
is the sixth most common cancer in Kazakhstan.
Transcriptome sequencing has become a powerful
method for detecting driver mutations in cancer, since
not only somatic point mutations but also aberrant RNA
variants such as fusion genes and alternative splicing can
be identified. The aim was to identify genetic basis of
ESCC by performing whole transcriptome sequencing
study in Kazakhstani patients
Methods: Whole transcriptome sequencing was
performed on 10 tissue samples (5 normal tissue samples
and 5 tumor tissue samples) from 5 patients. A pair of
fresh frozen EC and its adjacent normal tissue specimen
were obtained. Five pairs of EC samples subjected to
RNA-seq, total RNA was isolated and its quality was
assessed using Agilent Bioanalyzer, Qubit. cDNA library
were prepared following the Tru Seq RNA protocol and
sequenced using Illumina HiSeq2000 platform
Results: All generated *.BCL files were simultaneously
converted and demultiplexed using bcl2fastq application
and were aligned using the Tophat2 application. Gene
expression profiling was performed using HTSeq tool and
genes with different expression level were determined
by DESeq application. To determine the biological
functions and relations were used database MSigDB and
KEGG. Sequence alignment, gene expression profiling
and identifying genes with different expression level
procedures were performed. By the results of paired
analysis of normal and tumour tissues, we discovered
287 genes with reduced expression and 192 genes with
increased expression. Using MSigDB and KEGG databases
were found 10 and 4,respectively; 10 and 10,
respectively overlapping sets of genes with increased and
decreased gene expression.
Conclusion: ESCC is the most common histologic subtype
of esophageal cancer in our patients and is characterized
by a poor prognosis. Most patients diagnosed with late
stages T3-T4. Using high throughput sequencing
approach, we could be able to identify higher number of
crucial molecular pathways involved in esophageal
carcinogenesis that could facilitate the development of
new diagnostic and treatment strategies. The early
detection of EC gives hope of a long-term survival for
patients
Disclosure of Interest: None Declared
Oncology Center, Astana, Kazakhstan, Department of
Biochemistry and Molecular Biology, Genomic Medicine
Institute, Seoul National University College of Medicine ,
4
Seoul, Korea, Republic Of, NAZARBAYEV UNIVERSITY,
Center for Life Sciences, Astana, Kazakhstan
Objectives: To determine the phylogenetic relationship
between Negrito tribe, Senoi tribes and Proto Malay
tribes in Peninsular Malaysia.
Methods: We analysed 50 fresh blood samples of
selected Orang Asli tribes (Negrito, Senoi and Proto
Malays) from Peninsular Malaysia. These subjects were
selected based on a few criteria which include individual
of a population must be at least three generations of the
same population, no parental admixture and
communicate daily in local dialect. Phylogenetic analyses
of Beta Fibrinogen gene (730 base pairs) using four
methods, namely, neighbour-joining (NJ), maximum
parsimony (MP), and maximum- likelihood (ML) resulted
in similar statistically supported clades with minimal
change in branching order.
Results: Our results showed these three major groups,
Negrito, Senoi and Proto Malay, were closely related
with each other with small genetic distances and minimal
value for bootstrap supported values. This may be due to
the close geographical locations of their settlement,
which may have been derived from a single entry into
Peninsular Malaysia. Our result also suggested that
Negritos are the basal group within these three major
groups.
Conclusion: As a conclusion, our results support previous
studies which indicated that Negrito might be the earliest
settlers in Southeast Asia. Beta fibrinogen gene is a good
genetic marker in inferring the molecular phylogenetic of
selected Orang Asli tribes in Peninsular Malaysia.
Disclosure of Interest: None Declared
P061
TRANSCRIPTOME PROFILE OF ESOPHAGEAL SQUAMOUS
CELL CARCINOMA IN KAZAKHSTAN.
1,*
1
1
S. Rakhimova , A. Akilzhanova , U. Kairov , A.
1
2
3
4
Molkenov , Y. Zhukov , J. Y. Shin , Z. Zhumadilov
1
Department of Genomic and Personalized Medicine,
NAZARBAYEV UNIVERSITY, Center for Life Sciences,
P062
DNA SEQUENCING SERVICE AT IMCB
1,*
1
S. N. H. B. Mohamed Haron Narasib , C. Ah Keng , L.
1
1
Debbie , T. Alice
1
DNA Sequencing Facility, INSTITUTE OF MOLECULAR &
CELL BIOLOGY, SINGAPORE, Singapore, Singapore
92
Objectives: The DNA Sequencing Facility (DSF) at IMCB
provides Sanger sequencing service for all in house staff
using Applied Biosystems 3730xl instrumentation and
BigDye terminator chemistry. Users carry out their own
cycle sequencing reactions and submit the sequenced
samples to DSF for clean-up and capillary
electrophoresis. The service is also available to external
users for a fee that depends on level of service required
as well as the number of samples.
Service extended to A-STAR Research Institutes (RIs) as
well as Biopolis tenants and external organisations.
DSF is also involved in genome sequencing projects for
Fugu, Elephant Shark and Lamprey in collaboration with
Professor B. Venkatesh and Sydney Brenner
Methods:
1. Users carry out cycle sequencing
reactions
2. Submit requests on-line
3. Bring samples to DSF (5-24, Proteos)
4. Samples undergo magnetic beads clean-up
5. Run on ABI3730 Sequencers
6. Users download sequence files
Pictures shows different equipment used for different
process in the workflow.
Results: Sequencing Results Analysis
Different diagrams shows different sequencing
electrophoregram after capillary electrophoresis.
- High quality sequences
- Failed sequencing reactions
- G-C rich template
- Waterfall effect due to excess template quantity
- Presence of two primers in a single template
Conclusion: Sequencing Statistics (as of December 2014)
- Top 5 external users contribute to 80% of service
revenue
- Number of samples processed is ~150,000
Disclosure of Interest: None Declared
Pictures/Graph:
93
P063
RELATIONSHIP BETWEEN CHEMOKINE (C-X-C MOTIF)
LIGAND 12 GENE VARIANT RS1746048 AND
CARDIOVASCULAR DISEASES
1,*
1
2
3
S. Ikeda , K. T. T. Zaw , T. Arai , M. Mieno-Naka , M.
4
1
Sawabe , M. Muramatsu
1
Department of Molecular Epidemiology, Tokyo Medical
2
and Dental University, Department of Pathology, Tokyo
Metropolitan Geriatric Hospital and Institute of
3
Gerontology, Tokyo, Department of Medical Informatics,
4
Jichi Medical University, Tochigi, Section of Molecular of
Pathology, Tokyo Medical and Dental University, Tokyo,
Japan
P064
GENETIC POLYMORPHISMS OF SMAD7 IN MALAY
PATIENTS WITH VENTRICULAR SEPTAL DEFECTS
1,*
1
1
S. A. F. Mohamed Sadom , H. Hashim , S. Maran , T.
2
3
4
Hern-Tze , M. R. Mohd Zain , W. P. Wan Ibrahim , T.
1
Huay Lin
1
2
Human Genome Centre, Department of Immunology,
3
Department of Pediatrics , Universiti Sains Malaysia,
4
Kubang Kerian, Faculty of Medicine and Health Sciences,
Universiti Sultan Zainal Abidin, Kuala Terengganu,
Malaysia
Objectives: Ventricular septal defects (VSD) is the most
common form of cardiac malformations that accounts for
approximately over 20% of congenital heart disease.
SMAD7 antagonizes the signalling of TGF-β family
member and has been found in the development and
function of mouse heart models. The aim of this study
was to screen and to identify the polymorphisms of
SMAD7 gene in Malay population with ventricular septal
defects.
Methods: Peripheral blood samples were collected from
30 VSD patients that have been diagnosed by clinicians.
Of these cases: 19 were of membranous VSD, 10 cases of
muscular VSD and 1 case of infundibular VSD. The
genomic DNA was then subjected to PCR amplifications
using 10 sets of designed primers encompassing all four
exons of SMAD7. Subsequently, re-sequencing was
conducted to characterize the polymorphisms in SMAD7
of the patients. Observed polymorphisms then were
genotyped in 30 healthy controls free of cardiovascular
malformations, using both re-sequencing and allelespecific PCR techniques.
Results: A total of 10 variants were identified in the
patient populations. A synonymous novel variant
(p.T354T) located in the MH2 domain of the SMAD7 was
observed in a patient with muscular VSD but was absent
in the controls (Wang et al, 2013). This variant might be
of interest as MH2 domain plays an important role in the
inhibition of TGF-β and BMP signalling pathway. The
other variants are located in the 5’UTR (rs7236774 and
rs368427729), exon 4 (rs3809922 and rs3809923),
intronic regions (rs145686330, rs3764482 and
rs3736242) and 3’UTR (rs37544823 and rs16950113). Of
these SNPs, rs3736242 has been implicated to affect
splicing. Even though all of these variants did not affect
amino acid changes and thus did not affect the SMAD7
protein, they might influence the transcriptional
efficiency and stability at the mRNA level at a later stage.
Conclusion: Identification of these genetic variations
provides a new perspective on VSD causation.
References: Wang, E., Jin, W., Duan, W., Qiao, B., Shun,
S., Huang, G., Shi, K., Jin, Li. & Wang, H. (2013).
Association of two variants in SMAD7 with the risk of
congenital heart disease in the Han Chinese population.
PLoS One 8(9): e72423.
Disclosure of Interest: None Declared
Objectives: Cardiovascular disease (CVD) is one of the
leading causes of human death in the developed
countries. It is also becoming one of the major causes of
morbidity and mortality in the developing countries. CVD
is a complex disease, which results from the interaction
between genetic factors and environmental factors. It is
a challenge to elucidate the pathogenic mechanism of
the disease. Recently, GWAS have revealed that a single
nucleotide polymorphism (SNP) rs1746048 on
chromosome 10q11.21 is associated with CVD-cause
mortality. This loci is related to chemokine (C-X-C motif)
ligand 12 (CXCL12), which encodes a chemokine that
affects atherosclerosis, plaque rupture, and acute
thrombus formation. This study aims to examine
whether rs1746048 is associated with increased CVD
risks in Japanese elderly population.
Methods: A total of 1850 autopsy cases of elderly
Japanese subjects were enrolled in this study.
Phenotypes pertaining to CVD such as coronary stenosis
index (CSI), pathological atherosclerosis index (PAI), and
myocardial infarction (MI) were pathologically
determined. The rs1746048 was analyzed by TaqMan
SNP Genotyping assay system. Among the 1850 subjects,
1658 patients met the criteria of having adequate DNA
samples for the PCR experiments, well-determined
genotyping results and appropriate availability of their
clinical history. All the statistical analyses were
performed using SAS statistical software for Windows
ver.9.3.
Results: There were no association with the rs1746048
and MI, PAI, and CSI in our population, after adjusting for
age at death, gender, smoking history, and alcohol
intake. Significant associations were observed for
abdominal descending aortic aneurysm (AAA) (CT+TT:CC,
OR=2.00, 95%CI=1.19-3.37, p=0.009). We also found that
the rs1746048 was associated with increased risk of
atrial fibrillation (AF) (TT:CT+CC, OR=2.22, 95%CI=1.423.46, p<0.001) and arteriosclerosis obliterans (ASO)
(TT:CT+CC, OR=2.20, 95%CI=1.08-4.50, P=0.03).
Conclusion: The rs1746048 in CXCL12 gene may be a risk
factor for CVD such as AAA, AF, and ASO in Japanese
elderly population.
Disclosure of Interest: None Declared
94
P065
INHIBITION OF SIRT1 AND TREATMENT WITH
TOCOTRIENOL-RICH FRACTION MODULATE THE
EXPRESSION OF GENES INVOLVED IN THE REGULATION
OF CELL CYCLE AND APOPTOSIS
1,*
1
1
S. Makpol , F. Jaafar , Y. A. Mohd Yusof , W. Z. Wan
1
Ngah
1
Biochemistry, Universiti Kebangsaan Malaysia, Cheras,
Kuala Lumpur, Malaysia
Indeed, each individual receives half of its genetic
heritage of his mother and the other half of his biological
father. Thus, to be the father, an individual must share
with the child at least one of the two alleles of each
marker studied.
Rare cases of twin pregnancy were induced by
fertilization from two different parents. In this case it is a
superfecondation. This rare situation was often
suspected but rarely confirmed.
We report in this paper a case of genetically confirmed
superfecondation in the context of paternity by genetic
fingerprinting.
In the context of paternity, we performed a genetic study
of 4 members: a mother and her 2 twin infants, from the
same twin pregnancy and an alleged father.
Methods: This study involved the analysis of 15 STRs
markers by "PowerPlex 16 System" kit and by sequencer
"ABI Prism 310" among these four members.
Results: Genetic analyzes were performed under the
same technical conditions and showed that one of the
twins have the same alleles that his father, while the
other infant has different alleles compared with those of
the alleged father in 11 markers of 15. Therefore, despite
that these two children are twins, their biological fathers
are different.
Conclusion: The superfecondation is a rare and very
special obstetric situation. It is secondary to fertilization
of two eggs from the mother by two sperm each from a
different father.
In this work, we have confirmed this by using the tools of
molecular genetics. However, their clinical and biological
implications, if they remain unknown.
Objectives: In the present study we elucidated the
effects of tocotrienol-rich fraction (TRF) on the
expression of SIRT1 and genes that are involved in cell
cycle progression and its regulation.
Methods: Small interference RNA (siRNA) was used to
silence SIRT1 at transcriptional level while SIRT1 activity
was inhibited by sirtinol in young human diploid
fibroblasts (HDFs). TRF treatment was given for 24 h
before or after SIRT1 inhibition.
Results: Our results showed that silencing of SIRT1 gene
and inhibition of SIRT1 activity increased the percentage
of cells stained positive for senescence-associated bgalactosidase (SA b-gal) which was alleviated by TRF
treatment (p<0.05). TRF increased the expression of
SIRT1, up-regulated SIRT1 regulator E2F1 and upregulated Cyclin D1 (CCND1) (p<0.05). A similar CCND1
up-regulation was observed in HDFs treated with TRF
before or after inhibition of SIRT1 activity which
subsequently promoted cell cycle progression (p<0.05).
Inhibition of SIRT1 activity increased cyclin dependent
INK4a
kinase inhibitor p16
(CDKN2A) expression which was
CIP1
down-regulated with TRF treatment (p<0.05). p21
(CDKN1A) was up-regulated when SIRT1 activity was
inhibited and with TRF pre-treatment (p<0.05).
Treatment with TRF before SIRT1 silencing or before
SIRT1 activity inhibition increased the percentage of
apoptotic cells (p<0.05).
Conclusion: In conclusion, tocotrienol-rich fraction
prevents replicative senescence of HDFs by modulating
the expression of CCND1, E2F1 and CDKN2A genes which
were regulated by SIRT1. However, with the inhibition of
SIRT1 activity, tocotrienol-rich fraction induced apoptosis
by modulating the expression of CCND1 and CDKN1A
Disclosure of Interest: None Declared
References:
1]:
Blickstein
I.
Superfecundation and superfetation: lessons from
the past on early human development. J Matern Fetal
Neonatal Med. 2003 Oct;14(4):217-9.
[2]: Malinowski W, Waszyński E. Superfecundation in
etiology of twin pregnancy. Ginekol Pol. 2006
Oct;77(10):797-803.
[3]: Raczek E. Superfecundation and superfetation with
resulting heteropaternal twins--a possible resolution of
the phenomena in the era of DNA typing. Arch Med
Sadowej Kryminol. 2003 Jan-Mar;53(1):73-7.
Disclosure of Interest: None Declared
P066
INDISPUTABLE DOUBLE PATERNITY IN TWINS CAUSING
BY SUPERFECONDATION
1,*
1
1
1
W. Manoubi , A. Mili , A. M’sakni , A. Saad , M. Gribaa
MENDELIAN GENETICS
P067
IDENTIFICATION OF CAUSAL GENES THROUGH WHOLE
EXOME SEQUENCING IN A MALAYSIAN COHORT OF
CHARCOT-MARIE-TOOTH PATIENTS
1,*
1
2
2
A. Ahmad-Annuar , S. Tey , N. Shahrizaila , K.-J. Goh ,
3
456
456
G.-S. Ch'ng , G. Nicholson , M. Kennerson
1
Department of Biomedical Science, Faculty of Medicine,
2
Department of Medicine, Faculty of Medicine, University
3
of Malaya, Department of Genetics, Kuala Lumpur
4
Hospital, Kuala Lumpur, Malaysia, Sydney Medical
5
School, University of Sydney, Molecular Medicine
1
1
genetics, laboratory of cytogenetics and molecular
biology, Sousse, Tunisia
Objectives: The paternity allows within forensics, to
establish the legal relationship between a child and his
father looking if the alleged father is the biological father
or not.
Today, this research is based on DNA mainly using
microsatellites or short tandem repeats (STRs) markers.
95
6
Laboratory, Concord Hospital, Northcott Neuroscience
Lab, ANZAC Research Institute, Sydney, Australia
CBS gene (17 exons) was PCR amplified and
bidirectionally sequenced using standard protocols.
Results: The patient was found to be compound
heterozygous for two novel mutations. Four known
single nucleotide polymorphisms were also detected in
the CBS gene of the patient. The patient is heterozygous
for all the identified alleles.
Conclusion: This is the first mutational analysis of the
CBS gene done in a Filipino with Classical Homocystinuria
who presented with a novel duplication mutation and a
novel missense mutation. This study suggests that
Homocystinuria due CBS deficiency is a heterogeneous
disorder at the molecular level.
Disclosure of Interest: None Declared
Objectives: To identify the genetic causes of peripheral
neuropathies in a Malaysian cohort of Charcot-MarieTooth disease
Background: Hunting for genes has been greatly aided by
next generation sequencing techniques and here we
present data of an ongoing effort to map causal genes
for inherited peripheral neuropathies in Malaysia. Our
team has been involved in determining the pattern of
CMT genetics in our cohort of Malaysian patients and we
have identified several families with demyelinating or
axonal forms of Charcot-Marie-Tooth (CMT) disease
which are negative for mutations in the commonly
associated genes (PMP22, GJB1, MPZ and MFN2).
P069
CHARACTERIZATION OF MUTATIONS THROUGH WHOLE
GENE SEQUENCING OF THE GLUCOSE-6-PHOSPHATE
DEHYDROGENASE GENE AMONG FILIPINO CHILDREN
WITH G6PD DEFICIENCY
1,*
1
E. M. C. Cutiongco De La Paz , C. David-Padilla , M. M.
1
P. Baluyot
1
University of the Philippines Manila, Institute of Human
Genetics, National Institutes of Health, Manila,
Philippines
Methods: Whole exome sequencing was performed on
affected and unaffected family members using the
Illumina HiSeq 2000 platform and several bioinformatics
tools were used together with intuitive filtering and
segregation analysis to narrow down the candidate gene
lists.
Results: In one family, we were able to narrow down the
variants from over 80,000 to 4 variants in 4 novel
candidate genes. Analysis on the other families will
further add to the identification of new genes for CMT
and to the knowledge of the pathogenic pathways
involved.
Conclusion: Next generation sequencing technology has
enabled us to further characterise our CMT familes which
would otherwise be classified as genetically unknown
cases. In the case of identification of novel genes,
functional work will be performed to validate the
pathogenicity of the mutations.
Disclosure of Interest: None Declared
Objectives: Glucose-6-phosphate dehydrogenase (G6PD)
deficiency has a high prevalence among Filipinos. This
study aims to characterize the mutations and
polymorphisms in the G6PD gene among Filipino children
aged 0-12 months old with G6PD deficiency and to
document the mean enzyme activity associated with
each of the variants, and to establish a database of G6PD
variants in the Filipino population.
Methods: Patients aged 0-12 months confirmed with
G6PD deficiency through an enzyme assay were
recruited. Whole gene sequencing was performed
through PCR amplification of 12 protein-encoding exons
of the G6PD gene. Sequence variations were classified as
mutations, benign variants unrelated to disease, or
variations of unknown clinical significance.
Results: A total of 113 participants were recruited and
only 101 patients were confirmed to have G6PD
deficiency. Thirty of the G6PD deficient participants were
female while 71 were male. Preliminary results show that
majority of the patients (~67%) had the Viangchan
mutation followed by the Chatham (14%) and Union (8%)
variants. There are also less common variants in the
G6PD gene in the other cases. One male patient was not
found to have a pathogenic variant. All these variants
identified cause an amino acid substitution and have
likewise been reported in other Southeast Asian
populations.
Conclusion: Among Filipino newborns confirmed with
G6PD deficiency by enzyme assay, majority of the
patients have the Viangchan mutation.
Disclosure of Interest: None Declared
P068
CBS GENE MUTATIONS DETECTED IN A FILIPINO
INDIVIDUAL WITH HOMOCYSTINURIA
1,*
2
2
C. L. T. Silao , T. D. F. Fabella , K. I. D. Rama , S. C.
1
Estrada
1
Department of Pediatrics, University of the Philippines
2
College of Medicine Manila, Institute of Human
Genetics, National Institutes of Health Philippines,
Ermita, Manila, Philippines
Objectives:
Classical
Homocystinuria
due
to
cystathionine β-synthase (CBS) deficiency is an
autosomal recessive disorder of sulfur metabolism.
Clinical manifestations include mental retardation,
dislocation of the optic lens (ectopia lentis), skeletal
abnormalities and a tendency to thromboembolic
episodes. We present the first mutational analysis of the
CBS gene in a Filipino with Classical Homocystinuria.
Methods: Genomic DNA was extracted from peripheral
blood collected from a diagnosed Filipino patient with
Classical Homocystinuria. The entire coding region of the
96
1,*
P070
COMBINED
PITUITARY
HORMONE
DEFICIENCY:
MUTATION ANALYSIS OF POU1F1 AND PROP1 GENES IN
A COHORT OF MALAYSIAN PATIENTS
1,*
2
3
J. MOHD ALI , F. HARUN , L. KHA CHIN
1
DEPARTMENT OF MOLECULAR MEDICINE, FACULTY OF
2
MEDICINE, DEPARTMENT OF PEDIATRICS, FACULTY OF
3
MEDICINE, DEPARTMENT OF MOLECULAR MEDICINE,
UNIVERSITY OF MALAYA, KUALA LUMPUR, Malaysia
1
1
M. Dvorakova , P. Cibulkova , R. Krenkova , P.
1
1
Vanickova , A. Boday
1
Laboratory of Medical Genetics - Department of
Molecular Biology, Laboratore AGEL a.s., Novy Jicin,
Czech Republic
Objectives: Thoracic aortic aneurysms and dissections
(TAAD) are among the most common and serious chronic
diseases of the aorta and severe life-threatening
conditions. TAAD affects all parts of the thoracic aorta ascending aorta, aortic arch, descending aorta and
thoracoabdominal area of aorta. TAAD is a genetically
heterogeneous group of thoracic aorta disability with
reduced penetrance and variable expressivity. TAAD is
categorized into 2 broad groups: syndromic such as
Marfan syndrome, Loeys-Dietz syndrome, Ehlers-Danlos
syndrome type IV and arterial tortuosity syndrome
(associated with abnormalities of the other organ
system); and non-syndromic (with manifestation
restricted to the aorta). Non-syndromic is divided into
familial TAAD (FTAAD) and isolated or sporadic form. We
detected 2 mutations in 2 different genes (TGFBR2 and
ACTA2), which are responsible for FTAAD in a patient
with aortic aneurysm dissection during pregnancy and
with TAAD positive family history (two first-degree and
one second-degree relatives died of aortic aneurysm
dissection).
Methods: DNA was isolated from peripheral blood. The
main FTAAD genes TGFBR2, TGFBR1, ACTA2, SMAD3
and TGFB2 were analyzed. The DNA analysis of the
TGFBR2 and TGFBR1 genes included MLPA, separation of
PCR products of all 9 exons by SSCP and direct
sequencing of abnormal migrating patterns. ACTA2 and
other genes were analyzed by direct sequencing. Newly
detected sequence variant was subjected to in silico
predictions (for its effect on protein function).
Results: On the basis of different migration shift in SSCP
analysis of TGFBR2 gene, one previously described
change, c.383delA (p.Lys128SerfsTer35), was found in
patient’s DNA. This deletion is described as a somatic
mutation in esophageal and colorectal cancer, but not as
germline mutation and not with aortic aneurysm
phenotype. Direct sequencing of the ACTA2 gene
revealed one novel nucleotide change in exon 3,
c.143G>A (p.Gly48Glu). In silico analysis performed by
prediction software (PMut, PolyPhen-2) indicates this
change as pathogenic.
Conclusion: We wanted to analyze DNA of all family
members
to
assess
the
genotype-phenotype
correlations. We analyzed DNA from patient’s
asymptomatic daughter who has not proved the
presence of either mutation, because all symptomatic
family members have already died. There is no incidence
of any cancer in family history and so we assumed that
one of these mutations is responsible for FTAAD in this
family.
Disclosure of Interest: None Declared
Objectives: Combined Pituitary Hormone Deficiency
(CPHD) is a genetic disorder characterized by the
deficiencies of growth hormone (GH) and at least
another one of the other five anterior pituitary
hormones (APH). Many of the CPHD patients are
sporadic cases, although familial cases with autosomal
dominant, autosomal recessive and X-linked forms have
been reported. Ten genes have been reported to cause
CPHD (POU1F1, PROP1, HESX1, LHX3, LHX4, SIX6, OTX2,
PTX2, GLI2 and SOX3), and these genes encode signaling
proteins or transcription factors that are crucial for
pituitary development/organogenesis. Mutations in
PROP1 gene is the most prevalent cause of CPHD,
particularly among the familial cases. Despite the
identification of the ten causative genes, the etiology for
the majority of CPHD cases is unknown, including some
of the familial cases, and this highlights the significance
of further analysis to uncover the genetic basis of the
disease. To our knowledge, there has not been any
report of CPHD mutation analysis from the South East
Asian region. This study performed the mutation
screening of all coding exons of POU1F1 (CPHD1,
MIM#613038) and PROP1 (CPHD2, MIM#262600) in a
Malaysian cohort of 12 sporadic cases of CPHD (3
Malays, 5 Chinese and 4 Indians).
Methods: All of the patients included in this study have
GH deficiency, and deficiency in at least one of the other
APH. Four of the cases had small pituitary as revealed by
MRI. All of the coding exons, including the intron-exon
boundaries for the two genes were PCR-amplified and
screened using a combination of SSCP and heteroduplex
(HD) analysis. Sanger sequencing was carried out if
aberrant bands/HD-shift was detected.
Results: We detected four genomic sequence changes in
PROP1: c.27T>C [p.(=),[exon 1]; (c.424G>A, p.A142T)
[exon 3]; IVS1+13insG [intron 1] and IVS1+3 A>G [intron
1] .These are non-pathogenic variants which have been
reported in other studies. We did not detect any
sequence change in POU1F1.
Conclusion: This study shows a similar finding as of other
studies: PROP1 mutation is rare among sporadic cases of
CPHD. Whole genome sequencing or exome sequencing
might provide better approaches to detect disease
causing variants for the unresolved cases.
Disclosure of Interest: None Declared
P071
A PATIENT WITH AORTIC DISSECTION AS A RESULT OF
MUTATIONS IN TGFBR2 AND ACTA2 GENES
97
P072
POPULATION STUDY OF A CLASSICAL MENDELIAN
GENETIC MARKER FOR A TASTE SENSITIVITY TO
PHENYLTIOCARBAMIDE IN UKRAINE
1,*
1
2
O. V. Filiptsova , I. A. Timoshyna , Y. N. Kobets , I. S.
1
1
1
Burlaka , H. F. Chechui , P. V. Mirenkova
1
2
Biology Department, Department of Pharmaceutical
Marketing and Management, NATIONAL UNIVERSITY OF
PHARMACY, Kharkiv, Ukraine
P073
FKRP GENE SCREENING SHOULD BE CONSIDERED IN
DIAGNOSIS OF PATIENTS WITH DUCHENNE/BECKERLIKE PHENOTYPES
1
1
1
2
2
K. L. Ng , I. S. Tan , C. J. Y. Chia , S. Zhou , C. Liu , P.-S.
2
2
2,*
Low , S. Tay , P.-S. Lai
1
2
River Valley High School, National University of
Singapore, Singapore, Singapore
Objectives: Mutations in the Fukutin-related protein
(FKRP) gene result in muscular dystrophies with wide
phenotypic variability including the milder Limb-Girdle
Muscular
Dystrophy
2I
(LGMD2I)
and
more severe congenital muscular dystrophy type 1C
(MDC1C). However, LGMD2I and MDC1C show significant
overlaps with other muscle disorders not caused
by FKRP mutations such as Spinal Muscular Atrophy Type
I (SMA-1) and Duchenne Muscular Dystrophy (DMD) or
its milder form, Becker's Muscular Dystrophy
(BMD). Hence, misdiagnosis is a concern for patients with
DMD/BMD and SMA-like phenotypes. This study seeks to
identify cases of patients carrying FKRP mutations who
may have been misdiagnosed with DMD/BMD-like
phenotypes.
Methods: Seven patients with muscular dystrophy
phenotypes but without a conclusive clinical diagnosis
were recruited and analyzed for mutations in the FKRP
coding region. They had previously been screened
negative for mutations in common causative genes. A
quick screening method based on High Resolution Melt
(HRM) analysis was also developed, allowing quick
screening of family members of any proband carrying an
identified mutation.
Results: Mutation analysis of FKRP gene revealed a
homozygous missense mutation, p.Tyr182Cys in a
patient. The parents were found to be heterozygous
carriers. This mutation is predicted by SIFT to be
probably damaging as the altered tyrosine residue is
highly conserved. Only 6 other LGMD2I patients
worldwide have been reported to carry this same
mutation and associated with a mild disease course,
elevated CK levels, proximal muscle involvement starting
in the lower limbs and progressing to the upper limbs,
and calf hypertrophy. These symptoms are similar to
DMD/BMD.
Conclusion: FKRP mutations are reportedly rare in Asian
populations. There may be more undetected FKRP
mutations in misdiagnosed or undiagnosed cases of
LGMD2I or MDC1C patients. In patients presenting with
DMD/BMD-like phenotypes but negative for DMD gene
mutations, it is useful to screen FKRP gene. We found an
FKRP mutation in a patient not previously diagnosed with
LGMD2I. No FKRP mutations were found in the other
remaining subjects. HRM may be used as a quick
screening method for patients suspected to carry
mutations in the FKRP gene.
Disclosure of Interest: None Declared
Objectives: The taste sensitivity to phenylthiocarbamide
(PTC) is one of the classical genetic markers of a human.
PTC is a synthetic compound, which is felt bitter in some
individuals (tasters) and tasteless in other (non-tasters).
The molecular genetic nature of PTC was determined
when describing the gene of the sensitivity receptor to a
bitter taste hTAS2R38. PTC is of great interest from the
medical point of view since a number of associations of
the taster status with human diseases has been found.
The aim of this study was to analyze distribution of the
sensitivity to PTC in the sample of the population of
Ukraine presented by residents of Kharkov and some
other populations of Ukraine.
Methods: The study involved 255 people (47 males and
208 females) aged from 16 to 20. The PTC solution in the
concentration of 0.13% was prepared according to the
method of Harris and Kalmus.
Results: The design of the experiment corresponded to
the blind cohort cross-sectional study. When studying
the phenotype frequencies of PTC tasters and nontasters the data indicating that among all the population
studied there were 22% of PTC non-tasters were
obtained. There is a tendency of increase of the
frequency of non-tasters among males compared to
females (29.8% and 20.2%, respectively).
Conclusion: Based on the Hardy-Weinberg equation the
frequencies of three possible genotypes (dominant
homozygotes TT, heterozygotes Tt and recessive
homozygotes tt) were calculated. The frequencies of
alleles T and t obtained in the male and female
population under research are very close to the
frequencies of the same alleles in one of the populations
of India (Gujjar and Bakarwal, T and t are 0.44 and 0.56,
respectively among males, and T and t are 0.55 and 0.45,
respectively among females).
References: · Wooding S. Phenylthiocarbamide: a 75year adventure in genetics and natural selection.
Genetics 2006;172(4):2015-23.
· Shivaprasad HS, Chaithra PT, Kavitha P, Malini SS. Role
of phenylthiocarbamide as a genetic marker in predicting
the predisposition of disease traits in humans. J Nat Sc
Biol Med 2012;3(1):43-7.
· Yumnam Luxmi, Kapoor A.K. A Study of Taste Sensitivity
of Phenylthiocarbamide (PTC) and Colour Blindness
among the Rajputs of Dadra and Nagar Haveli.
Anthropologist 2011;13(2):163-5.
Disclosure of Interest: None Declared
98
P074
FINDING THE CAUSATIVE GENE MUTATION IN A
CONSANGUINEOUS FAMILY WITH CHARCOT-MARIETOOTH (CMT) DISEASE
1,*
2
3
4
S. Tey , N. Shahrizaila , A. Drew , K. J. Goh , G.
356
356
1
Nicholson , M. Kennerson , A. Ahmad Annuar
1
Department of Biomedical Science, Faculty of Medicine,
2
Department of Medicine, Faculty of Medicine, University
3
of Malaya, Kuala Lumpur, Malaysia, Northcott
Neuroscience Laboratory, ANZAC Research Institute,
4
Sydney, Australia, Department of Medicine, University of
5
Malaya, Kuala Lumpur, Malaysia, Molecular Medicine
6
Laboratory, Concord Hospital, Sydney Medical School,
University of Sydney, Sydney, Australia
P075
SEVERE OBESITY, TYPE 2 DIABETES MELLITUS,
INTELLECTUAL DISABILITY AND HYPOGONADOTROPHIC
HYPOGONADISM IN A FAMILY SEGREGATING WITH A
TRUNCATING MUTATION IN THE CARBOXYPEPTIDASE-E
(CPE) GENE
1,*
1 2
1 3
S. I. Alsters , A. P. Goldstone , J. L. Buxton , A.
1
1
1
4
Zekavati , A. Sosinsky , A. M. Yiorkas , S. Holder , R. E.
2
2
5
16
Klaber , N. Bridges , M. M. van Haelst , C. W. le Roux ,
1
7
1
A. J. Walley , R. G. Walters , A. I. Blakemore
1
2
Imperial College London, Imperial College healthcare
3
NHS trust, UCL Institute of Cardiovascular Science,
4
North West London Hospitals NHS Trust, London, United
5
Kingdom, University Medical Center Utrecht, Utrecht,
6
Netherlands, University College Dublin, Dublin, Ireland,
7
University of Oxford, Oxford, United Kingdom
Objectives: To identify the novel gene mutation causing
CMT in two affected brothers from a consanguineous
family.
Background: Charcot-Marie-Tooth (CMT) disease is a
clinically and genetically heterogeneous group of
disorders affecting the motor and sensory neurons with
an estimated prevalence of 1 in 2500 people. Over eighty
genes have been identified for CMT and related
peripheral neuropathies, however there are many cases
yet to be resolved. We have identified an autosomal
recessive CMT family in which all known recessive genes
have been excluded. This family therefore provides the
opportunity to identify a novel causative gene mutation
using next generation sequencing and traditional gene
mapping strategies.
Methods: Whole exome sequencing (WES) was
performed on two affected brothers, parents and an
unaffected brother. From intuitive data filtering, 152
candidate variants were found to be shared in the
affected brothers and absent in the unaffected family
members. To further reduce the number of variants, we
performed linkage analysis with SNP genotypes from the
WES data using MERLIN however the mapping
information was not informative. Further mapping of the
disease locus using the six family members was
performed using Golden Gate Linkage V panel and
several suggestive linkage peaks (LOD>2.0) were
obtained. After recruitment of additional family
members we were able to reduce the suggestive linkage
regions to 2 loci (chr12 and chr14) using microsatellite
markers. Homozygosity mapping was performed on the
consanguineous family and a region of homozygosity was
found to overlap with the linkage region on chromosome
14.
Results: By combining the mapping strategies and the
WES data, 4 candidate genes have been identified which
are currently under investigation.
Conclusion: The combination of next generation
sequencing, linkage analysis and bioinformatics
strategies is a powerful tool for identifying causative
candidate genes in family disease analysis. Using these
methods, we have potentially identified a new gene for
autosomal recessive CMT.
Disclosure of Interest: None Declared
Objectives: Whole exome sequencing (WES) has
revealed a number of new loci causing monogenic
obesity. We have investigated a consanguineous
Sudanese family with a Mendelian pattern of extreme
obesity in an attempt to identify the cause of their
disease. The proband was a 20 year old female with
childhood-onset morbid obesity (current body mass
2
index (BMI) 51.5 kg/m ), intellectual disability, type 2
diabetes mellitus (T2D) and hypogonadotrophic
hypogonadism.
Methods: WES was carried out on the proband, and also
her mother and sister, who each had less severe obesity
2
(BMI of 36.0 and 31.9 kg/m respectively), and no other
symptoms. Sanger sequencing was used to confirm
findings and undertake segregation analysis and
quantitative RT-PCR was performed on RNA isolated
from whole blood samples.
Results: Analysis of WES data revealed a homozygous
deletion (c.76_98del) in exon 1 of the CPE gene in the
proband, which results in a p.E26RfsX68 truncation of
the protein. Sanger sequencing confirmed homozygosity
in the proband and heterozygosity in her mother, sister
and two non-obese brothers. Another unaffected sister
did not carry the deletion. No DNA was available from
the father, nor from a diseased older brother with a
similar phenotype as the proband. No CPE expression
was detected in blood derived RNA from the proband,
and expression in the heterozygous sister was lower than
the range seen in six controls matched for obesity, age
and T2D.
Conclusion: As far as we are aware, this is the first
homozygous null CPE mutation described in humans.
Carboxypeptidase E is, among others, involved in
processing peptides active in the leptin-melanocortin
appetite pathway and glucose metabolism. The morbid
obesity, intellectual disability, diabetes and the
hypogonadism seen in this proband and her brother,
recapitulates the phenotypes of the previously-described
fat/fat and Cpe knockout mouse models. Our data add to
the growing number of monogenic obesity loci known in
man.
Disclosure of Interest: None Declared
99
1,*
1
2
3
H. A. Osman , H. Hasan , R. Suppian , A. Abdul Rahim ,
4
4
5
5
S. Hassan , D. Z. Andee , N. Abdul Majid , B. A. Zilfalil
1
2
Medical microbiology and parasitology, Biomedicine
3
4
5
program, medicine, Surgery, Paediatrics, Universiti
Sains Malaysia, Kubang kerian, Kelantan, Malaysia
MICROBIAL GENOMICS
P076
GENUS RATIO OF PREVOTELLA TO BACTEROIDES AS A
MICROBIAL MARKER IN OBESITY
1 2,*
12
12
A. Shafiq , T. Lay Kek , I. Rose Iszati , L. Lian Shien
1
1 3
4
4
, Y. Hartini
, A. Aminuddin , O. Mazlifah
, R.
4
12
Thuhairah , S. Mohd Zaki
1
Integrative Pharmacogenomics Institute (iPROMISE),
2
3
Faculty of Pharmacy , Faculty of Health Sciences ,
Universiti Teknologi MARA, Puncak Alam Selangor,
4
Faculty of Medicine, Universiti Teknologi MARA , Sungai
Buloh Selangor , Malaysia
Objectives: Helicobacter pylori is one of the most
common worldwide human pathogens and is associated
with gastritis, peptic ulcer, gastric cancer and gastric
mucosa-associated
lymphoid
tissue
lymphoma.
Helicobacter pylori cytotoxin-associated antigen A (CagA)
gene, the most virulence factor contains four segments
flanking the EPIYA motifs, EPIYA-A, -B, -C, or -D, are
believed to play an important role in gastroduodenal
disease. The aim of this study was to determine the type
of EPIYA Motifs in different ethnic groups.
Methods: This is a cross sectional study conducted
between July 2012 to January 2014 among 226 dyspeptic
patients at the Endoscopy Unit of Hospital Universiti
Sains Malaysia and Hospital Kuala Lumpur. H. pylori cagA
variable EPIYA motif was screened by polymerase chain
reaction from gastric biopsies.
Results: Overall 105 (46.5%) were confirmed H. pylori
positive, out of this cagA was detected in 73 (69.5%).
The cagA genotype was mainly Western type (54. 79%)
followed by the East Asian type (38.36%) and (6.85%)
were unclassified (A-B type). Majority of Chinese (88.9%
and Indian (82.8) patients were predominantly infected
with CagA type A-B-D and A-B- C strain respectively.
Malays have mixed strains of ABD (30.8%) and ABC
(53.8%). There were statistically significant difference
(P<0.001) between race and cagA EPIYA motifs.
Conclusion: This study shows that EPIYA A-B-D is
predominant in ethnic Chinese while EPIYA ABC was
more common in Indians and Malays. There were
significant difference (P<0.001) between ethnicity and
cagA EPIYA motifs.
Disclosure of Interest: None Declared
Objectives: To determine the variability in the taxonomic
composition of fecal microbiomes in obesity.
Methods: The gut microbiota of three different groups of
urban Malay male adults (lean, obese Type 1 and obese
Type 2) were sequenced using shotgun metagenomics
sequencing. A paired-end, 2 x 300 bp sequencing run was
performed using the Illumina MiSeq platform. The
taxonomic analysis of the metagenomics reads used the
web application server MG-RAST.
Results: An average of 6,562,502 high quality sequences
of 260 base pairs in length were successfully obtained.
Based on the rarefaction curve plot analysis, the gut
microbiota species richness of each sample were
comparable between samples. At the phyla level,
Bacteroidetes was seen as the most abundant gut
microbiota in all samples except for one sample from
obese Type 2 group. The taxonomical composition at
genus and species level showed that Prevotella copri was
the dominant gut microbiota in both obese Type 1 and
Type 2 groups. Within the lean group, Bacteroides spp.
was the most abundant gut microbiota followed by
Prevotella copri. The gut microbiota fit into the
enterotype categorization of enterotype 2 (Genus
Prevotella) and enterotype 1 (Genus Bacteroides). The
mean ratio of the composition for genus Prevotella to
Bacteroides was 2-fold higher in obese Type 1 and Type 2
groups compared to lean group (1.5 vs 0.7). Enterotype
classification of gut microbiota has been linked to
individual long-term dietary pattern. Enterotype 1 had
been significantly linked with Western diet while
enterotype 2 were associated with carbohydrate rich
diet. High Prevotella to Bacteroides ratio has been linked
with atherosclerosis and cardiovascular disease risk.
Conclusion: The composition ratio of Prevotella to
Bacteroides could be a useful marker for clustering of gut
microbiota in association with obesity. However, a larger
sample size is required to validate the taxonomic
distribution of microbiota specific for obesity as a
signature for our local population.
Disclosure of Interest: None Declared
P078
UNDERSTANDING THE GENOME OF BURKHOLDERIA TO
UNRAVEL THE EVOLUTION OF PLANT-MICROBE
INTERACTION
1,*
1
1
N. Najimudin , A. H. Ahmad Ghazali , S. Shaffie , N. Ab.
1
1
1
Aziz , A. F. Mohamad , A. Y. Abdul Rahman
1
SCHOOL OF BIOLOGICAL SCIENCES, UNIVERSITI SAINS
MALAYSIA, PENANG, Malaysia
Objectives: Burkholderia vietnamiensis is a member
species known for its rhizosphere colonizing ability and
its ability to fix nitrogen gas. B. vietnamiensis forms fanshaped nodules in the root of the legume Mimosa pigra
and M. pudica and fixes nitrogen from the atmosphere
by converting it to ammonia. B. vietnamiensis is also
known as a member of the “cepacia group” (Vandamme
and Dawyndt, 2011). It is interesting to note that the
pathogenic
Burkholderia
strains,
including
B.
pseudomallei and B. cepacia infect humans and animals
whilst B. vietnamiensis infects both plants and humans as
P077
DIVERSITY OF HELICOBACTER PYLORI CAGA EPIYA
MOTIFS IN DIFFERENT DIFFERENT ETHNIC GROUPS
100
an opportunistic agent (Stone et al., 2014). In this study,
the genome of Burkholderia sp. B20, an isolate from root
nodules of Mucuna bracteata, was obtained to
understand the evolutionary pathway of infection within
the Burkholderia species
Methods: Genomic sequencing was performed using the
Illumina and PacBio sequencing platforms.
Results: A genome size of 7,742,526 bp with a GC
content of 66.85% was determined. The highest Average
Nucleotide Identity was with Burkholderia cepacia
GG4. Although it was isolated from a nodule, neither the
nod nor nif genes were present. Its rDNA sequence as
well as that of the ferric uptake regulator (fur) gene
showed highest identity to B. vietnamiensis and B.
cepacia. This was also supported by a phylogenomic
analysis on its genome. A fur negative mutant was
successfully constructed revealing that it is genetically
amenable.
Conclusion: Based on its physiology and genetic
tractability, isolate Burkholderia sp. B20 can be used as a
model system to understand the evolution of plantmicrobe interactions.
References: 1. Stone JK, DeShazer D, Brett PJ, Burtnick
MN. 2014. Melioidosis: molecular aspects of
pathogenesis. Expert Rev. Anti. Infect. Ther. 12:1487-99.
2. Vandamme P, Dawyndt P. 2011. Classification and
identification of the Burkholderia cepacia complex: Past,
present and future. Syst Appl Microbiol. 2011
Apr;34(2):87-95.
Disclosure of Interest: None Declared
distribution of frequency of MCP-1 allele AA and GG+GA
genotype were 19(44.2%) and 24(55.8%) respectively in
control group and 9(20.0%) and 36(80.0%) respectively in
LTBI positive group. The CCR2 A/G allele AA and GG+GA
genotype were 19(43.2%) and 25(56.8%) respectively in
control group and 8(18.2%) and 36(81.8) respectively in
LTBI positive. Distribution of CD209 A/G allele AA and
GG+GA genotype were 37(86.0%) and 6(14.0%)
respectively for controls group and 39(86.7%) and
6(13.3) for LTBI positive group respectively. The allele G
frequency was higher in all the three genes among LTBI
positive group compared to A in controls group. The
MCP-1 and CCR2 were significantly associated with risk
of TB (OR 3.16: CI 95% (1.22-8.15): (P= 0.015)) and (OR:
3.42: CI95%: (1.29-9.03) (P=0.011) respectively. No
significant difference was found in CD209 and risk of TB
OR: 95%CI : 0.9(0.28, 3.20), (P=0.932).
Conclusion: Conclusions: The findings of this study
revealed that the MCP-1 -2518 A/G and CCR2 A/G
genotype and presence of the G allele may be associated
with risk of developing active TB among LTBI individuals.
References: LTBI, SNP analysis, MCP-1, CCR2 and CD209
genes, Peninsular Malaysia
Disclosure of Interest: None Declared
P080
WHOLE GENOME SEQUENCING AND COMPARATIVE
ANALYSIS OF BARTONELLA ELIZABETHAE
1,*
1
2
23
S. T. Tay , K. L. Kho , W. Y. Wee , S. W. Choo
1
Department of Medical Microbiology, Faculty of
2
Medicine, Department of Oral Biology and Biomedical
3
Sciences, Faculty of Dentistry, Genome Solutions Sdn
Bhd, Suite 8, Innovation Incubator UM, Level 5, Research
Management & Innovation Complex, University of
Malaya, Kuala Lumpur, Malaysia
P079
MCP-1−2518 A/G, 336A/G CD209, AND CCR2 V64 A/G
GENES POLYMORPHISMS INCREASES THE LIKELIHOOD
RISK OF DEVELOPING TUBERCULOSIS OR AGAINST WITH
LTBI INDIVIDUALS IN PENINSULAR MALAYSIA
1,*
2
1
3
O. S. Elmi , H. Hasan , S. Abdullah , M. Z. Mat Jeab , B.
4
1
Zilfalil , N. N. Naing and non
1
Unit of Biostatistics and Research Methodology, School
of Medical Sciences, USM, Universiti Sains Malaysia,
2
Kubang Kerian, Department of Medical Microbiology
and Parasitology, School of Medical Sciences, Universiti
3
Sains Malaysia, Respiratory Unit, Department of
Medicine, Hospital Raja Perempuan Zainab II Kota Bharu,
4
Department of Paediatrics, School of Medical Sciences,
Universiti Sains Malaysia, Kelantan, Malaysia
Objectives: Bartonella elizabethae has been reported as
a causative agent of human endocarditis and
neuroretinitis. The bacterium has been isolated from
small mammals including rodents. A B. elizabethae strain
(designated as BeUM) isolated from a wild rat in
Malaysia was sequenced in this study for investigation of
the genetic difference between rodent-borne and human
strain.
Methods: B. elizabethae strain BeUM was sequenced
using Illumina HiSeq 2000 paired-end sequencing
platform. Gene prediction and annotation was
performed using RAST (Rapid Annotation using
Subsystem
Technology)
server.
Comparative
pathogenomic analysis of strain BeUM with two human
strains (ATCC49927 and F9251) were carried out.
Sequences from each strain were searched against
Virulence Factor Database (VFDB) for prediction of
virulence genes. Genomic island was predicted using the
IslandViewer software.
Results: The Illumina sequencing reads were
preprocessed and assembled using SPAdes, resulting in
76 contigs. Scaffolding of these contigs using SSPACE
generated 39 scaffolds with a genome size of
Objectives: This study was aimed to determine the
presence of Single Nucleatide Polymorphisms(SNP) and
the allele frequency among three candidate genes MCP1, CCR2 and CD209 which are resistance or susceptible to
TB of household contacts of MDR-TB cases.
Methods: Methods: Genomic DNA was extracted from
88 subjects and were genotyped for the three candidate
genes by polymerase chain reaction-based restriction
fragment length polymorphism assay (PVUII) and FokI.
Data were analysed by Hardy-Weinberg equilibrium
Results: Results: A total of 88 subjects were studied
which comprised 44 cases and 44 controls. The
101
1,959,141bp and N50 of 279,295bp. Using the RAST
server, 5,605 predicted coding sequences were
identified. The draft genome of strain BeUM
contained 1,958 protein-coding
and
42
RNA
genes. Comparative genomic analysis identified several
genes which were unique to the strain BeUM. The
analysis also identified a putative intact prophage which
was conserved among all B. elizabethae strains
investigated in this study. Comparative pathogenomics
analysis indicated that the human and rodent strains
shared a large number of putative virulence genes.
Interestingly, a genomic island was identified in the
strain BeUM. Majority of the putative genes (9 out of 11
predicted genes) in the genomic island were virulence
genes, suggesting that this is likely a pathogenicity island.
Conclusion: The whole genome sequencing and
comparative analysis of a rodent-borne B. elizabetahe
strain is reported in this study. Investigation of the highly
divergent and virulence genes of B. elizabethae strains
will be able to provide insights on the evolution and
adaptability of this bacterium in different hosts.
Disclosure of Interest: None Declared
There are clear examples of bacterial Gsts representing
zeta and beta classes that can be observed from the
molecular phylogeny. There are 29 bacterial species that
possess Gsts and these species are made up of 19
genera. On average, each species has about four Gsts.
Variation in microbial detoxification genes may help
explain inter-individual variation in drug response,
metabolism of toxins and diseases associated with
insufficient detoxification.
Conclusion: A search for Gsts in human associated gut
microbiome has revealed 103 proteins that should be
further characterized for their biochemical roles to gain
an insight on their detoxification potential.
References: 1) Fonseca R. R. da, Johnson W. E., O’Brien
S. J., Vasconcelos V., Antunes A., 2010 Molecular
evolution and the role of oxidative stress in the
expansion and functional diversification of cytosolic
glutathione transferases. BMC Evol. Biol. 10: 281.
Disclosure of Interest: None Declared
BIG DATA
P082
CLOUD-BASED VARIANT ANALYSIS SOLUTION USING
CONTROL-ACCESSED SEQUENCING DATA
1,*
1
1
C. Xiao , E. Yaschenko , S. Sherry
1
NCBI, National Institutes of Health, Bethesda, United
States
P081
MOLECULAR EVOLUTION AND INDIVIDUALITY OF
DETOXIFICATION SYSTEM IN HUMAN MICROBIOME
1,*
1
1234
W. Y. Low , N. S. Che Wahid , C. Luo
1
Centre for Bioinformatics, Perdana University, Serdang,
2
3
Malaysia, Fibonacci Technologies, Beijing, China, Broad
Institute of MIT and Harvard, Harvard Medical School,
4
Sequana Computing LLC, Cambridge MA, United States
Objectives: Variation analysis plays an important role in
elucidating the causes of various human diseases. The
drastically reduced costs of genome sequencing driven
by next generation sequence technologies now make it
possible to analyze genetic variations with hundreds or
thousands of samples simultaneously, but currently with
the cost of ever increasing local storage requirements.
The tera- and peta-byte scale footprint for sequence data
imposes significant technical challenges for data
management and analysis, including the tasks of
collection, storage, transfer, sharing, and privacy
protection. Currently, each analysis group facing these
analysis tasks must download all the relevant sequence
data into a local file system before variation analysis is
initiated. This heavy-weight transaction not only slows
down the pace of the analysis, but also creates financial
burdens for researchers due to the cost of hardware and
time required to transfer the data over typical academic
internet connections.
Methods: To overcome such limitations and explore the
feasibility of analyzing control-accessed sequencing data
in cloud environment while maintaining data privacy and
security, here we introduce a cloud-based analysis
framework that facilitates variation analysis using direct
access to the NCBI Sequence Read Archive through NCBI
sratoolkit, which allows the users to programmatically
access data housed within SRA with encryption and
decryption capabilities and converts it from the SRA
format to the desired format for data analysis.
Objectives: The detoxification potential of human
associated microbes is less investigated compared to that
of human cells. This study investigates the evolution of
detoxification related genes such as the phase II
multigene family Glutathione S-transferases (Gsts) in the
human gut microbiome. We provide in-depth insights on
the Gst genes in this study and offer methods scalable
for other detoxification related genes. Lastly, we also aim
to identify the patterns in the bacterial detoxification
assemblages in human guts, which have essential
implications in human health.
Methods: A list of 41 Gsts representing 15 classes of this
1
multigene family was compiled from the literature .
Then, a list of reference bacterial genomes and individual
samples corresponding to gastrointestinal tract were
downloaded from the HMP (Human Microbiome Project)
(http://www.hmpdacc.org). The list of Gsts was used as
input for BLASTP searches against the HMP reference
genomes and individual metagenomic data. Significant
matches were extracted and subsequently aligned for
bootstrapped maximum-likelihood tree construction.
Individuality patterns in microbiome detoxification
system were analyzed and various analyses were
performed to infer the evolutionary rate in each of such
patterns.
Results: A list of 103 predicted bacterial proteins was
found from the gastrointestinal tract reference genomes.
102
Results: A customized machine image (swift) with
preconfigured tools (including NCBI sratoolkit) and
resources essential for variant analysis has been created
for instantiating an EC2 instance or instance cluster on
Amazon
cloud.
Performance
of
this
framework has been evaluated and compared with that
from traditional analysis pipeline, and security handling
in cloud environment when dealing with controlaccessed sequence data has been addressed. We
demonstrate that it is cost effective to make variant calls
using control-accessed SRA sequence data without first
transferring the entire set of aligned sequence data into
a cloud storage environment.
Conclusion: This direct data access approach using NCBI
sratoolkit from cloud for next generation sequencing
analysis is more cost-effective in terms of time and disc
spaces being used for the analysis, and thus will
accelerate variation discovery using control-accessed
sequencing data.
cancer sample and cell line panels provides opportunities
for the identification of drug targets as key drivers in
cancer regulation.
Disclosure of Interest: None Declared
P084
ICLIKVAL: COMMUNITY RESOURCE FOR CURATING THE
VAST WEALTH OF SCIENTIFIC LITERATURE THROUGH
THE POWER OF CROWDSOURCING
1,*
1
T. D. Taylor , N. Kumar
1
Center for Integrative Medical Sciences, RIKEN,
Yokohama, Japan
Objectives: There are currently over 24 million citations
to various forms of scientific literature in PubMed.
Searching this vast resource does not always give
desirable or complete results due to a number of factors
such as: missing abstracts, unavailability of full-article
text, non-English articles, lack of keywords, etc. Ideally,
each and every citation should include a complete set of
keywords or terms that describe the original article in
enough detail that searches, using natural language,
return more relevant results; however, this would
require countless hours of manual curation. Our
objective is to make manual curation ‘fun’ and social and
self-correcting, thus enriching resources such as PubMed
so that users are able to extract more valuable and
relevant results.
Disclosure of Interest: None Declared
P083
SYSTEMATIC ANALYSIS OF BIG DATA FOR CANCER DRUG
DISCOVERY
1,*
1
N. Kim , S. Yoon
1
Center for advanced bioinformatics and systems
medicine, Dept of Biological Sciences, Sookmyung
Women's University, Seoul, Korea, Republic Of
Objectives: An integrative approach of large-scale omics
and drug response data on various cancer types enables
us to identify the cellular signaling and drug sensitivity in
cancer. Signatures in different levels of biological process
such as gene expression, protein expression and protein
activation have applications in finding novel diagnostic or
prognostic biomarkers. They are also key components in
accelerating mechanism-based drug discovery or
repositioning. Here we represent system-level analysis of
cell line and patient’s tissue sample data for target
identification in cancer drug discovery.
Methods: Association study with the genotypic
classification was performed on drug response and omics
data such as transcriptome, proteome, and
phosphateome on human cancer cell lines. Further, we
carried out the expanded analysis using next generation
sequencing data obtained from TCGA (The Cancer
Genome Atlas).
Results: Through a multidimensional analysis of drug
response and omics data on cell line panels, we
identified drug targets to be regulated by a mutation of
STK11/LKB1 in lung cancer. Among them, overexpression of PDE4D gene was represented on STK11mutated lung cancer cell lines and tissue samples.
Furthermore, we confirmed that PDE4-specific inhibitors
selectively inhibited the growth of STK11-mutated lung
cancer lines.
Conclusion: This study shows that a systematic analysis
of multi-level omcis data generated on various clinical
Methods: We have constructed a cross-browser and
platform-independent application using the latest web
technologies and a NoSQL database. Users perform
searches to identify articles of interest, mark articles for
later review or review them immediately or add them to
a review request queue, load PDFs into the viewer, select
annotations (values) within the text, and add appropriate
keywords (keys). Article-specific comments can be made,
key-value pairs can be edited and rated, live chats
between users working on the same article can be held,
etc. Users can even add annotations via Twitter.
Results: We have developed a web-based open-access
tool for manual curation of PubMed articles, and other
media types, using a crowdsourcing approach which we
believe the community will enjoy using. While we
encourage the use of ontology terms and support them
as auto-suggest keyword terms, we do not restrict users
to these terms because we do not want to impose,
within reason, any limitations on the types of annotation
that one may provide. Non-English annotation is also
supported.
103
Picture/graph (P083)
Methods: We will be working with authors to make the
raw data, computational tools and data processing
pipelines described in the GigaScience papers available
and, where possible, executable on an informatics
platform. We hope that by making both the data and
processes involved in their analysis freely accessible, this
novel form of publication will help articles published in
GigaScience to have a much higher impact in the
scientific literature, and maximize their reuse within the
community. We also provide a rapid data release
mechanism for datasets that are not associated
with GigaScience articles that have not previously been
published elsewhere by giving each the dataset a DOI,
making them citable in a standard (and countable)
manner in the reference section of papers that use these
data.
In future GigaDB will link with GigaDV (presented by
OMERO), which is a data viewer for GigaDB image files to
aid readers in visualizing the imaging datasets. GigaDB
will also integration with the BGI Cloud, and with the
Galaxy software tools to enable users to directly upload
files to Galaxy for further analysis.
Results: To date, GigaDB comprises over 133
datasets(>30TB in size) – all under a CC0 Waiver(the
most open sharing waiver available). The GigaDB
includes the Rice 3000 genome project, the first
nanopore dataset, the first ~50 bird genomes from the
10,000 genome project. GigaDB also host lots of nongenomic
datasets
(eg.
Imaging,
proteomic,
metabolomics, software etc.) We are willing to discuss
any datatypes related to biological sciences.
Conclusion: GigaDB is an open-access repository aim to
let the results published in scientific aritcles also have to
be reproducible and maximizing the reuse of published
data.
Conclusion: The more annotations that accumulate in
the database the more our semantic search feature will
improve, and users will be able to precisely filter the
results. Rather than compete with other curation
projects, we wish to work with them to incorporate their
valuable data, and, via our REST API, to make the
accumulated annotations easily accessible to the
research community. We recently opened iCLiKVAL and
user feedback has been very positive. We hope this will
become the default resource for community-based
curation of all online scientific literature.
References:
PubMed: http://www.ncbi.nlm.nih.gov/pubmed
Disclosure of Interest: None Declared
P085
GIGADB：PROMOTING DATA DISSEMINATION AND
REPRODUCIBILITY
1,*
1
1
1
X. Sizhe , C. I. Hunter , P. Li , R. Davidson , S. C.
1
1
Edmunds , L. Goodman
1
Gigascience, Hong Kong, Hong Kong
Objectives: GigaScience journal is an Open Access, Open
Data, scientific journal that aims “to revolutionize data
dissemination, organization, understanding, and use.”
Beyond the traditional publication, GigaScience is linked
to GigaDB, a new integrated database of ‘big-data’
studies from the life sciences. The initial goals of GigaDB
are to assign DOIs to datasets to allow them to be
tracked and cited, and to provide a user-friendly web
interface to provide easy access to selected GigaDB
datasets and files.
104
We wish to solicit open discussions from others to help
our
future
developments.(database@gigasciencejournal.com)
Disclosure of Interest: None Declared
Objectives: The frequency of EGFR mutations in nonsmall-cell lung cancer (NSCLC) was determined in 2184
Malaysian patients analysed in Subang Jaya Medical
Centre (SJMC).
Methods: Tissue biopsies received were tested for EGFR
mutation using the cobas� EGFR Mutation Test. The CEIVD marked allele-specific realtime PCR assay is designed
to detect 41 somatic EGFR mutations in exons 18, 19, 20
and 21.
Results: Of 2184 patients analysed, 56.4% were males.
Patients’ age ranged from 15 to 97 years old with a mean
and median age of 61 years. The predominant ethnic
group was Chinese (48%), followed by Malay (32%),
Indian (4%) and others (16%). EGFR mutation status was
successfully identified in 2135 patients (97.8%). The
commonest cause for testing failure was insufficient
number of tumour cells. A higher mutation rate of 57.8%
was found in female patients, although 56.4% of the
patients are males. EGFR mutations were detected in 844
cases (39.5%), with 38.6% of the cases harbouring at
least one mutation. The most prevalent mutation type
detected was exon 19 deletion (57.6%), followed by exon
21 L858R mutation (32.7%). 4.6% of the cases showed
multiple mutations, with 38 cases showing double
mutations and 1 case showing a triple mutation. The
exon 20 T790M resistance mutation was detected
together with the initial sensitizing mutations,
accounting for 2.3% of all the mutated cases. Out of 39
cases of multiple mutations, 19 cases harboured the
exon 20 T790M mutation (48.7%), with exon 21 L858R as
the most prevalent initial sensitizing mutation.
Conclusion: Our data showed that the most prevalent
type of mutation is exon 19 deletion (57.6%), followed by
exon 21 L858R (32.7%). The EGFR TKI resistant mutation,
exon 20 T790M, was detected together with its initial
sensitizing mutation (2.3%). EGFR mutation detection
should be considered for all patients with possible
adenocarcinoma component on histology, regardless of
clinical parameters such as age, sex or smoking history.
The high percentage of EGFR negative cases highlights
the importance showed the significance of identifying
other mutations.
Disclosure of Interest: None Declared
CANCER GENOMICS
P086
7X LOW-DEPTH GENOMIC SEQUENCING IS SUFFICIENT
FOR CLINICAL ANALYSIS OF A GIST FFPE TUMOUR
SAMPLE
1,*
1
1
1
A. Amin , S. Abdul Karim , S. M. Ching , H. Isa , Y. S.
1
1 2
1
1
Leong , J. Y. Chia , K. W. Chong , F. Wahid , T. M.
3
1
1
14
Pasupati , R. G. Hercus , P. Suwinski , L. Croft
1
2
MGRC, Mid Valley, University of Malaya, Kuala Lumpur,
3
4
Clinipath Malaysia, Klang, Monash University Malaysia,
Sunway, Malaysia
Objectives: A feasibility test of low coverage clinical
genomic sequencing for solid tumours.
Methods: 7x genome coverage using Illumina HiSeq
2000, 2x100nt paired end reads from formalin fixed
paraffin embedded tumour tissue slide. Analysis of SNV,
structural variations, CNVs, and text-mining of data using
MGRC's OneClick Pipeline.
Results: Low depth 7x genomic sequencing of a
gastrointestinal stromal tumour (GIST) histopathology
sample is sufficient to identify driver mutations and
accessory advantageous mutations. Based upon these
results tailored therapeutic intervention is possible. This
GIST sample had no c-KIT mutation but a stop codon in
PDGFRA, among other potentially oncogenic mutations.
PDGFRA is a tyrosine-kinase which is found mutated,
usually by truncation, in approximately 5% of GIST
tumours.
Conclusion: This low depth approach is sufficient to
identify common driver mutations within the
heterogenous pool of mutations present in a single solid
tumour.
Disclosure of Interest: A. Amin Employee of: MGRC, S.
Abdul Karim Employee of: MGRC, S. M. Ching Employee
of: MGRC, H. Isa Employee of: MGRC, Y. S. Leong
Employee of: MGRC, J. Y. Chia Employee of: MGRC, K. W.
Chong Employee of: MGRC, F. Wahid Employee of:
MGRC, T. Pasupati Employee of: Clinipath Malaysia, R.
Hercus Employee of: MGRC, P. Suwinski Employee of:
MGRC, L. Croft Employee of: MGRC
P088
EXTRACELLULAR MATRIX PROTEINS SECRETED BY
MESENCHYMAL STEM CELLS INDUCE PROSTATE CANCER
CELL MIGRATION IN VITRO
1,*
2
2
C. Maercker , M. Boutros , F. Graf
1
ESSLINGEN UNIVERSITY OF APPLIED SCIENCES, Esslingen,
2
German Cancer Research Center (DKFZ), Heidelberg,
Germany
P087
DETECTION OF EPIDERMAL GROWTH FACTOR
RECEPTOR (EGFR) MUTATIONS IN NON-SMALL-CELL
LUNG CANCER PATIENTS IN MALAYSIA
1 2,*
1
2
1
C. W. Tay , S. B. Yousoof , Y. K. Cheah , P. Rajadurai
1
Molecular Diagnostic Laboratory, Subang Jaya Medical
2
Centre, Petaling Jaya, Selangor, Department of
Biomedical Science, University Putra Malaysia, Serdang,
Selangor, Malaysia
Objectives: Some cancers show a strong tendency to
metastasize to bone, a tissue of mesenchymal origin and
a prominent site of mesenchymal stem cells (MSC) in an
adult. Recent reports have suggested that bonemetastasizing cancers may mimic the process of homing
of hematopoietic stem cells to their bone niche, in which
105
MSC play a crucial role. In light of the growing awareness
that MSC play a potentially important role in cancer, we
aim to dissect the interaction and the dynamics between
tumor cells and MSC in metastasis formation. We found
that prostate cancer cell lines, which form bone
metastasis in animal models, show a characteristic
migration pattern towards MSC, displaying dose
dependency along a protein-based chemotactic gradient.
This effect was stronger towards naïve MSC compared to
MSC undergoing differentiation, fibroblasts and other
cell types tested. This indicates that specific molecules
secreted by MSC are responsible for stimulating
migration.
Methods: The cell culture supernatant of MSC isolated
from healthy donors and cultivated in protein free
medium was investigated for its migration promoting
activity for prostate cancer cells (PC3 cells) in an
impedance based high-throughput trans-well migration
assay. After size exclusion chromatography of the MSC
supernatant, the ~1000 kD fraction had the strongest
chemotactic activity. Another peak was at about 100 kD.
The ~1000 kD fraction then was fractionated again by ion
exchange chromatography (IEX), showing the strongest
migratory activity at ~300 – 350 mM NaCl.
Results: we were able to identify a number of
extracellular matrix (ECM) proteins or ECM-associated
proteins by electrospray-ionization mass spectrometry,
which obviously are responsible for cell migration. Based
on these results, recombinant or isolated candidates
were tested in the trans-well migration assay.
Interestingly, some molecules, which are potential
mediators of cancer progression, only showed low
migratory activity, others induced a stronger response.
Also the migration dynamics were individually different.
Whereas some candidates induced a rapid migration
response, other proteins showed a gradual and linear
increase of PC3 cell migration over time.
Conclusion: This argues for specific functions of ECM
proteins secreted by MSC in different tissues mediating
multiple cellular processes such as adhesion, migration,
tissue architecture, and proliferation at the different
stages during metastasis.
Disclosure of Interest: None Declared
TNBC. In this study, we dissect the AP-1 – ZEB2 axis in
TNFa-induced EMT in TNBC cells.
Methods: Chromosome conformation capture assay (3C)
was used.
Results: In this study, we demonstrate that the
inflammatory cytokine TNFa induces EMT in TNBC cells
via activation of AP-1 signaling and subsequently induces
expression of the EMT regulator ZEB2. We also show that
TNFa activates both the PI3K/Akt and MAPK/ERK
pathways, which act upstream of AP-1. We further
investigated in detail AP-1 regulation of ZEB2 expression.
We show that two ZEB2 transcripts derived from distinct
promoters are both expressed in breast cancer cell lines
and breast tumor samples. Using the chromosome
conformation capture assay, we demonstrate that AP-1,
when activated by TNFa, binds to a site in promoter 1b of
the ZEB2 gene where it regulates the expression of both
promoter 1b and 1a, the latter via mediating long range
chromatin interactions. The finding of AP-1 activation of
ZEB2 expression was further supported by clinical data
showing a significant positive correlation between AP-1
and ZEB2 expression.
Conclusion: Overall, this work provides a plausible
mechanism for inflammation-induced metastatic
potential in TNBC, involving a novel regulatory
mechanism governing ZEB2 isoform expression.
References: Zhao C, Qiao Y, Jonsson P, Wang J, Xu L,
Rouhi P, Sinha I, Cao Y, Williams C and Dahlman-Wright
K.
Genome-wide
Profiling
of
AP-1-Regulated
Transcription Provides Insights into the Invasiveness of
Triple-Negative Breast Cancer. Cancer Res. 2014;
74(14):3983-3994.
Disclosure of Interest: None Declared
P089
AP-1-MEDIATED CHROMATIN LOOPING REGULATES
INDUCED EPITHELIAL–MESENCHYMAL TRANSITION IN
TRIPLE-NEGATIVE BREAST CANCER
1,*
C. Zhao
1
Department of Biosciences and Nutrition, KAROLINSKA
INSTITUTET, Stockholm, Sweden
Objectives: To establish a resectable VX-2 rabbit brain
tumor model for assessment of intraoperative local
administration of drugs.
Methods: 26 New Zealand White rabbits were implanted
with VX-2 cells and their survival was monitored with
(n=9) or without (n=13) resection. 4 animals underwent
surgery in combination with AdLac-Z gene transfer.
Results: We show that VX-2 rabbit brain tumor model is
reproducible and technically relatively easy to use.
Importantly, it has similarities in growth and pathology to
aggressive brain tumors. Tumor resection significantly
improves the survival of animals, yet all of them finally
develop large residive tumors leading to death. Thus, this
model mimics the clinical reality in patients. Notably, it
allows evaluation of locally administrated novel therapies
P090
RESECTABLE VX-2 RABBIT BRAIN TUMOR MODEL FOR
DEVELOPMENT
OF INTRAOPERATIVE LOCAL ADMINISTRATION OF
DRUGS
1,*
1
1
F. Ahmad , A. Pacholska , V. Tuppurainen , S. Ylä1
1
Herttuala , A. Hyvarinen
1
A.I Virtanen Institute, University of Eastern Finland,
Kuopio, Finland
Objectives: Objectives: The molecular determinants of
malignant cell behaviour in triple-negative breast cancer
(TNBC) are poorly understood. Recent studies have
shown that regulators of epithelial-mesenchymal
transition (EMT) are potential therapeutic targets for
106
in combination with surgical debulking. We show
successful marker gene transfer with adenovirus vector
injected into resection cavity walls after tumor resection.
Conclusion: VX-2 rabbit brain tumor model is useful for
preclinical evaluation of novel therapies that require
local administration in combination with surgery.
References: 1. Barker FG 2nd, Chang SM, Larson DA,
Sneed PK,WaraWM,Wilson
CB, Prados MD (2001) Age and radiation response in
glioblastoma
multiforme. Neurosurgery 49(6):1288–1297, discussion
1297–8
2. Carson BS, Anderson JH, Grossman SA, Hilton J, White
CL 3rd,
Colvin OM, Clark AW, Grochow LB, Kahn A, Murray KJ
(1982)
Improved rabbit brain tumor model amenable to
diagnostic
radiographic procedures. Neurosurgery 11(5):603–608
3. Claes A, Schuuring J, Boots-Sprenger S, HendriksCornelissen S,
Dekkers M, Van der Kogel AJ, Leenders WP, Wesseling P,
Jeuken
JW (2008) Phenotypic and genotypic characterization of
orthotopic
human glioma models and its relevance for the study of
anti-glioma
therapy. Brain Pathol 18(3):423–433
4. Ng WH, Wan GQ, Too HP (2007) Higher glioblastoma
tumour
burden reduces efficacy of chemotherapeutic agents: in
vitro
evidence. J Clin Neurosci 14(3):261–266
5. Stewart LA (2002) Chemotherapy in adult high-grade
glioma: a
systematic review and meta-analysis of individual patient
data from
12 randomised trials. Lancet 359(9311):1011–1018
Disclosure of Interest: None Declared
study was to identify circulating miRNAs in NPC patients
and controls.
Methods: Plasma samples were collected from 8 NPC
patients and 6 controls. Extraction of RNA from plasma
samples was performed with miRNeasy micro kit. The
samples were prepared for small RNA sequencing using
TruSeq Small RNA Prep Kit and libraries were sequenced
TM
on Illumina HiSeq 2000. Alignment were performed
with novoAlign and Strand NGS followed by differential
expression analysis with Mann Whitney test, edgeR and
DESeq.
Results: A total of 557 human miRNAs and 16 EpsteinBarr virus miRNAs were detected in plasma samples of
NPC patients and controls. Top 100 most abundant
miRNAs in NPC plasma samples were identified. Of these
abundant miRNAs, about 80 of them were found to be
differentially expressed in the various methods of
analysis.
Conclusion: Lists of differentially expressed miRNAs
between NPC and controls had been generated using
various small RNA analyses. This is an on-going project
and the sequencing results will be validated in qPCR
platform with a larger cohort of patients and controls. It
is hoped that a biomarker profile can be obtained for the
classification of NPC patients and controls.
Disclosure of Interest: None Declared
P092
ADRA2A GENE POLYMORPHISM IS ASSOCIATED WITH
BREAST CANCER SEVERITY
1 2 3,*
2 4
1 2 5
G. Belaaloui
, B. Kaabi , W. Benbrahim
, K.
125
6
6
137
Hamizi , M. Sadelaoud , W. Toumi , H. Bounecer
1
2
3
Faculty of Medicine, Hadj Lakhdar University, GRIAS
4
laboratory. Faculty of Medicine, Faculty of Sciences,
5
6
7
Anti-Cancer Center, LAM laboratory, Epidemiology
Unit. University Hospital Center, Batna, Algeria
Objectives: The SNPs rs1800544 and rs553668 of
ADRA2a were associated with obesity, metabolic
syndrome and type-2 Diabetes mellitus, known prognosis
and risk factors for breast cancer (BC). This is the first
investigation of the association of these SNPs with BC
severity.
Methods: DNA was extracted from peripheral blood
samples of 100 women treated for BC in the Anti-Cancer
Center of Batna. SNPs were analyzed using TaqMan SNP
Genotyping Assays. Prognostic indicators: TNM stage,
SBR grade and tumor expression of progesterone or
estrogen receptors and human epidermal growth factor
receptor-2 HER2, were obtained from medical records.
Results: Mean patients age was 48.28±1.04y. Table 1
shows genotype frequencies:
rs1800544
rs553668
CC
35.7%
GG
60.2%
GC
41.8%
AG
30.6%
GG
22.4%
AA
9.2%
P091
CIRCULATING MICRORNAS AS BIOMARKER FOR THE
DIAGNOSIS OF NASOPHARYNGEAL CARCINOMA
1,*
1
2
1
G. W. Tan , A. S. B. Khoo , T. Y. Tan , L. P. Tan and The
Malaysian Nasopharyngeal Carcinoma Study Group
1
Molecular Pathology Unit, Institute for Medical
2
Research,
Kuala
Lumpur,
Department
of
Otorhinolaryngology, Sarawak General Hospital, Kuching,
Malaysia
Objectives: Nasopharyngeal Carcinoma (NPC) arises as
tumour from the epithelial cells of nasopharynx. Due to
the hidden location of the tumour, there could be no or
apparently trivial symptoms. About 75% of NPC cases
presented in advance stage and late stage lead to poor
outcome. Diagnosis at early stage can increase the
survival rate. Circulating microRNAs (miRNAs) are stable
small RNAs which can potentially be used as non-invasive
biomarkers for the early diagnosis of NPC. The aim of this
Loci were in Hardy-Weinberg equilibrium. There was no
association between rs553668 and prognostic indicators.
107
However, there was a significant association between AA
genotype and premenopausal status (OR=17.19,
p=0.008). rs1800544 G allele was associated to advanced
TNM stages III-IV (OR=2.8, p=0.02), and its GC genotype
was associated to SBR3 grade (OR=4.64, p=0.03).
Although its GG genotype seemed to be associated with
premenopausal status, this was not significant (OR=3.21,
p=0.05).
We found indirect indicators of an association between
these SNPs and BC risk: their minor allele frequencies are
different from what was described in healthy persons;
this may be explained by ethnicity or health status.
Conclusion: This is the first report on ADRA2A gene
polymorphism in BC. rs1800544 is associated to bad
prognostic stages TNM/SBR while rs553668 is associated
to premenopausal status. The role of ADRA2A SNPs in BC
prognosis requires investigation in a larger study, and
their eventual association with BC susceptibility is
ongoing.
genes, which matched the Cancer Census Gene List, were
identified.
Conclusion: Candidate genes were identified and are
being validated.
Disclosure of Interest: None Declared
P094
PREVENTING BREAST AND OVARIAN CANCERS IN
MALAYSIAN BRCA MUTATION CARRIERS
1,*
2
3
4
H. Sa'at , Y. Sook-Yee , W. Yin-Ling , K. Rahmat , Y.
5
2
2
1
Cheng-Har , T. Soo-Hwang , T. Hassan , T. Gie-Hooi , S.
1
1
6
1
Mee-Hoong , S. Jamaris , T. Meow-Keong , N. A. Taib
1
Department of Surgery, University Malaya Medical
2
Centre, Kuala Lumpur, Cancer Research Initiatives
3
Foundation, Selangor, Department of Obstetrics and
4
Gynecology, Department of Biomedical Imaging,
5
University Malaya Medical Centre, Kuala Lumpur, Sime
6
Darby Medical Centre, Selangor, Department of
Pediatrics, University Malaya Medical Centre, Kuala
Lumpur, Malaysia
Disclosure of Interest: None Declared
Objectives: Risk management clinic (RMC) was
established in 2008 at University Malaya Medical Centre
as part of Malaysian breast cancer genetic study
(MyBrCa). Patients who found as BRCA mutation positive
were offered to attend RMC to discuss on risk-reducing
strategies (RRS). Hitherto, the extent to what influenced
RRS uptake in Malaysia is not well characterized. This
study aims to describe the uptake of RRS in Malaysian
BRCA carriers and explore their experience in RRS
decision making.
Methods: 129 affected BRCA carriers were identified
between Jan 2003 and Dec 2013. These patients were
followed up and the information was collected
retrospectively including the status of BRCA result
disclosure, RMC visit history and their decision of RRS. As
semi-structured interview was used to explore RRS
decision making experience. The interview was audiotaped and transcribed verbatim. NVivo 10 software tool
was used to assist data analysis.
Results: Of the 129 BRCA carriers, 62 had attended RMC.
10 (20.4%) chose to have risk-reducing contralateral
mastectomy (RRM). 37 (71.4%) opted for intensive
breast screening, while one also opted for
chemoprevention using tamoxifen. Of the 49 carriers
without previous gynae surgery, 24 (49%) chose to have
risk-reducing bilateral oophorectomy. 18 (36.7%) chose
ovarian screening. In qualitative study, 8 affected carriers
were interviewed and several themes emerged. The
main barriers of RRS were to preserve femininity. The
impact of previous cancer experience make them only
consider surgery if problem is found to the organ
involved. The main motivators were completed
childbearing and felt obliged to maximize survival for the
sake of their children. The support from husband and
doctor were crucial in decision making. Patients' gap of
knowledge has been identified, particularly on
understanding of risks and the optimal benefit form each
RRS.
P093
ANALYSIS OF CANCER SUSCEPTIBILITY GENES IN CASES
OF FAMILIAL NASOPHARYNGEAL CARCINOMA
1,*
1
1
2
H. Akmal Hisham , T. Lu Ping , K. W. Ric , L. C. Lun , P.
3
4
5
6
K. Choo , Y. Y. Yap , D. B. Dass , T. T. Yong , G. K.
7
1
Govindasamy , A. Khoo Soo Beng and The Malaysian
Nasapharyngeal Carcinoma Study Group#
1
Molecular Pathology Unit, Institute for Medical
2
Research, Kuala Lumpur, ENT Department, Queen
3
Elizabeth Hospital, Kota Kinabalu, Department of
Otorhinolaryngology, Hospital Pulau Pinang, Penang,
4
Department of Surgery, Clinical Campus Faculty of
Medicine and Health Sciences, University Putra Malaysia
5
at
Hospital
Kuala Lumpur,
Department
of
Otorhinolaryngology, Hospital Kuala Lumpur, Kuala
6
Lumpur, Department of Otorhinolaryngology, Head and
Neck Surgery, Sarawak General Hospital, Jalan Hospital,
7
Sarawak, Department of Otorhinolaryngology, Faculty of
Medicine, University of Malaya, Kuala Lumpur, Malaysia
Objectives: Nasopharyngeal carcinoma (NPC) is the
fourth most common cancer in Malaysia. Familial
clustering is known to occur in NPC but cancer
susceptibility genes are not known for this cancer. The
objective of the study is to identify cancer susceptibility
genes in familial NPC.
Methods: Constitutional DNA from 25 cases of NPC with
a family history of the cancer was subjected to exome
sequencing using the Illumina Next Generation
Sequencing Platform. Sequence analysis was carried out
using Novoalign, Picard, SAMtools, SnpEff and SNPsift,
Variant Studio Software, COSMIC, TCGA, dbSNP, ClinVar,
SIFT and PolyPhen.
Results: Over 20,000 non-synonymous mutation and 300
frameshift and stop-gain mutations per sample were
found and subjected to filtering. Several candidate
108
Conclusion: This findings will direct future research
towards the development of intervention to assist
decision making in Malaysia BRCA carriers.
an evolutional differentiation of progenitor tumoral cells
to MCL
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P096
MICRORNA EXPRESSION PROFILES AND COPY NUMBER
ALTERATIONS IN ACUTE PROMYELOCYTIC LEUKAEMIA
PATIENTS: A PRELIMINARY STUDY.
1 2,*
3
4
2
I. Ismail
, S. Sulong , M. F. Md Ahid , S. Ghazali , A.
2
2
2
Cheng Yong , N. A. F. Abdullah , N. M. K. Nik Man , Z.
4
5
2
Zakaria , A. Mansoor , R. Hassan
1
Universiti Sultan Zainal Abidin, Kuala Terengganu,
2
3
Haematology Department, Human Genome Centre,
4
Universiti Sains Malaysia, Kubang Kerian, Cancer
Research Centre, Institute For Medical Research, Kuala
5
Lumpur, Malaysia, Division of Hematology & Transfusion
Medicine, Department of Pathology & Laboratory
Medicine, University of Calgary/CLS, Calgary, AB, Canada
P095
CCND1
REARRANGEMENT
AS
A
SECONDARY
MOLECULAR EVENT IN MANTLE CELL LYMPHOMA
1,*
2
1
1
H. Elghezal , A. alzahrani , I. ben abdallah , K. alfayez ,
3
4
S. sobki , G. Elyamany
1
2
3
cytogenetics, oncology, central medical laboratory and
4
blood bank, hematopathology, Prince Sultan Military
Medical City, riyadh, Saudi Arabia
Objectives: World Health Organization classification
defines mantle cell lymphoma (MCL) as a distinct entity
characterized by a unique immunophenotype and a
molecular hallmark of chromosomal translocation
t(11;14), which considered as the primary molecular
event juxtaposing CCND1 gene with IgH gene and
resulting in the overexpression of cyclin D1
Here, we describe an unusual case of MCL characterized
by the detection of t(11;14) as a secondary molecular
event in tumoral cells whereas chromosome 1 inversion
was detected as primary chromosomal rearrangement
This report allows as to reassess our knowledge
concerning molecular pathogenesis of MCL
Methods: A 64-year-old male presenting MCL confirmed
by BM morphologic and Immunophenotyping.
Cytogenetic analysis was performed on BM samples
using Conventional G-banding. At least 20 metaphases
were
analyzed.
FISH
was
performed
using
IgH/CCND1 dual color DNA probes. Slides were prepared
for FISH analysis according to the manufacturer's
protocol. A total of 200 interphase cells and 20
metaphasis were scored
Results: Karyotyping revealed the presence of a tumoral
clone characterized by only chromosome 1 inversion.
Clonal evolution was detected with t(11;14) in 70% of
cells presenting chromosome 1 inversion. FISH identified
the IGH/CCND1 fusion in 44% of the scored cells.
Chromosome 1 inversion was observed in all metaphasis
positive for IGH/CCND1 rearrangement but 3 among 10
metaphasis with chromosome 1 inversion are negative
for IGH/CCND1 rearrangement.
Conclusion: MCL is genetically characterized by the
t(11;14). We report a unique case of MCL with CCND1
rearrangement detected as a clonal evolution of tumoral
cells presenting a chromosome 1 rearrangement as a
primary genetic event. In one previously reported case of
composite lymphoma with MCL and DLBCL FISH for the
t(11;14) showed a fusion in the MCL, but not in the
DLBCL component, suggesting that these 2 populations
of tumoral cells have arisen from a common progenitor
clone and differentiation to MCL was a second event
associated with the expression of the t(11;14). Our case
support strongly this hypothesis and suggest that in
cases of MCL CCND1 rearrangement can be observed as
Objectives: Deregulation of microRNAs (miRNAs) and
alteration in copy number variations (CNV) have been
suggested to play roles in the pathogenesis of acute
promyelocytic leukaemia (APL). In the present study, we
investigate the miRNAs expression profiles and alteration
in CNV in APL patients.
Methods: The microRNA expressions in APL patients
were evaluated using the Agilent miRNA microarray
platform. Following hybridization and data acquisition,
we used GeneSpring Software V13.0 to determine
statistically significance differences in miRNA expression
profiles in APL patients. Targeted genes of particular
miRNAs were identified using miRWalk database and
pathway analysis was performed using DAVID database.
For array-based comparative genomic hybridization
(CGH) analysis, we analyzed DNA from APL patients by
using commercially available oligonucleotide microarrays
slide (Agilent Technologies) according to the
manufacturer’s protocol. Data analysis was carried out
using Cytogenomics V2.0.6.0. PML- RARα transcripts
were detected in all patients’ RNA, confirming the clinical
diagnosis of APL.
Results: We found up regulation of sixteen miRNAs and
seven miRNAs were found to be down regulated in APL
patients. The most up regulated miRNAs in APL patients
is miR-181b. MiR-181b targets the tumour suppressor
RASSF1 gene in APL. In the present study we also found
that miR-125b is predicted to target CBFB, a transcription
factor that has been involved in haematopiesis. MiR125b controls apoptosis by down-regulating genes
involved in the p53 pathway including BAK1 and
TP53INP1. Chromosomal deletion on subband 5q13.2,
8p23.1 and 16p12.3 were commonly seen in APL patients
(75%) and gain of 2p11.2 and 14q32.33 were found in all
cases.
Conclusion: These results indicate copy number
alterations specifically targeting miRNAs are uncommon
in APL. However, the functional impacts of such regions
need to be extensively investigated in a large number of
109
samples and further validation assay for both tests are
warranted. To the best of our knowledge, the current
study represents the first aCGH and miRNAs profiling
exploration in understanding the pathogenesis of APL in
Malaysia.
Disclosure of Interest: None Declared
P097
EXPRESSION
DATA
IDENTIFIES
DEREGULATED
IMPRINTED GENES IN NASOPHARYNGEAL CARCINOMA
1,*
1
I. M. Alhwij , A. Soosay
1
University Sarawak Malaysia, Kota samarahan,
Malaysia
P098
IDENTIFICATION OF BRCA1 AND BRCA2 MUTATIONS IN
BREAST CANCER IN BRUNEI DARUSSALAM
1
2
F. N. Mohd Jaya , S. N. I. Haji Matusin , D. N. H. Pg Haji
3
2
2
4
Mumin , H. Zainal Abidin , X. Y. Lim , H. M. S. Abdullah ,
5
2,*
D. B. Sukumaran , M. R. W. Haji Abdul Hamid
1
Faculty of Medicine, Imperial College of Science,
Technology and Medicine, Hammersmith Campus,
2
London, United Kingdom, PAPRSB Institute of Health
Sciences, Bandar Seri Begawan, Brunei Darussalam,
3
Department of Oncology, Weatherall Institute of
4
Molecular Medicine, Oxford, United Kingdom, Raja Isteri
5
Pengiran Anak Saleha Hospital, The Brunei Cancer
Centre, Bandar Seri Begawan, Brunei Darussalam
Objectives: Imprinted genes involve in growth and
development, behavioral aspects and metabolism at
both embryonic and adult stages. Loss of imprinting (LOI)
by genetic (e.g. deletion, duplication and UPD) or
epigenetic (e.g. aberrant DNA methylation) mutations
can cause either activation of a silent allele or repression
of the expressed one of an imprinted gene, leading to
serious disease, including cancers. Moreover, almost
one-third of known human imprinted genes are
implicated in various types of human malignancies. In
cancer such as nasopharyngeal carcinoma (NPC) almost
all of tumor suppressor genes associated with NPC are
inactivated by DNA hypermethylation and LOH. This
might be explained by the fact that NPC development is
associated with environmental factors including salted
preserved food and EBV virus infection which enhance
epimutations. For this reason, it is suggested that such an
epigenetic mutations could lead to LOI of imprinted
genes. The study is designed to identify differentially
expressed imprinted genes in undifferentiated NPC,
using previously published expression analysis of data of
microarray and next-generation sequencing (NGS).
Methods: All dysregulated genes in the six microarray
were converted from their input GeneChip IDs (e.g.,
UniGene ID and Affymetrix Probeset ID) to Entrez Gene
ID and gene symbol using g:profiler bioinformatic tool
(http://biit.cs.ut.ee/gprofiler/gconvert.cgi),
and
integrated in one data set. The microarray and NGS data
were matched with the imprintome data set to identify
differentially expressed imprinted genes in NPC.
Results: Twenty-eight known imprinted genes were
found to be differentially expressed (11 from microarray
and 21 from NGS data; 4 genes are overlapped). To our
knowledge, there are 100 bona fide human imprinted
genes to date and 30 genes have been previously shown
to be deregulated in various types of human cancers
including NPC, including14/28 of the identified imprinted
genes in this study.
Conclusion: In conclusion, analysis of expression data
has indicated that human imprinted genes may be
involved in the pathogenesis of NPC.
Objectives: This is an ongoing study on determination of
BRCA1 and BRCA2 mutations in breast cancer cases in
Brunei Darussalam.
Methods: Subjects are patients diagnosed with breast
cancer at The Brunei Cancer Centre from 2010 to 2013.
Statistical analysis is used to compute the data
appropriately. Blood samples are taken from consented
patients for DNA analysis. Genomic DNA isolation, PCR
and DNA sequencing are respectively performed
according to Qiagen, Malone et al.,(2006) and Applied
Biosystems. Data are analysed by sequencing analysis
softwares (Applied Biosystems). Data obtained so far
include 26 cases of breast cancer analysed for BRCA1 and
BRCA2 mutations.
Results: Twenty-six index cases of breast cancer aged 30
to 62 are studied. The ethnicity is made up of Malay,
Chinese and others. The mean age of diagnosis is 47.9
(8.55). Early findings identified 12 genetic variants in
exon 11 of BRCA1 which include a rare 2376delG
mutation (3.9%) and a 2566T>Y variant (3.9%). Ten
common polymorphisms are also identified namely
2612C>T, 2612C>Y, c.2082C>T, c.2082C>Y, c.2311T>C,
c.2311T>Y, c.3113A>G, c.3113A>R, 3548A>G and
3548A>R. Of the polymorphism 19.2% and 42% are
homozygous and heterozygous respectively. Data from
more cases will be presented.
Conclusion: Twenty-six index cases show respective
variants in exon 11 of BRCA1. A rare 2376delG mutation
could be interesting as this mutation was not found in
any other cases unlike the other ten polymorphisms
which are identified in more than one case. 2566T>Y is
also identified in one other case only. The significance of
2376delG in this case is to be elucidated. Further
recruitment of cases is continuing and more
determination of BRCA1 and BRCA2 mutations will be
performed and reported.
References: Malone K E et al;(2006). Cancer Research
(66):8297-8308. Thirthagiri E et al.,(2008). http://breastcancer-research.com/ content/10/4R59. Toh GT et
al.,(2008). www.plosone.com.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
110
P099
IMAGE-BASED HIGH THROUGHPUT SIRNA LIBRARY
SCREENING PLATFORM FOR CANCER TARGET
DISCOVERY
1,*
1
M. Song , S. Yoon
1
Center for advanced bioinformatics and systems
medicine, Dept of Biological Sciences, Sookmyung
Women’s University, Seoul, Korea, Republic Of
P100
AMPLIFICATION OF CHROMOSOME 1Q AND DELETION
OF CHROMOSOME 8Q WAS ASSOCIATED RECURRENCE
IN EARLY STAGE OF HCC AFTER RESECTION- ANALYSIS
OF FFPE SPECIMEN BY AFFYMETRIX ONCOSCAN
PLATFORM
1,*
2
3
M.-C. Yu , Y.-S. Lee , C.-N. Tsai
1
Department of Surgery, Chang Gung Memorial Hospital,
2
Taoyuan, Department of Biotechnology, Ming Chuan
3
University, Graduate Institute of clinical medical
sciences, CHANG-GUNG UNIVERSITY, Taoyuan, Taiwan,
Province of China
Objectives: RNA interference (RNAi) has become a
powerful tool for drug target discovery, and the
systematic loss-of-function screens using RNAi libraries
can now be performed to identify the biological
functions of specific genes or pathways in various
diseases. Cancer target discovery studies on clinically
relevant drug applications and their mode of actions can
be accelerated by integrating multi-level omics data such
as genome, transcriptome, proteome and phosphatome
data together with siRNA screening data.
Methods: We introduce the siRNA screening platform
composed of the image-based assay optimization,
primary screening, data analysis and hit selection criteria
using some studies to investigate novel therapeutic
targets in cancer. We applied two different samples to
siRNA screening. One example is a study using a specific
gene-knockdown cell line. In this study, in order to
identify novel therapeutic targets in STK11-deficient lung
cancer cells, we utilized a large-scale siRNA screening to
identify genes that would sensitize STK11-deficient lung
cancer cells (A549) with or without AMPK. And another
example is a genome-wide siRNA screening using a
sphere-forming (3D) culture system similar to in vivo. 3D
growths of cancer cells in vitro are more reflective of in
situ cancer cell growth than growth in monolayer (2D).
This study is designed to identify genes reducing sphere
size on 3D as compared to 2D.
Results: In the study using a stable knockdown cell line,
the perturbation of several genes exhibited significant
inhibitory effect on the growth of AMPK-knockdown
cells. And we identified that specific hits inducing
inhibition of cell growth with AMPK knockdown were
related to metabolism and signal transduction among
various functional categories. These results highlight the
potential of synthetic lethal siRNA screens with AMPK
inhibitors to define new determinants of potential
therapeutic targets. And in another screening using 3D
culture system, we found specific genes reducing sphere
formation. These hits were related to lipid metabolism.
From these results, we can find new therapeutic targetrelated drugs for inhibition of tumor progression and
metastasis.
Conclusion: This screening platform can be provided as a
valuable tool to find novel therapeutic targets and drugs
for cancer therapy. We now provide this platform service
to academic and industrial organizations.
Disclosure of Interest: None Declared
Objectives: Hepatocellular carcinomas (HCC) is one of
the most common cancers worldwide. It is the third
highest cause of cancer mortality worldwide and is also
ranked in the annual report of the Department of Health
(DOH) in Taiwan as the first cause of cancer mortality in
men and the second in women. Early detection and
coupling appropriate treatments of HCC is still the gold
standard for favored outcome of HCC patients;
nevertheless, a small portion of small HCC (<5 cm)
patients got poor prognosis. Therefore, the aim of this
study was to explore the potential genetic signature for
small HCC as prognostic factors.
Methods: Total 110 paraffin embedded HCC specimen
were enrolled in this study, most of them were stage I
and II HCC. The genomic profile of these HCC was
examined by Affymetrix OncoScan® FFPE Assay Kit.
Genomic gains, losses, and loss-of heterozygosity (LOH)
were associated with clinical data of these HCC patients.
Results: Among these genome aberrations, third-one
LOH, thirty-four chromosomal amplification, and twentynine chromosomal deletions were associated with
recurrence of early stage of HCC (or small HCC).
Significant CNV in HCC samples were chromosomal
amplification in 1q, 6p, 7q, 8q, 11q, 17q, and 20q ;
chromosomal deletion in 1p, 4q, 6q, 8p, 9p, 13q, 16q,
and 17p. However, the most significant differences in
disease-free survival of early stage HCC (or small HCC)
was found to be associated with amplification of
chromosome 4p and 8q and deletion of chromosome 1q
and 8p. (p < 0.05).
Conclusion: Our result indicated that the presence of
aberrations in chromosome 1q, 4p, 8p, and 8q were
associated recurrence of early stage HCC (or small HCC)
after resection.
Disclosure of Interest: None Declared
P101
INFLUENCED OF HTERT MRNA EXPRESSION AND
TELOMERASE ACTIVITY IN MALAYSIAN CML PATIENTS
TREATED WITH IMATINIB MESYLATE
1,*
22
2
1
M. S. watihayati , A. husin , R. hassan , A. ravindran ,
3
1
A. A. baba , S. sulong
1
2
3
Human Genome Center,
Hematology,
internal
medicine, UNIVERSITI SAINS MALAYSIA, KOTA BHARU,
Malaysia
111
Objectives: Since year 2001, Imatinib Mesylate (IM) has
been introduced as a first-line treatment for CML
patients and showed an excellent feedback. Despite
majority of patients gave response to the treatment, up
to one third of patients showed primary resistance or
relapse after an initial response. Resistant to treatment
might be related with telomerase complex as some of
the BCR-ABL independent mechanism involved the
activation of enzyme(s) responsible for cell proliferation
and immortalization. We performed an analysis on
expression of hTERT gene in combination with detection
of telomerase activity in Malaysian CML patients treated
with IM to elucidate the influence of telomerase
component in IM resistance.
Methods: Ninety-two patients undergoing for at least 12
months of IM treatment were recruited from Hospital
USM and other hospitals under Malaysia Ministry of
Health. Patients were divided into group of resistant and
respond to IM. Relative expression levels were
determined by ddCt method with expression levels
normalized to RPL27 gene while telomerase activity was
detected using TRAPEZE® Telomerase Detection Kit.
Results: Our data showed 21% and 19% of CML patients
have less than 1 fold difference of hTERT expression
respectively in resistant and respond group. 79% of
resistant group and 81% of respond group showed more
than 1 fold difference with majority of patients detected
with telomerase activity. A recent study by using sublines
from a Bcr-Abl positive cell line showed a putative
involvement of telomerase in the promotion of imatinib
resistance. However, statistical analysis of our results
showed no significant difference between both groups
which suggested that IM have non-direct causal
relationship to the resistant of the treatment.
the core components of telomerase enzyme. Upregulation of telomerase is in general associated with
tumorigenesis.
This study aimed to detect gene copy number of TERC
gene in K562 cell line using FISH technique.
Methods: In myeloid cell line, K562 and a lymphoma cell
line, RL were analyzed by FISH for TERC gene
amplification using a commercially two-color FISH
probes. Slide preparation from human peripheral blood
(normal control) and cell lines was done using cytospin
and conventional cytogenetics.
Results: The FISH analysis was successfully optimized in
detection of TERC gene amplification in normal sample
and K562 cell line using both methods of sample
preparation. The FISH signal pattern seen in normal
sample indicates the presence of two copies of TERC
gene. Amplification of TERC gene was detected in K562
cells in which there were more than three copies of TERC
gene.
Conclusion: This study showed the increase of TERC gene
copy number in K562 cells using FISH techniques. The
high expression and activity of telomerase found in
leukemic cells and lymphoma may be partially explained
by amplified TERC genes. Application of FISH technique in
detection gene amplification may play an important role
in monitoring and management of cancer patients.
Disclosure of Interest: None Declared
P103
DETECTION
OF
MLH1
AND
MSH2
BY
IMMUNOHISTOCHEMISTRY ASSESSMENT IN NEPALESE
PATIENT
WITH
HEREDITARY
NONPOLYPOSIS
COLORECTAL CANCER
1,*
2
1
N. A. Gandah , M. Bhattarai , B. A. Zilfalil , T. R.
2
Shrestha
1
Department of Pediatric, Universiti Sains Malaysia,
2
Kubang Kerian, Malaysia, Central Department of
Biotechnology, Tribhuvan University, Kathmandu, Nepal
Conclusion: hTERT expression and telomerase activity
might not have a major role in mechanism of IM
resistance in our CML patients. Further study in relation
to this resistance may reveal the mechanism involved in
the regulation of telomerase and the effect of IM on
telomerase activity that has not yet defined.
Disclosure of Interest: None Declared
Objectives: Hereditary nonpolyposis colorectal cancer
(HNPCC), also known as Lynch syndrome is the most
common inherited colon cancer and accounting for 510% of total colon cancer. HNPCC is caused by the
presence of several mutations in MLH1 and MSH2
mismatch repair gene (MMR) which lead to the
production of proteins that can be detected using
commercially available monoclonal antibodies (antiMLH1 and anti-MSH2). This study aims to investigate the
feasibility of these monoclonal antibodies to be used for
the detection of MLH1 and MSH2 protein expression in
formalin-fixed paraffin-embedded (FFPE) tissue samples
of Nepalese patient diagnosed with colorectal cancer.
Methods: Forty three FFPE tissue samples of patients
with colorectal cancer were examined and subjected to
immunohistochemistry (IHC) using two antibodies (antiMLH1 and anti-MSH2). Staining pattern assessment and
semi-quantitative scoring method was performed.
Patient with FFPE sample showing abnormal staining
P102
GENE COPY NUMBER STATUS OF TERC IN CANCER CELL
LINES MODEL WITH SPECIAL EMPHASIS ON
FLUORESCENCE IN SITU HYBRIDIZATION (FISH)
ANALYSIS
1,*
1
2
N. Mohd Adam , S. Sulong , J. Mohamed
1
Human Genome Centre, School of Medical Sciences,
Health Campus, Universiti Sains Malaysia, Kubang Kerian,
2
Kelantan, Faculty of Health Sciences, Universiti
Kebangsaan Malaysia, Kuala Lumpur, Malaysia
Objectives:
Genetic
abnormalities have
been
documented in human cancers such as chromosomal
translocation, gene deletion, gene mutation and gene
amplification. The human telomerase RNA gene (TERC) is
located in the chromosome 3q26 region, which is one of
112
pattern for MLH1 and/or MSH2 was grouped as HNPCC
positive.
Results: 39.5% (n=17) of patients were grouped as
HNPCC positive, where 18.6% (n=8) of the patient
showed abnormal staining pattern for MLH1, 11.6% (n=5)
showed abnormal staining pattern for MSH2 and 9.30%
(n=4) showed abnormal staining pattern for both
antibody. Meanwhile 60.5% (n=26) were found negative
for HNPCC.
Conclusion: Percentage of HNPCC found in this study was
relatively high (> 5-10%), suggesting that the IHC can be
considered as the first line screening for patient with
possible risk of HNPCC. However, further analysis using
genetic screening is required to determine the specificity
and the sensitivity of this method. This study
demonstrates the potential use of IHC in detecting
HNPCC in Nepalese population.
Disclosure of Interest: None Declared
all types of GAs separately. Surprisingly, one combination
of aligner and GAs didn’t perform well for all types of
GAs. As an example, BreakDancer performed well in
terms of sensitivity (0.87) and precision (0.9) with
Novoalign to map deletions, however, it could not
identify inversion with any aligner used.
Conclusion: In essence, this study compared the
performance of 30 pipelines for identification of GAs
which will help the scientific community to design
experiments and choose the best combination of
softwares according to their data. The results suggested
that no single pipeline can identify all types of GAs with
100% accuracy, therefore, a specific combination of
aligner and GAs software should be used to identify each
type of GAs.
References: Li H, Durbin R (2009) Fast and accurate short
read alignment with Burrows-Wheeler transform.
Bioinformatics 25: 1754–1760.
Disclosure of Interest: None Declared
P104
A COMBINATORIAL APPROACH TO CUSTOMIZE
PIPELINE FOR
IDENTIFICATION
OF
GENOMIC
ALTERATIONS USING NEXT GENERATION SEQUENCING
DATA
1,*
1
P. Narang , A. Lynn
1
School of Computational & Integrative Sciences,
Jawaharlal Nehru University, New Delhi, India
P105
TREATMENT-FOCUSED GENETIC TESTING (TFGT). IS IT
TOO SOON FOR MALAYSIA?
1,*
2
3
R. A. Mazlan , K. Barlow-Stewart , M. Gleeson , T. Soo
4
4
1
1
Hwang , Y. Sook Yee , T. Gie Hooi , T. Meow Keong , N.
1
A. Mohd Taib
1
University Malaya Medical Centre, Kuala Lumpur,
2
3
Malaysia, University of Sydney, Sydney, Hunter Family
4
Cancer Service, Newcastle, Australia, Cancer Research
Initiatives Foundation, Kuala Lumpur, Malaysia
Objectives: Cancer, a worldwide disease driven by the
acquisition of genomic alterations (GAs) of various types
i.e. deletions, insertions, inversions and translocations
etc. Over the last few years, various sequencing projects
are generating huge amount of omics data and a number
of softwares are continuously being developed to
identify GAs in cancer genomes with an increase in
accuracy. The identification of GAs is affected by various
sequencing metrics and thus choosing best of existing
softwares for custom data has become difficult for end
users. To this aim, we screened the performance of 30
pipelines comprising five aligners and six GAs callers to
identify GAs in cancer genomes.
Methods: To generate cancer genome, first we created a
diploid genome using human genome assembly (UCSC
build hg19). Next, a total of 2500 GAs comprising 1700
deletions, 500 insertions, 200 balanced translocations
and 100 inversions were incorporated randomly in the
diploid genome using RSVSim. Paired end reads of length
100b with mean fragment size of 400b were generated
using ART and mapped against hg19 using five aligners.
GAs were mapped by six softwares.
Results: Identification of GAs was affected by aligner and
GA software both as varying number of GAs were
identified by each combination. For instance,
Breakdancer identified 1926, 2422, 4416, 2490 and 4439
GAs for BWA, Bowtie, Stampy, Novoalign and Smalt
respectively. Using Novoalign, we identified 2490, 5595,
36, 3448, 872 and 3092 GAs for BreakDancer, CNVnator,
Crest, Delly, Pindel and Meerkat respectively. Next, we
compared the sensitivity and precision of softwares for
Objectives: The knowledge of a woman’s BRCA mutation
status around the time of breast cancer diagnosis can be
used to guide surgical treatment and preventative
options for women. This concept, known as treatmentfocused genetic testing (TFGT), has been previously
reported to be acceptable in a population of Australian
women. However, little is known of the acceptability of
TFGT to women with breast cancer in Malaysia. The
benefits in terms of risk management options and the
potential reduction in incidence and mortality of breast
cancer that may follow the introduction of TFGT in
Malaysia are considerable.
Methods: A qualitative study was performed with 20
Malaysian women who attended the Breast Clinic at
University Malaya Medical Centre (UMMC). A modified
semi-structured interview was used to explore their
hypothetical views on TFGT (as if they were being offered
the testing if it was available in Malaysia). All interviews
were audio-recorded, transcribed and analysed for
concordance by three independent coders. Thematic
analysis was facilitated by NVivo 10.0 software (QSR
International).
Results: Major challenges to implementing TFGT in
Malaysia were identified including limited knowledge of
health and the genetics of breast cancer, cultural
aspects, attitudes towards risk-reducing surgery and the
cost of genetic testing. Most participants had difficulty
understanding the concept of TFGT. Risk reducing
113
mastectomy was perceived to be too extreme, with
significant concerns raised about body image. Social
stigmatization about a breast cancer diagnosis and being
a BRCA mutation carrier, along with the high cost of
genetic testing were other identified barriers.
Participants preferred face-to-face discussion with their
treating doctor rather than written materials, and
information regarding TFGT soon after a diagnosis was
felt to be too much to receive at that time.
Conclusion: The lack of understanding of genetic testing
and poor health literacy are barriers to the introduction
of TFGT in Malaysia. Further education in the role of
genetics in breast health is essential but there is also a
need to consider cultural influences before TFGT
implementation. This study provides important insights
into the challenges to breast healthcare and cancer
genetic counseling in Malaysia.
Disclosure of Interest: None Declared
patients might contribute to the negative mutation
finding. Future study should be directed towards finding
more potential exons by selecting patient in advance
stage in order to yield higher mutation frequency.
Additional clinical and pathogenetic studies are needed
to understand the association between PDGFRA and IMresistant CML.
References: Cools, Jan, et al. "A tyrosine kinase created
by fusion of the PDGFRA and FIP1L1 genes as a
therapeutic target of imatinib in idiopathic
hypereosinophilic syndrome." New England Journal of
Medicine 348.13 (2003): 1201-1214.
Disclosure of Interest: None Declared
P107
TRANSFER RNA SIGNATURES AS PROGNOSTIC MARKERS
FOR BREAST CANCER
1,*
2
3
3
S. Damaraju , P. Krishnan , S. Ghosh , J. Mackey , O.
4
Kovalchuk
1
2
Laboratory Medicine and Pathology, Laboratory
3
Medine and Pathology, Oncology, University of Alberta,
4
Biological Sciences, University of Lethbridge, Edmonton,
Canada
P106
DETECTION OF PDGFRA MUTATIONS AT EXON 12 AND
18 AMONG MALAYSIAN CHRONIC MYELOID LEUKEMIA
PATIENTS TREATED WITH IMATINIB MESYLATE
1,*
2
3
1
R. H. Razali , R. Hassan , A. Husin , S. Sulong
1
2
3
Human Genome Center,
Hematology,
Medical
Department, USM, Kota Bharu, Malaysia
Objectives: Our objective is to identify and validate
biomarkers (tRNAs) of higher sensitivity and specificity to
aid in treatment decisions and improve outcomes
(Overall Survival, OS and Recurrence Free Survival, RFS)
in breast cancer. Small non-coding RNAs are
biomolecules with <200 nt in length such as microRNA,
snoRNA, transfer RNA (tRNAs) etc. While many studies
have focused on miRNAs as prognostic markers for
various cancer types, the role of other small RNAs is now
gaining prominence but literature is scanty on such
characterized prognostic markers in BC. Among the other
small RNA types, tRNAs (73-92nt) are of special interest
as they are involved in protein translation and have only
recently been reported as promising biomarkers for BC.
Methods: Small RNA profiles from 104 breast tumor
tissues were generated from Illumina Genome Analyzer
IIx and analyzed using Partek Genomics Suite 6.6.
Univariate and multivariate Cox proportional hazards
regression model (including permutation test at p<0.1 for
univariate analysis) and risk score analysis was
performed (R program and SAS 9.3) to identify tRNAs
significant for OS and RFS. Patients were dichotomized
into high-risk and low-risk groups based on risk scores
using Receiver Operating Characteristics Curve. Statistical
significance in tests is defined at p<0.05.
Results: A total of 571 tRNAs were captured, of which
only 216 were retained after filtering (minimum 10 read
counts in at least 90% of the samples). Risk scores were
constructed for OS and RFS separately using significant
RNAs identified from permutation test. Multivariate
analysis showed that the risk signature is an independent
prognostic factor for OS (Hazard ratio = 2.782, p =
0.0008) and RFS (Hazard ratio = 1.858, p =0.0197).
Kaplan-Meier plots with log rank p< 0.05 revealed that
Objectives: Imatinib mesylate (IM) resistance is a major
challenge in the treatment of patients with chronic
myeloid leukaemia (CML). BCR-ABL independent
pathway was investigated; the involvement of PDGFRA
mutation as a mechanism of resistance in patients with
Philadelphia positive CML patients treated with IM. The
PDGFRA belongs to the tyrosine kinase Class III; it has
been implicated in cancers. Mutation of PDGFRA leads to
constitutive
activation
causing
spontaneous
proliferation.
Methods: 86 patients from 5 tertiary hospitals around
peninsular Malaysia in different phases of Philadelphiapositive CML who were treated with IM from 2010 until
2013 were evaluated (IM-responsive patients, n= 43; IMresistant patients, n=43). 32 patients had chronic phase;
7 patients had accelerated phase; and 4 patients had
blastic phase. Patients aged from 20 until 73 years were
categorized into a range of age group. PCR amplifications
were performed on exon 12 and exon 18 followed by
screening for mutations by direct sequencing.
Sequencing results were aligned by using BLAST to
compare a query sequence with a reference sequences.
Results: Resistant patients predominate by female and
the median age was 43. 74% of the resistant CML were in
chronic phase. None of the CML patients in this study
exhibit any mutation on the hotspot exons 12 and 18 in
PDGFRA.
Conclusion: Higher frequency of IM resistance notable in
female and mainly in younger age population. The
absence of PDGFRA mutation at exon 12 and 18 may
suggest that other regions of this gene could be involved.
Majority of the study samples were from chronic phase
114
patients belonging to the higher risk group exhibited
poorer OS and RFS.
Conclusion: This is the first study to identify tRNAs as
prognostic markers for BC. Profiling using NGS platform
enables genome wide profiling of all the RNAs unlike
array based technologies. However, the identified
signatures require further validation and biological
insights to ascertain their role as valuable biomarkers for
BC.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P108
PROTEOMIC DYNAMICS IN CERVICAL CANCER TUMORS
FROM THE CANCER CELL LINES
REVEALS AN
IMPORTANT ROLE OF GLUTATHIONE -S-TRANFERASES.
1,*
1
1
S. M. Encarnacion , A. Checa-Rojas , L. Delgadillo-Silva
1
Center for Genomic Sciences, UNIVERSITY OF MEXICO,
Cuernavaca, Mexico
Objectives: The behavior of colorectal cancer without
lymph node metastasis is heterogeneous. The clinical,
pathological, and molecular determinants of subsequent
metastasis and clinical outcome are controversial.
Methods: We retrospectively collected 120 cases of
adenocarcinoma of sigmoid colon without initial lymph
node
metastasis
between
1996
and
2004.
Immunohistochemical method was used to assess p53,
epidermal growth factor receptor, MLH1, and MSH2
status. KRAS mutation was examined by direct
sequencing. The correlation between metastasis
incidence, prognosis, clinical, pathological, and molecular
features was checked by univariate and multivariate
analysis.
Results: There were 33 cases (27.5%) developing
metachronous metastasis. By multivariate analysis, the
incidence of distant metastasis was associated with
female gender (p=0.035), abnormal carcinoembryonic
antigen (CEA) level (p=0.041), and MLH1 overexpression
(p=0.003,). According to Kaplan-Meier estimate and Cox
proportional hazard regression model, cases with female
gender (p=0.048,), abnormal CEA level (p=0.001), and
MLH1 overexpression (p=0.015) had worse prognosis.
The overall survival of cases with MSH2 overexpression
was more favorable (p=0.016).
Conclusion: In patients with stage I-II colon cancer,
female gender, abnormal CEA data, and MLH1
overexpression are indicators for distant metastasis and
poor outcome. MSH2 overexpression is a predictor for
longer overall survival. The above clinical parameters
coupled with 3-tier stratification of MLH1 and MSH2
immunoreactivity could be an alternating approach to
select high-risk patients for adjuvant treatment or
intense surveillance.
Disclosure of Interest: None Declared
P109
THE PROGNOSTIC IMPLICATIONS OF OVER-EXPRESSION
OF MLH1 AND MSH2 FOR STAGE I-II COLON CANCER
PATIENTS
1 2,*
2
S.-F. Huang , S.-C. Huang
1
Institute of Molecular and Genomic Medicine, National
2
Health Research Institutes, Miaoli County, Pathology,
Chang Gung Memorial Hospital, Taoyuan, Taiwan,
Province of China
Objectives: Protein turnover are the most important
metabolic and regulatory mechanisms in establishing
proteome homeostasis, impacting many normal and
pathological processes. Applications in the biomedical
field allow to identify changes in protein expression in
pathological tissues, which help to elucidate the
processes involved in the homeostasis deregulation and
propose strategies to combat diseases such as cancer.
The study of proteome dynamics in cancer is critical since
the change on the deregulation of proteins involved in
the tumorigenic process can be observed. During tumor
development (TD) changes in the proteome of cancer
cells support growth and disrupts the normal tissue
homeostasis of the organism. Measuring changes in the
proteome during TD may help us to elucidate the
interplay between cellular processes and to understand
the early events that lead to its progression.
Methods: Using 2D-PAGE followed by MALDI-TOF-MS we
have identified differentially expressed proteins over
tumor development of CuCa tumors, from inoculated
female nude mice with the cancer cell lines HeLa and
SiHa.
Results: Once we established the proteomic dynamics
over this period of time, we select the GSTP1 and GSTM3
proteins because of their strong expression and
biological function. GST´s are detoxification enzymes and
conjugate the tripeptide glutathione to a wide variety of
endogenous
metabolites,
xenobiotics,
and
chemotherapeutics. We hypothesized that GSTs play a
main role in maintenance and proliferation of CC
tumors. Therefore, first we assessed whether treatment
with morpholine anti-GSTs in vitro. Remarkably, antiGSTs treatment resulted in the cellular decrease in GSTs
sensitive cancer cells in contrast with their control.
Subsequently, we assess morpholino treatment in a
murine model. Our in vitro studies were similar to those
in vivo, with the most dramatic decrease in tumor cells.
Conclusion: Our results indicate that GSTs play an
important role in cell maintenance and survival during
tumor development in cervical cancer.
P110
WHOLE GENOME GENE EXPRESSION PROFILING
IDENTIFIES KEY BIOLOGICAL PATHWAYS DIFFERENTIAL
IN EARLY AND LATE ONSET BREAST CANCER
1,*
1
2
3
S. Malvia , S. A. R. Bagadi , D. Arora , R. Sarin , C.
4
1
Chintamani , S. Saxena
1
Tumor Biology, National Institute of pathology,
2
3
4
Pathology,
Surgery, Apollo Hospital,
Surgery,
Safdarjung hospital, New Delhi, India
115
Objectives: To understand molecular point of view:
pathogenesis & biomarker
Methods: Study includes 40 histologically confirmed
breast cancer patients with age ranging in two groups,
Early aged <40yrs and Late aged >55yrs. Core biopsy
tissue collected from tumor (40) and adjacent normal
area (12) in RNA later was used for gene expression
study using Ilumina Human HT-12vA Expression bead
chip array.
Results: Breast cancer patients in India are about one
decade younger in developing countries than their
counterparts in developed nations. The proportions
of young patients (< 35 years) vary from about 10% in
developed to up to 25% in developing Asian countries,
which carry a poorer prognosis. Changes in gene
expression pattern that reset a cell program from a
normal to a diseased state involve creating a
characteristic signature of gene expression that defines
the cell's unique identity. Identification of Gene
expression signatures in cancer has significant value in
predicting the prognosis and treatment outcome. Here
we identified key pathways getting dysregulated
including mainly Axon Guidance, Cell Cycle, Viral
carcinogenesis, Focal adhesion, Cyotkine Receptor
Interaction, Neuroactive ligand receptor interaction.
We identified various differential gene sets amongst
Early vs Late, having significant role in cancer. Gene
regulator network modelling helped in identifying key
differentially regulated genes amongst TNBC vs TPBC,
different STAGE’s of breast cancer
Conclusion: In this study we identified specific genes
playing role in early aged onset of breast cancer
Disclosure of Interest: None Declared
endometrial cancer have Lynch syndrome. It involves the
alteration of mismatch repair (MMR) genes; MLH1,
MSH2, MSH6 and PMS2. In this study, we analyzed the
correlation between immunohistochemical assessment
(IHC) of MMR protein in Malay cohorts with the germline
mutations in MLH1 and MSH2 genes.
Methods: All patients fulfilled at least one of the
Bethesda criteria in which colorectal cancer was
diagnosed in a patient with the age of less than 50 years
old, and/or have synchronous and/or metachronous
colorectal cancer and with a strong positive family
history. The germline mutations were screened by using
polymerase
chain
reaction
(PCR)
and
immunohistochemistry was performed on paraffin
embedded tumour tissue samples using two antibodies;
MLH1 and MSH2. Germline testing in the cohort was
done regardless of the IHC result.
Results: Three polymorphisms were detected in this
study within the exon 6 of MSH2 gene, c.984C>T
(rs4987189) and , c.965G>A (rs4987188). Out of 22
patients, 5 patients (23%) were identified as a carrier for
a polymorphism within the 5’ UTR of MLH1 gene,c.93G>A (rs1800734). The presence of polymorphism in
these patients were accompanied by the normal protein
expression by immunohistochemistry except for a
patient which demonstrated loss of protein expression in
MLH1 protein in the presence of polymorphisms in the
promoter region, c.-93G>A (rs1800734).
Conclusion: The polymorphism in the promoter region of
MLH1 could be the predominant variation of Malaysian
HNPCC as this findings was concordant with the previous
study of HNPCC in Malaysian cohorts. The other two
polymorphisms have not been reported in Malay cohorts
and remain Variants of Uncertain Significance.
Disclosure of Interest: None Declared
P111
MLH1 AND MSH2 GENE POLYMORPHISMS IN MALAYS
WITH HEREDITARY NONPOLYPOSIS COLORECTAL
CANCER (HNPCC)
1,*
2
W. K. Wan Juhari , K. B. Ahmad Amin Noordin , W. F.
3
4
Wan Abdul Rahman , A. S. Mohd Sidek , M. R. Abu
5
6
6
7
Hassan , J.-P. Plazzer , F. Macrae , A. D. Zakaria , B. A.
1
Zilfalil
1
Department of Paediatric, School of Medical Sciences,
2
Universiti Sains Malaysia, School of Dental Sciences,
3
Universiti Sains Malaysia, Department of Pathology,
School of Medical Sciences, Universiti Sains Malaysia,
4
Surgery Department, Hospital Raja Perempuan Zainab 2,
5
Kota Bharu, Clinical Research Centre, Hospital Sultanah
6
Bahiyah, Alor Setar, Malaysia, Department of Colorectal
Medicine and Genetics, Royal Melbourne Hospital,
7
Melbourne, Australia, Department of Surgery, School of
Medical Sciences, Universiti Sains Malaysia, Kota Bharu,
Malaysia
GENERAL GENETICS & GENOMICS
P112
MRI OF THE BRAIN IN CORNELIA DE LANGE SYNDROME
AND CORRELATION WITH BEHAVIOUR
1,*
2
T. R. Roshan Lal , A. Kline
1
2
Medical Genetics, Johns Hopkins, Medical Genetics,
Harvery Institute of Human Genetics, Greater Baltimore
Medical Centre, Baltimore, United States
Objectives: Neurobehavioural and developmental issues
with a broad range of deficits are prominent features of
Cornelia de Lange syndrome, a disorder due to disruption
of the protein complex cohesin. Some autopsies have
noted hypoplasia of cerebellum, corpus callosum,
septum pellucidum and brainstem, and brain CT or MRIs
have shown enlarged ventricles, thinning of white matter
and brainstem and cerebellar hypoplasia. Findings on
brain MRI should be correlated with phenotypic findings,
and with molecular changes if available, similarly
addressed in other developmental disorders, including
22q11 deletion syndrome and Rett syndrome, and with
behaviour, previously correlated in children with autism
spectrum disorder. This study assesses retrospectively
Objectives: Hereditary nonpolyposis colorectal cancer
syndrome (HNPCC), is an inherited tendency to develop
colorectal, endometrial (uterine) and other cancers.
Although most cancers are not inherited, about 5
percent (%) of people who have colorectal or
116
brain MRIs compared to behaviour at the time of the
scan using the Aberrant Behavior Checklist (ABC), a
validated behavioral assessment tool, and other clinical
features.
Methods: We reviewed MRI scans on 14 individuals with
CdLS age 2 years and higher, collected medical records,
and had parents complete the ABC for behaviour at the
time of MRI
Results: Half of the MRI scans were abnormal, showing
cerebral atrophy, white matter changes and cerebellar
hypoplasia. Acquired findings included pituitary tumors,
several cysts, and one Chiari I malformation. Abnormal
behavioural scores included 64% with inappropriate
speech, 57% with irritability/agitation, 50% with
lethargy/social withdrawal, 43% with hyperactivity/
noncompliance
and
14%
with
stereotypic
behavior/repetitive movements. Lethargy was noted in
the patients with cerebral atrophy. The single patient
with all areas of behaviour involved on the ABC had a
normal brain MRI, and all of the patients with normal
structural MRI’s had abnormal ABC scores. Normal ABC
scores were noted in 57% of the patients with abnormal
MRI changes.
Conclusion: Abnormal behaviors occur in patients with
CdLS with normal brain MRI’s. This supports our longterm anecdotal observations that patients with less
structural malformations have more severe behaviors in
general. Cohesin disruption is known to affect the CNS in
other organisms (e.g. drosophila, mice), and the volume
of normal protein is lower in the CNS than in other
organs. The mechanisms that lead to the abnormal
behaviours may therefore stem not from gross brain
structure but more on a molecular level.
References: Beck B. Epidemiology of Cornelia de Lange’s
syndrome. Acta Paediatr Scand
65:631-638, 1976
Disclosure of Interest: None Declared
sources of haplotypic data - Hapmap and the thousand
genome project (1000g).
Methods: We retrieved 245 Thai individuals with 52,160
SNPs covered all chromosomes from the Pan-Asian SNPs
database. To test yield and accuracy, 5% of the SNPs
were randomly masked. SHAPEIT software was used to
pre-phased the genotypes. Haplotypic data from Chinese
combined with Japanese from the international Hapmap
project phase 2 release #22 or haplotype of combined
samples from the 1000g were separately used as
references in SHAPEIT v2 and IMPUTE2. Imputation was
performed using IMPUTE2 to recover the masked SNPs.
Each chromosome were analyzed separately. We varied
posterior probability to illustrate the optimum threshold.
The imputed SNPs were then verified with the masked
SNPs to access the yield and accuracy of each posterior
probability.
Results: The results shown the inverse correlation in
yield and accuracy. Increasing posterior probability cutoff
(0.5-1) resulted in decreasing yields (92.65-12.27% in
Hapmap panel; 97.41-36.22% in 1000g panel) but
increasing accuracy increased (87.46-99.69% in Hapmap
panel;84.32-99.19% in 1000g panel). In Thai population,
using data from Hapmap as a reference showed better
accuracy (posterior probability = 0.9, accuracy = 97.38%
in Hapmap panel; 94.50% in 1000g panel) but lower yield
than the 1000g data (posterior probability = 0.9, yield =
59.50% in Hapmap panel; 68.77% in 1000g panel). The
cutoff threshold between 0.8-0.9 shown optimal in both
reference panels (accuracy =91.96-97.38%; yield = 59.5077.07%).
Conclusion: We used a simple pipeline process with
publicly available database to investigate the imputation
in Thai population. Hapmap panel gave higher accuracy
but less yield than 1000g panel. The balancing between
the yield and accuracy could be further adjusted by
selecting posterior probability threshold.
Disclosure of Interest: None Declared
P113
GENOTYPE IMPUTATION IN THAI POPULATION.
1 2,*
23
W. Lert-Itthiporn , P. Suriyaphol
1
Molecular Medicine Graduate Program, Faculty of
2
Science,
Division of Bioinformatics and Data
Management for Research, Department of Research and
Development, Faculty of Medicine Siriraj Hospital,
3
Center for Emerging and Neglected Infectious Diseases,
Mahidol University, Bangkok, Thailand
P114
ASSOCIATION BETWEEN ACE GENE VARIATION AND
PHYSICAL FITNESS PARAMETERS OF MALAY FEMALE
ATHLETES AND NON ATHLETES IN MALAYSIA
1,*
1
2
23
X. Li , F. K. Ooi , Z. Bin Alwi , Y. Surini
1
Sport Science Unit, School of Medical Sciences,
2
Department of Paediatric, School of Medical Sciences,
3
Human Genome Center, Universiti Sains Malaysia, kota
bharu, Malaysia
Objectives: Genome-wide association study (GWAS) is a
method to identify single nucleotide polymorphisms
(SNPs) that associated with a disease. Despite large
amount of markers on GWAS genotyping panel, the
number of SNPs are still limited. Some SNPs are also lost
in analysis due to low call rates or poor quality, resulting
in loss of analysis power. Imputation can fulfill the
missing SNPs using haplotypic reference. The choice of
references is not obvious for population that are not
included in reference set such as Thai. Here, we
investigated yield and accuracy relationship using 2
Objectives: Human ACE gene contains a restriction
fragment length polymorphism which consists of the
insertion, I (presence of Alu repeat) and deletion, D
(absence of Alu repeat) of 287 bp of Alu repeat located in
intron 16. In this study, we aimed to investigate the
association between ACE I/D polymorphism and the
physical fitness parameters of Malaysian female athletes
and non athletes.
Methods: The ACE I/D polymorphism was genotyped in
Malay female athletes (n=33) and non athletes (n=33) by
117
using PCR technique. Physical fitness parameters such as
body composition, resting heart rate, blood pressure,
muscular strength and power, flexibility, and lung
function were measured. Hardy-Weinberg equilibrium
with the study groups was tested using chi-square test.
One way analysis of variance (ANOVA) was used for
comparisons of physical fitness abilities between groups
with different genotype.
Results: The frequency of II, ID, DD genotypes among
female athletes was 21.2%, 63.6%, and 15.2%
respectively, while those among female non athletes was
48.5%, 39.4%, and 12.1%, respectively. There was no
statistically significant difference in the distribution of
the genotypes between both groups. Female athletes
with DD genotype showed statistically significant higher
percent body fat than female athletes with ID genotype
(26.74 ± 7.3 % vs. 20.03 ± 4.83 %, p=0.046). Meanwhile,
female athletes with ID genotype showed statistically
significant higher explosive leg power measured via
standing long jump test compared to female athletes
with DD genotype (154.81 ± 16.60 cm vs. 130.00 ± 23.75
cm, p=0.034). In non athletes, no statistically significant
differences in all the measured physical fitness
parameters among II, ID, DD genotypes.
Conclusion: In Malay female athletes, the frequency of
ID was the highest among the genotypes. Malay female
athletes with ID genotype exhibited lower percentage of
body fat and higher value of explosive leg power
compared to female athletes with DD genotype.
Key words: ACE, physical fitness, explosive leg power,
Malay
References: Joyner, M.J. and E.F. Coyle, Endurance
exercise performance: the physiology of champions. J
Physiol, 2008. 586(1): p. 35-44.
Woods, D., et al., Elite swimmers and the D allele of the
ACE I/D polymorphism. Hum Genet, 2001. 108(3): p. 2302
heterozygous SAO. The mother (R2) and a son (R6) were
heterozygous with mutation G701D. The children (R3,
R4, and R5) were clinically affected and diagnosed as
compound heterozygous with mutation G701D/SAO. The
microscopic examination of the R1 shows ovalocytic
stomatocytes. R2 and R6 appear normal. R3, R4 and R5
peripheral blood films were evidence of hypochromic
microcytic with mild haemolytic anemia.
Conclusion: The AE1 gene G701D/SAO mutation has
been reported earlier. The previous finding shows coinheritance of SAO and dRTA does not cause more
severity clinically and hematologically compared to
classical dRTA. This study adds more values to the earlier
findings that compound heterozygous AE1 gene
polymorphism causes autosomal recessive dRTA in SAO.
References:
1. Yenchitsomanus, P.T., et al.,
Autosomal recessive distal renal tubular
acidosis caused by G701D mutation of anion exchanger 1
gene. Am J
Kidney Dis, 2002. 40(1): p. 21-9.
2. Yenchitsomanus, P.T., et al., Anion exchanger 1
mutations associated with distal renal tubular acidosis in
the Thai population. J Hum Genet, 2003. 48(9): p. 451-6.
3. Vasuvattakul, S., et al., Autosomal recessive distal
renal tubular
acidosis associated with Southeast Asian ovalocytosis.
Kidney Int,
1999. 56(5): p. 1674-82.
4. Bruce, L.J et.al., D.L. Cope et. al, G.K. Jones et. al,
A.E. Schofield et. al, M.Burley et. al, S.Povey et. al,
R.J.Unwin et. al, O.Wrong et. al, and M.J.A. Tanner et. al.
Familial Distal Renal Tubular Acidosis Is Associated with
Mutations in the Red Cell Anion Exchanger (Band 3, AE1)
Gene. Clin. Invest, 1995. 100:1693–1707
Corresponding author’s email: fkooi@usm.my
Disclosure of Interest: None Declared
P116
PHARMACOGENETIC ASPECTS OF PLANT AND ANIMAL
PRODUCTS CONSUMPTION
1
2
2,*
O. V. Filiptsova , M. N. Kobets , Y. N. Kobets , I. A.
1
Timoshyna
1
2
Biology Department, Department of Pharmaceutical
Marketing and Management, NATIONAL UNIVERSITY OF
PHARMACY, Kharkiv, Ukraine
Disclosure of Interest: None Declared
P115
TITLE: DRTA AND SAO IN MALAYSIA: CLINICAL AND
MOLECULAR FEATURES
1,*
1
2
Y. Raman , N. M. Yusoff , Z. Alwi
1
Advance Medical And Dental Institute, University Science
2
Malaysia, Pulau Pinang, HUSM, USM, Kelantan,
Malaysia
Objectives: The aim of the present study was to analyze
the available information about potential interactions of
the drugs and products of plant and animal origin, which
are used in human nutrition and as a remedies of the
traditional medicine.
Methods: The paper used desk research, conducted
content analysis.
Results: The paper studies the effect of traditional and
new food and herbs, which are used in traditional
medicine, on the activity of cytochrome P-450 family
enzymes involved in the metabolism of drugs. The use of
grapefruit juice (a potent inhibitor of CYP3A4) during
therapy with drugs that are substrates of cytochrome
Objectives: AE1 mutations phenotypically can be
recessive or dominant dRTA depending on the position of
the amino acid change in the protein. This study provides
description about clinical and molecular features of dRTA
and SAO.
Methods: DNAs were extracted and molecular analysis
was performed by PCR amplification and direct
sequencingin a Malay family with 3 children.
Results: The molecular diagnosis results of this study
shows the father (R1) has been diagnosed as
118
CYP3A4 refers to the examples of the negative nature of
the interaction. Subsequent studies have shown that
grapefruit juice reduced first-pass metabolism of
felodipine by selective post-translational reduction of
the expression of CYP3A4 in the intestinal wall. The
effect on the activity of several cytochrome P450
(CYP1A1, CYP1A2, CYP2E1 and CYP3A11) of six tropical
fruits, namely, banana, mangosteen, guava, pineapple,
mango and papaya was investigated in a recent study in
mice. In vitro study, it was shown that the wild honey
Tualang, found in Malaysia inhibited CYP2C8 activity, at
the level of macroorganism could potentially lead to a
change in the metabolism of drugs, which are
metabolized by this enzyme, in particular, of a potent
opioid buprenorphine.
Conclusion: Presented problems is the basis for a
thorough medical history analysis in the order of the
ways of life (food, bad habits) of the patient in the
appointment of appropriate therapy.
References: Arayne M.S. Grape fruit juice-drug
interactions / M.S. Arayne, N. Sultana, Z. Bibi // Pak J
Pharm Sci. – 2005. – Vol.18, No.4. – P.45-57.
Effect of St John's wort on drug metabolism by induction
of cytochrome P450 3A4 enzyme / J.S. Markowitz, J.L.
Donovan, C.L. DeVane eta al. // JAMA. – 2003. – Vol.290,
No.11. – P.1500-4.
In-vitro inhibitory effect of Tualang honey on cytochrome
P450 2C8 activity / Y.D. Muthiah, C.E. Ong, S.A. Sulaiman
et al. // J Pharm Pharmacol. – 2012. – Vol.64, No.12. –
P.1761-9.
Methods: TALEN pairs targeting exon 2 of TNFR gene
have been designed and constructed using the Golden
Gate cloning approach. The constructions of TALENs
were confirmed by restriction enzyme digestion and
sequence analyses of DNA plasmids. Transfection for the
human liver adenocarcinoma SK-Hep1-endothelial cell
line was optimized using nucleofection technology with
high efficiency (~75%). Each pair of TALENs was in vitro
transcribed into mRNA and transfected into SK-Hep1
cells. TALEN protein expression was detected with antiAcv5 tag using western blot.The expression level of GFP
and surface TNFR1 were measured after 18h, 24h, 48h
and 72 of TALEN mRNA transfection.
Results: The results indicate that introducing TALEN
mRNA does not alter GFP expression from the control
plasmid, and does not alter surface expression of TNFR1
within the time-course of transfection. Genetics
examination of TALEN target sites shows that TALEN
pairs unable to induce mutation on target sites, this
could be because TALEN found to be sensitive to DNA
methylation and single nucleotide polymorphisms
(SNPs).
Conclusion: Sensitivity of TALENs to DNA methylation
and SNPs may drastically restrict the range of their
applications, suggesting using the newest alternative
technology for genome engineering known as CRISPR
(Cas-based RNA-guided DNA endonucleases).
Disclosure of Interest: None Declared
P118
ACCURATE VARIANT DETECTION USING MOLECULAR
BARCODES
1,*
2
2
2
C. Y. Lee , H. Johansson , J. Chi , K. Zobeck , L.
2
2
3
Forsmark , M. Isaksson , H. Hogrefe
1
AGILENT TECHNOLOGIES, SIngapore, Singapore,
2
3
AGILENT TECHNOLOGIES, Santa Clara, AGILENT
TECHNOLOGIES, La Jolla, United States
Disclosure of Interest: None Declared
GENOMICS TECHNOLOGIES
P117
GENERATION
AND
CHARACTERISATION
OF
TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASES
(TALENS) TARGETING TNFR1 GENOME EDITING
1,*
1
1
1
A. Alotiby , L. Fairclough , I. Todd , P. Tighe
1
Immunology, Nottingham university, Life science school,
Nottingham,UK, Nottingham, United Kingdom
Objectives: HaloPlex is an amplicon based method for
targeted sequencing. The protocol utilizes specificity
gained
from
restriction
enzyme
recognition,
hybridization and DNA ligation to capture molecules
originating from the target region to be sequenced. The
target region is fully customizable from a single gene up
to several thousand discrete regions. Amplicon based
methods for multiplex target enrichment are, in general,
convenient methods for capturing a wide range of target
region sizes. However, in contrast to hybridization
capture methods where random shearing is deployed, it
is not possible for Haloplex or other amplicon based
techniques to use the start point of paired end reads to
identify duplicate reads. Duplicate read information can
be useful for improving base calling accuracy and to
monitor sampling to determine the degree of confidence
to assign calls at different presumed allelic fractions. For
somatic variants, which are generally present at a lower
than 50% allelic fraction, it is even more advantageous to
know how many molecules have been sampled when
calling a particular base.
Objectives: TALENs are important new tools for the next
generation of genome engineering. They are created by
fusion of a transcription activator-like effectors DNA
binding domain to a DNA cleavage domain, FokI
nuclease. TALENs bind and cleave the target site in pairs,
which leads to FokI catalysed double-strand breaks that
stimulate error-prone non-homologous end joining.
Customized TALENs can be used to generate
physiologically relevant human cell line models of genetic
diseases by altering the endogenous alleles. This study
aims to generate and characterize TALENs that targets
TNF receptor 1 (TNFR1) gene and produce human cell
lines expressing TRAPS-associated TNFR1 mutations.
TRAPS (TNF receptor associated periodic syndrome) is an
autoinflammatory disease caused by mutations in the
TNFR1 gene.
119
Methods: To enable identification of duplicate reads
from libraries prepared with Haloplex, we have added a
molecular barcode to the introduced primer cassette.
The molecular barcode consists of ten degenerate bases
allowing for over one million unique sequences to be
present for tagging of molecules.
Results: Using information derived from the molecular
barcode sequences we demonstrate observation of
variants down to 5% allelic fraction in multiple molecules
tagged with different molecular barcodes.
Conclusion: The new protocol has, besides the
introduction of molecular barcodes, been optimized in a
few additional aspects. Due to improved reagent
formulations and streamlining of workflow, complete
target enrichment can now be completed in less than 5
hours. Using 50 ng input we demonstrate >85%
specificity and above 90% of target regions being
covered at >10% of average depth.
Disclosure of Interest: None Declared
albus. Our annotation engine also identified 78 antibiotic
resistance genes out of which 18 were present in all the
samples. Further in-depth analysis revealed six out of 78
pathogens harbored at least one of the 18 common
antibiotic resistant genes.
Conclusion: To the best of our knowledge, this is the first
shotgun metagenome dataset of paper currency notes
and provides a conceptual framework for future
applications including bio-surveillance of exchangeable
fomites for infectious agents.
Disclosure of Interest: None Declared
P120
DIFFERENTIAL UPREGULATION OF THE HYPOTHETICAL
TRANSMEMBRANE PROTEIN 66 (TMEM66) IN BAHRAINI
MULTIPLE SCLEROSIS PATIENTS WITH POTENTIAL
INFLAMMATORY RESPONSE
1,*
1
1
S. M. Taha , M. O. Bakhiet , M. J. Aljishi
1
Molecular Medicine, ARABIAN GULF UNIVERSITY,
Manama, Bahrain
P119
SHOTGUN
METAGENOME
SEQUENCING
FOR
SCREENING OF CURRENCY NOTES FOR MICROBIAL
PATHOGENS AND ANTIBIOTIC RESISTANCE GENES
1,*
1
1
1
S. Jalali , S. Kohli , C. Latka , S. Bhatia , S. K. Vellarikal
1
1
1
1
, S. Sivasubbu , V. Scaria , S. Ramachandran
1
CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE
BIOLOGY (CSIR-IGIB), DELHI, India
Objectives: To understand the molecular mechanisms
involved in the disease process, the present work utilized
the microarray technology to study differentially
expressed novel genes in MS Bahraini patients compared
to healthy matched subjects.
Methods: The microarray technology was utilized to
study differentially expressed novel genes in MS Bahraini
patients compared to healthy. The expression of the
upregulated genes were confirmed by real time PCR.The
TMEM66 gene was cloned, purified and tested for
immunologic activity on human healthy peripheral blood
mononuclear cells (PBMCs). cDNA synthesis and Roche
Real-Time PCR.
Objectives: Fomites are a well-known source of microbial
infections and previous studies have extensively
characterized the resident microbiome of a variety of
fomites. Paper currency notes are one of the most
commonly exchanged objects and its potential to
transmit pathogenic organisms has been well recognized.
Approaches to identify the microbiome associated with
paper currency notes have been largely limited to culture
dependent approaches, though recently the taxonomic
classification of the resident microbiome of paper
currency notes based on 16S ribosomal RNA has been
attempted. Shotgun metagenome sequencing approach
provides an additional advantage to traditional 16S rRNA
based approaches as it provides insights into the gene
repertoire, in addition to taxonomic classification, thus
providing a better overview of the functional potential of
the metagenome.
Methods: We used shotgun metagenome coupled with a
comprehensive annotation engine to characterize the
pathogenome and antibiotic resistome of currency
notes.
Results: Analysis of the data revealed presence of both
eukaryotic and prokaryotic genera on currency notes.
The taxonomic distribution at kingdom level revealed
contigs mapping to Eukaryota (70%), Bacteria (9%),
Viruses (1%) and Archaea (<1%). We identified 78
pathogens
including
Staphylococcus
aureus,
Corynebacterium glutamicum, Enterococcus faecalis, and
75 cellulose degrading organisms including Acidothermus
cellulolyticus, Cellulomonas flavigena, Ruminococcus
Results: The results depicted that 493 transcripts were
differentially expressed out of about 50,000 transcripts;
among these, 230 transcripts were upregulated while
263 were downregulated, in MS patients compared to
the healthy controls, as Fold Change (FC) was 1.5p-Value
of <0.05.. A few genes were found to be of unknown
function such as the transmembrane protein 66
(TMEM66), which exhibited a 3 times more expression in
the Bahraini MS patients compared to healthy
subjects. The TMEM66 protein induced significant
proliferation (p<0.05) and augmented induction of the
proinflammatory cytokines IL-6, IFN-g, TNF-a and the
chemokines CCL5 and CCR5, MIP-1a, MIP-1b in a kinetic
manner, but not the anti-inflammatory cytokine IL-4 or
IL-2 which were not expressed.
Conclusion: Thus, finding a unique gene that is
preferentially
expressed
in
a
certain
population,demonstrating a potential immune activity by
the protein encoded in this gene is the first step to
develop targeted diagnostics and therapeutic
approaches to achieve more personalized management.
TMEM66 might be a possible candidate . Further analysis
are required to study the expression of this protein in MS
patients from Middle East and Gulf region during
120
different stages of the disease before considering it as a
relevant diagnostic, therapeutic and follow up
it's biomarker.
References: Aljumah, M., Alroughani, R., Alsharoqi, I.,
Bohlega, S. A., Dahdaleh, M., Deleu, D., Daif, A. (2013).
Future of management of multiple sclerosis in the middle
East: a consensus view from specialists in ten countries.
Mult
Scler
Int,
2013,
952321.
Alroughani, R. A., & Al-Jumah, M. A. (2014). The need for
a multiple sclerosis registry in the Gulf Region.
Neurosciences
(Riyadh),
19(2),
85-86.
Ascherio, A. (2013). Environmental factors in multiple
sclerosis. Expert Rev Neurother, 13(12)
Disclosure of Interest: None Declared
increased response to oxidative stress pathway as well as
LT-TRF.
Conclusion: In conclusion, LT-TRF modulated more genes
expression compared to ST-TRF and may showed more
beneficial effects in preventing age-related deterioration
as it can increased protection to oxidative stress, induced
cell proliferation and apoptosis, while suppressed
cholesterol and lipid biosynthesis.
Disclosure of Interest: None Declared
P122
MULTIPLEX
LIGATION-DEPENDENT
PROBE
AMPLIFICATION (MLPA) FOR DETECTION AND
QUANTIFICATION
OF
MITOCHONDRIAL
DNA
MUTATIONS IN PATIENTS WITH MITOCHONDRIAL
DISORDERS
P121
SHORT- AND LONG-TERM TOCOTRIENOL RICH
FRACTION (TRF) SUPPLEMENTATION MODULATES GENE
EXPRESSION DURING AGEING IN MICE
1,*
1
S. M. Abdul Ghani , W. Z. Wan Ngah , N. A. Abdul
2
Hamid
1
Biochemistry, Universiti Kebangsaan Malaysia, Cheras,
2
Basic Medical Sciences, Cyberjaya University College of
Medical Sciences (CUCMS), Selangor, Malaysia
1,*
1
1
2
Y. Yakob , H. Ruslan , N. A. Abd Azize , C. Yew Sing , N.
3
Lock Hock
1
Unit of Molecular Diagnostics & Protein, Specialised
Diagnostics Centre, Institute for Medical Research,
2
3
Prince Court Medical Centre, Genetic Department,
Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
Objectives:
Multiplex
Ligation-dependent
Probe
Amplification (MLPA) is a new molecular genetics
method enabling multiplex detection and quantification
of its changes. In this study we evaluated a usefulness of
MLPA by comparing with DNA sequencing using samples
from patient with known mitochondrial disorders,
looking at mitochondrial DNA (mtDNA) mutations and
deletions. To the best of our knowledge there is no
publication focusing on the diagnostics value of MLPA in
detecting mtDNA mutations in patients.
Methods: We studied blood, muscle and urine samples
from 22 patients with known mitochondrial mutations
such as in MELAS (n=16), MERRF (n=2), NARP/Leigh
Syndrome (n=3) and KSS (n=1) which were previously
referred to our laboratory for molecular investigations.
Fifteen DNA from blood and urine of normal individuals
were used as controls. DNA were extracted using
standard laboratory protocol. PCR amplifications were
carried out in triplicate followed by MLPA. Mutation
analysis were performed by GeneMapper and Coffalyser
analysis software.
Results: The MLPA method detected reliably all
previously identified single point mutations (m.3243A>G,
m.8344A>G, m.8993T>C and m.11788G>A) in all cases.
2
There was a good correlation (r =0.96) between level of
heteroplasmy (i.e co-existence of normal and mutant
allele) for the m.3243A>G mutation determined by MLPA
and direct sequencing method. The degree of
heteroplasmy detected for m.3243A>G mutation was
from as low as 6%, which are usually not easily
recognized by RFLP and sequencing, therefore making
MLPA one of the sensitive method. Approximately 6.5kb
deletion of mtDNA encompassing the major arc of
mtDNA was detected in the urothelial cells of one patient
with KSS.
Objectives: Ageing is characterized by progressive
functional decline of multiple organs and tissues reserve
over time. Nutrigenomic studies have shown the
nutrient-gene interaction can promote beneficial effects
in preventing age-related deterioration. Tocotrienol-rich
fraction (TRF), the powerful lipophilic antioxidant
compound of vitamin E has been reported to modulate
enzymes and several transcription factors which are
closely linked to its potential as anticarcinogenic,
antiproliferative, pro-apoptotic and anti-inflammatory
activities in numerous studies using cancer cells and
animal models. Therefore, the aim of this study is to
determine the effect of short- (ST-TRF) and long-term
TRF (LT-TRF) supplementation on liver gene expression
during ageing in mice.
Methods: In this study, young (5 month-old) male
C57BL/6 mice were randomly assigned to receive either
RBDPO (control group) or 30 mg/kg TRF (study group)
supplementation daily. ST-TRF was treated for 2 months
while LT-TRF was treated for 13.5 months. Total RNA in
the liver tissue was extracted, hybridized and injected
into Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays.
Results: Using a T-test unpaired at 1.2-fold cut-off and
false discovery rate <0.05, our results indicated that the
expression of 63 genes (34 overexpressed, 29 genes
underexpressed) and 73 genes (35 overexpressed, 38
underexpressed) was altered by ST- and LT-TRF,
respectively. Based on functional classification, LT-TRF
increased response to oxidative stress (Hmox2, Txnip),
cell proliferation (Dbp) and apoptosis (Zbtb16) pathways,
whereas cholesterol (Hao1) and lipid (Elovl3)
biosynthetic process were down-regulated. Meanwhile,
just 2 months TRF (ST-TRF) supplementation was able to
121
Conclusion: In conclusion, MLPA analysis is a useful
diagnostic tool and may support genotype-phenotype
correlations in mitochondrial disorders particularly in
determining the heteroplasmy. It is important because if
it present in mother, it means she can be a carrier and
her children can be affected as well. Furthermore with
the ability to detect common point mutations in one
assay, it is feasible to use MLPA for molecular diagnosis
of patients with suspected mitochondrial disorders.
Disclosure of Interest: None Declared
Disclosure of Interest: None Declared
P124
GENOME-WIDE MAP OF POTENTIAL LONG NONCODING
RNA MEDIATED DNA:DNA:RNA TRIPLEXES IN THE
HUMAN GENOME
1,*
1
S. Jalali , V. Scaria
1
CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE
BIOLOGY (CSIR-IGIB), DELHI, India
Objectives: Long noncoding RNAs are a recently
discovered class of noncoding functional RNAs. Though
only a handful of the lncRNAs have been extensively
characterized, they are largely thought to modulate
regulation through interacting with other biomolecules
in the cell: DNA, RNA and protein. Though the lncRNAmiRNA and lncRNA-protein interactions have been
studied to great detail by our group and others, the
interaction of lncRNAs with DNA has not been studied
extensively. In the present study, we explore whether
lncRNAs could modulate genomic regulation by
interacting with DNA through the formation of highly
stable DNA:DNA:RNA triplexes.
Methods: We employed a computational approach to
screen the human genome for potential triplexes
mediated through lncRNAs. We screened for 23,898
transcripts annotated as lncRNAs in the recent GENCODE
annotation (v19) across the human genome (hg19) for
potential triplex forming sequence stretches (PTS). The
PTS frequencies were compared across 5 major features,
namely 5’UTR, CDS, 3’UTR, Introns, Promoter and 1000
bases downstream of the transcription termination sites.
Additionally, annotation of these regions was done by
mapping of experimental regulatory regions, different
classes of repeat regions and transcription factors (TF)
derived from UCSC Table Browser.
Results: We identified a total of 20,04,034 PTS sites in
the human genome. The sites were found to be enriched
in promoters and introns. Additional analysis of the
association of PTS with core promoter elements
including CpG islands, TF binding sites and enhancers
revealed a systematic paucity of PTS in all of these
regulatory regions, except for TF binding sites. Evaluation
of association of PTS with experimental available
datasets for TF binding sites revealed a total of 25 TFs
showed significant association with PTS in the genome in
majority of the cell lines analyzed. Analysis also
suggested that PTS are largely associated with repeats,
especially simple repeats.
Conclusion: Our study provides the first evidence
supporting that the lncRNAs are capable of acting as a
Triplex forming oligonucleotide (TFO) in DNA:DNA:RNA
triplexes. The enrichment of PTS in the promoters of
genes suggests its role in gene regulation, consistent
with the known role of some lncRNAs in transcriptional
and epigenetic regulation of genes. To the best of our
knowledge, this is the first comprehensive genome-wide
map of PTS mediated through lncRNAs.
Disclosure of Interest: None Declared
NON-CODING RNA
P123
TOCOTRIENOL-RICH
FRACTION
PROMOTES
DIFFERENTIATION OF HUMAN SKELETAL MUSCLE
MYOBLAST
1,*
1
A. M. Binti Razak , N. Binti Abdul Karim , S. Binti
1
Makpol
1
Biochemistry, Universiti Kebangsaan Malaysia, Cheras,
Malaysia
Objectives: This study aimed to elucidate the role of TRF
in promoting myoblast differentiation.
Methods: Human skeletal muscle myoblast (HSMM)
were cultured until reached population doubling of 14
(young) and 21 (senescent). The cells were treated with
50 ▫▫g/mL TRF for 24 hours before and after
differentiation induction. Effects of TRF on myoblast
differentiation were quantified as fusion index and
myotubes surface areas with fluorescent imaging and
MicroRNAs with myoblast gene expressions were
calculated. All parameters were recorded over a period
of 24 hours (day 1), 56 hours (day 3) and 104 hours (day
5).
Results: Ageing causes a significant reduction in
differentiation rate as observed in reduction of fusion
index and myotubes surface areas in senescent group
(p<0.05). However, no changes on surface area of
senescent myotubes were observed at day 1. Treatment
with TRF significantly increased differentiation with
increment in fusion index and myotubes surface areas at
day 1, day 3 and day 5. However, in young group treated
with TRF, no significant difference was observed on
myotubes surface area at day 5. Senescent groups
showed increased expression of miR-133b, miR-206, miR486, MYOD, MYOG and Myf5 while reducing target genes
of miR-206 and miR-486 which were PTEN and Pax7.
Meanwhile, target of miR-133b, IGF1R was increased
during early differentiation state and reduced at late
differentiation. In young myoblast, TRF promoted
differentiation by modulated the expression of miR-133b
and miR-206. Treatment showed reduction in their
targets while enhancing the expressions of MYOD, MYOG
and Myf5.
Conclusion: TRF promotes myoblast differentiation by
increasing the fusion index, myotubes surface areas as
well as myogenic transcriptional factors which were
associated with miR-133b, miR-206 and miR-486.
122
P125
DISTINCT AND MODULAR ORGANIZATION OF PROTEIN
INTERACTING SITES IN LONG NON-CODING RNAS
1,*
1
S. Jalali , V. Scaria
1
GN Ramachandran Knowledge Center for Genome
Informatics, CSIR INSTITUTE OF GENOMICS AND
INTEGRATIVE BIOLOGY (CSIR-IGIB), DELHI, India
Large-scale analyses of full-length cDNA sequences have
led to the identification of a diverse class of noncoding
RNAs known as long noncoding RNAs across a wide
variety of organisms including humans. LncRNAs are
emerging as key regulators of the epigenome, influencing
transcriptional networks and multicellular development.
Though the catalogue of the zebrafish lncRNAs has been
generated, the spatiotemporal expression features of
these lncRNAs in zebrafish are yet to be explored.
Therefore, we aim at constructing a spatio-temporal map
of lncRNAs for the embryonic development stages and
tissues in zebrafish using genome-wide datasets from a
number of sources available in public domain.
Methods: We have attempted to construct a spatiotemporal map of lncRNAs by integrating publically
available RNA seq data encompassing different
development stages as well as few adult tissues in
zebrafish. We mapped the RNA seq data using Tophat
followed by transcript annotation by Cufflinks.
Thereafter annotation of lncRNAs was performed using
stringent parameters of nucleotide length of more than
200 and ORF length of less than 30 amino acids. Further
we assessed the coding potential using Coding Potential
Calculator (CPC) and the transcripts with negative CPC
scores were retained to be annotated as predictive
lncRNAs. The differential expression of lncRNAs was
analyzed using another module Cuffdiff from the
Cufflinks package.
Results: We identified a putative novel set of 307 long
non coding RNAs having dynamic expression across 5
tissues and 11 developmental timepoints thus providing
an evidence of lncRNA involved in early development as
well as organogenesis of zebrafish. Comparative analysis
revealed tissue as well as stage specific expression of
these putative lncRNAs. A correlative expression pattern
analysis between protein coding and lncRNAs gave a
glimpse of the regulatory role of these non coding
transcripts in embryonic development and organ
formation.
Conclusion: We provide a large scale integrated
expression map of 45,120 transcripts including 2,266
known and 307 novel lncRNAs in zebrafish for the
embryonic development stages and tissues which would
provide an in-depth knowledge to further investigate the
role of lncRNAs in regulation of gene expression in
various biological processes as well as pathological
conditions.
Disclosure of Interest: None Declared
Objectives: The application of tiling microarrays and
deep sequencing methods on the human genome have
discovered a class of long noncoding RNA (lncRNA)
transcripts which are >200 nucleotides in length and
have no ORFs coding more than 30 amino acids. These
long non-coding RNAs are known to be involved in
regulatory roles via interactions with DNA, RNA, proteins
and other biomolecules in the cell. Experimental
methodologies like CLIP-seq allow us to gain insights into
the target sites of RNA binding proteins (RBP) at genome
scale. Presently lncRNA-protein interactions are
understood for only a few candidates like HOTAIR, Anril
and Xist. In this study, we aim to perform transcriptome
wide characterization of lncRNA-protein interactions.
Methods: From 29 datasets of CLIP-seq for RNA binding
protein available publicly, we determined protein-RNA
interaction sites by processing them through a
standardized computational pipeline that uses peak
calling which indicate protein-RNA interaction sites.
Results: Our present analysis reveals a set of interesting
characteristics of protein-RNA interaction in the context
of lncRNAs: 1) the density of interaction sites of these
proteins are significantly higher for lncRNAs compared to
protein coding transcripts; 2) substantial differences in
frequency of RNA-protein interaction sites across
different subclasses of lncRNAs; 3) significant overlaps of
interaction sites for different RNA binding protein; and 4)
positional preference for the binding sites across the
transcript length, suggesting a modular organization of
these elements in lncRNAs.
Conclusion: We have comprehensively analyzed RNA
binding protein interaction sites in lncRNAs. We identify
a previously uncharacterized set of RNA-protein
interactions modulated through lncRNAs. We
additionally characterize potential functional domains in
lncRNAs, which are also characterized by a paucity of
genomic variations suggesting they are under selection.
This study is the first comprehensive analysis of proteininteraction sites in lncRNAs.
Disclosure of Interest: None Declared
P126
A SPATIO-TEMPORAL MAP OF LONG NONCODING RNAS
IN ZEBRAFISH DEVELOPMENT
1,*
1
1
1
S. Kapoor , V. E. Leonard , A. Sivadas , S. Sivasubbu ,
1
1
C. Sachidanandan , V. Scaria
1
CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE
BIOLOGY (CSIR-IGIB), DELHI, India
PERSONALISED MEDICINE
P127
NOVEL AND RARE FUNCTIONAL GENOMIC VARIANTS IN
MULTIPLE AUTOIMMUNE SYNDROME
1,*
2
2
H. R. Patel , A. Johar , M. Arcos-Burgos
1
Genome Discovery Unity, John Curtin School of Medical
2
Research, Genome Biology Department, John Curtin
School of Medical Research, Australian National
University, Acton, Australia
Objectives: Noncoding RNAs play a key role in regulating
the gene expression for various biological processes.
123
Population Health Sciences, University College London,
3
Imperial Weight Centre, Imperial College Healthcare
NHS Trust, St. Mary’s Hospital, Imperial College London,
4
London, Diabetes Complications Research Centre,
Conway Institute, School of Medicine and Medical
5
Science, University College Dublin, Ireland, Clinical Trial
Service Unit and Epidemiological Studies Unit, University
of Oxford, Oxford, United Kingdom
Objectives: Exomic rare genome variants are associated
to complex traits. They can be successfully identified by
whole exome sequencing (WES) of extreme phenotypes.
The multiple autoimmune syndrome (MAS), which
represents the best example of polyautoimmunity, is the
most conspicuous extreme autoimmune phenotype.
Methods: The DNA of eight patients affected by MAS
along with 38 unaffected individuals, and four patients
affected by Sjogren’s syndrome were subject to WES.
Filters to identify novel and rare functional (pathogenicdeleterious)
homozygous
and/or
compound
heterozygous variants in these MAS patients were
applied. Bioinformatics tools such as the Human Gene
Connectome (HGC) as well as pathway and network
analysis were applied to test overrepresentation of genes
harbouring these variants in critical pathways-networks
involved in autoimmunity.
Results: Ten novel and rare functional variants were
identified harboured in MACF1, KIAA0754, DUSP12, ICA1,
CELA1, LRP1/STAT6, GRIN3B, ANKLE1, TMEM161A, and
FKRP. Intriguingly, the LRP1/STAT6 novel mutation is
homozygous in one MAS affected patient (Autoimmune
Thyroid disease (AITD), Rheumatoid Arthritis (RA), and
Sjogren’s syndrome (SS)), and heterozygous in other MAS
patient (AITD, SS, and vitiligo). LRP1/STAT6 are involved
in extracellular and intracellular anti-inflammatory
pathways that play key roles in maintaining the
homeostasis of the immune system. Further, Networks,
pathways, and interaction analyses showed that LRP1 is
functionally related to the HLA-B and IL10 genes and it
has a substantial impact within immunological pathways
and/or reaction to bacterial and other foreign proteins
(phagocytosis, regulation of phospholipase A2 activity,
negative regulation of apoptosis and response to
lipopolysaccharides). Further, ICA1 and STAT6 were also
closely related to AIRE and IRF5, two very well known
autoimmunity genes.
Conclusion: We have identified novel and rare exonic
mutations that may account for the MAS phenotype.
Among those, the LRP1/STAT6 novel mutation has the
strongest case for being categorised as potentially
causative of MAS given the presence of intriguing
patterns of functional interaction with other major genes
shaping autoimmunity.
Disclosure of Interest: None Declared
Objectives: A 593 kb deletion of 16p11.2 (Chr16:29.5–
30.1Mb, build hg19) results in an increased risk of
obesity as well as being an underlying causative mutation
in 1% cases of autism. We have estimated the prevalence
of this deletion in morbidly obese UK subjects seeking
surgical treatment. Obesity surgery is not considered
appropriate for some cases of inherited obesity, we
therefore also examined weight loss trajectories after
gastric bypass to assess whether obesity surgery is an
effective treatment for carriers of this deletion.
Methods: A real-time PCR copy number assay for the
TAOK2 gene (QIAGEN) within the deletion was used to
screen participants in the “Personalised Medicine for
Morbid Obesity” cohort (UKCRN ID:12440). The
calibrator genome method was used to calculate the
predicted TAOK2 copy number in test samples.
Confirmation of the predicted deletion was carried out in
one subject by whole exome sequencing. For those
carriers who had already undergone laparoscopic Rouxen-Y gastric bypass (LRNYGB), weight loss data at 12 and
24 months post-surgery were analysed and compared to
data from non-carriers.
Results: The 16p11.2 deletion was identified in 4 of 751
bariatric surgery patients (0.5%). The mean body mass
index (BMI) of deletion carriers was 48.50 compared to
47.81 in 747 non-carriers. None of the carriers had any
reported learning disability. Three deletion carriers had
undergone LRNYGB and at 12-month follow-up had lost
an average 30% of their initial body weight compared to
patients without 16p11.2 deletion who lost an average of
29% of initial body weight.
Conclusion: The prevalence of this deletion is similar to
that reported in morbidly obese subjects from European
1
general population cohorts (0.7%) . Diagnosis remains
important, however, because of the increased risk of
obesity and autism in family members: genetic
counselling should be offered. Our data so far indicate
that LRNYGB is an appropriate therapeutic approach for
patients with this deletion.
References: 1. Walters RG et al. (2010). Nature 463, 671–
67510.1038/nature0872
Disclosure of Interest: None Declared
P128
PREVALENCE OF 16P11.2 DELETION CARRIERS AMONG
UK OBESITY SURGERY PATIENTS AND IMPLICATIONS
FOR THEIR WEIGHT LOSS OUTCOMES
1,*
1
1
N. H. Ramzi , N. A. Nor Hashim , S. I. M. Alsters , J. L.
2
1
1
3
Buxton , A. M. Yiorkas , J. Murphy , H. S. Chahal , S.
3
3
4
Purkayastha , A. R. Ahmed , C. W. le Roux , R. G.
5
1
Walters , A. I. F. Blakemore
1
Section of Investigative Medicine, Division of Diabetes,
Endocrinology and Metabolism, Faculty of Medicine,
2
Imperial College London, Centre for Cardiovascular
Genetics, Institute of Cardiovascular Science, Faculty of
P129
PREDICTING INSULIN USE IN CHINESE PATIENTS WITH
TYPE 2 DIABETES USING CLINICAL AND GENETIC
INFORMATION
1,*
1
1
1
1
R. C. W. Ma , C. Tam , G. Jiang , Y. Wang , H. M. Lee ,
1
1
1
C. Lim , W. Y. So , J. C. Chan
124
1
1,*
Department of Medicine and Therapeutics, The Chinese
University of Hong Kong, Hong Kong, Hong Kong
1
2
1
C.-P. Fang , S.-C. Wang , H.-H. Tsou , Y.-S. Chang , I.-K.
34
1
1
14
Ho , H.-W. Kuo , S.-W. Liu , Y.-L. Liu
1
2
Center for Neuropsychiatric Research, Division of
Biostatistics and Bioinformatics, Institute of Population
Health Sciences, National Health Research Institutes,
3
Miaoli County, Center for Drug Abuse and Addiction,
4
China Medical University Hospital, Graduate Institute of
Clinical Medical Science, China Medical University,
Taichung, Taiwan, Province of China
Objectives: Type 2 diabetes is a heterogeneous disease
with insulin resistance and progressive beta-cell
dysfunction being the key pathophysiological defects.
Patients who do not achieve adequate glucose control on
oral medications should be commenced on insulin
therapy, though there is often a delay in initiating insulin.
The majority of recently discovered genetic variants
associated with type 2 diabetes appear to affect beta-cell
function. Our study aims to identify clinical and genetic
predictors of progressive beta-cell failure and need for
insulin therapy among Chinese patients with type 2
diabetes.
Methods: We followed up the clinical course for patients
with type 2 diabetes in the Hong Kong Diabetes Registry.
We defined oral drug failure as commencement of at
least 6 months of continuous insulin use based on drug
prescription information. We compared the baseline
clinical variables for patients who required insulin during
follow-up with subjects who remained on oral drug
therapy. Genotyping for the TCF7L2 rs7903146 variant
for type 2 diabetes was performed using Centaurus
(Nanogen) platform. Independent predictors for insulin
use were examined using Cox-regression analysis.
Results: During follow-up, 1463 out of 4738 subjects
(30.9%) were started on insulin therapy. Independent
clinical predictors for insulin use include: younger age at
diagnosis, increased HbA1c at baseline, lower eGFR at
baseline, and presence of metabolic syndrome traits. The
type 2 diabetes risk-conferring T allele at the TCF7L2
rs7903146 variant was associated with shorter time-toinsulin during follow-up.
Conclusion: Using prospective follow-up of the Hong
Kong Diabetes Registry, we identified clinical and genetic
factors associated with earlier need for insulin therapy
among patients with type 2 diabetes. Further studies to
examine the functional implication of recently identified
T2D genetic variants on the risk of diabetes progression
is warranted. Incorporating clinical and genetic
information may help to identify patients at risk of betacell failure for earlier insulin therapy to optimize
metabolic and other outcomes.
References: 1. Tam CH, So JK, Wang Y, et al. Use of Net
Reclassification Improvement (NRI) Method Confirms the
Utility of Combined Genetic Risk Score to Predict Type 2
Diabetes. PLoS One 2013; Dec; 8: (12): e83093
Acknowledgement: Research Grants Council Themebased Research Scheme (T12-402/13)
Disclosure of Interest: None Declared
Objectives: Delta opioid receptor (DOR) is a well known
receptor involved in heroin dependence. This study
tested the hypothesis of whether the single nucleotide
polymorphisms (SNPs) in the opioid receptor delta 1
(OPRD1) gene encoding region were associated with
treatment responses in a methadone maintenance
therapy (MMT) cohort from Taiwan.
Methods: 344 MMT patients were recruited from 6
hospitals. Treatment outcomes of severity of
dependence scale (SDS), diastolic /systolic blood
pressure, heart rate, chemokine interferon gammainduced protein 10 (IP-10) and treatment emergent
symptom scale (TESS) for the side effects were recorded.
25 SNPs located within the OPRD1 genetic region were
selected and genotyped from the genomic DNA of all 344
participants.
Results: Ten SNPs, from rs797397 to rs421300 in the
intron 1 region, showed significant associations in both
genotypes and allele types with SDS (GLM P≤0.031 and
P≤0.007, respectively), with diastolic blood pressure
(GLM P≤0.016 and P≤0.006, respectively), with dry
mouth side effects (GLM P≤0.043 and P≤0.005,
respectively) and plasma concentrations of IP-10 (GLM
P≤0.049 and P≤0.015, respectively). Individuals with the
allele types associated with a higher SDS showed a lower
diastolic pressure, lower dry mouth symptom score, and
lower plasma concentration of IP-10 than their counter
allele type carriers. rs2234918 in exon 3 is significantly
associated with the corrected QT (QTc) interval change in
the electrocardiogram in both genotype (GLM P=0.002)
and allele type (GLM P=0.001). The minor allele carriers
showed a greater QTc change than the major allele
carriers. More replications are essential for this
observation.
Conclusion: These results indicated the OPRD1 genetic
variants may be influential to the severity of
dependence, diastolic blood pressure, dry mouth side
effects, and plasma chemokine IP-10 concentrations in
this MMT cohort.
Disclosure of Interest: None Declared
P131
GENETIC ASSOCIATION OF PDYN POLYMORPHISMS
AMONG MALAYSIAN OPIOID DEPENDENTS.
1,*
2
1
1
D. Nagaya , Z. Zahari , M. Salem , B. H. Yahaya , T. S.
3
4
1
Choon , R. Ismail , N. Mohd Yusoff
1
Regenerative Medicine Cluster Advanced Medical and
Dental Institute, Universiti Sains Malaysia, Kepala Batas,
2
Department of Pharmacy, Hospital Universiti Sains
PHARMACOGENOMICS
P130
GENETIC POLYMORPHISMS AT INTRON 1 OF OPRD1 ARE
ASSOCIATED WITH SEVERITY OF DEPENDENCE,
DIASTOLIC BLOOD PRESSURE, CHEMOKINE IP-10 AND
DRY MOUTH SIDE EFFECT
125
3
Malaysia, Kota Bharu Kelantan, Institute of Research In
Molecular Medicine, Universiti Sains Malaysia, Penang,
4
Centre of Excellence for Research in AIDS, Universiti
Malaya, Kuala Lumpur, Malaysia
genetic information. Pharmacogenetic core markers in
several genes (UGT family, CYP450 family, NAT2, DPYD)
are reported to be associated with adverse side effects
and drug toxicities. However, both identification of DPYD
genetic variants and determination of DPYD enzyme
activity have not been well studied in the Korean
population.
Methods: In order to analyze the association between
DPYD single nucleotide polymorphisms (SNP) and DPYD
enzyme activity in the Korean population, we screened
the polymorphisms by direct sequencing using the ABI
3730 and analyzed the enzyme activity using HPLC in 73
healthy Korean subjects. Association analyses were
conducted using SAS.
Results: A total of 83 SNPs were observed. Among the
identified genetic variants, 32 were polymorphic,
including 3 core such as DPYD*9A (Cys29Arg), DPYD*5
(Ile543Val), and DPYD*6 (Val732Ile) and 11 novel SNPs.
Enzyme activity assay showed that activity value ranged
between 44 pmole/min/mg protein (unit) and 588 units
with an average value 201.38 units. Association analysis
between SNPs and enzyme activity in showed that two
novel SNPs, -832G>A and -131C>A, induced a significant
difference in enzyme activity (P < 0.05). Individuals with
the GG genotype at -832G>A showed significantly higher
DPYD enzyme activity than those with the AG genotype
at -832G>A (206.87 ± 16.37 units, 73.31 ± 11.35 units,
P=0.0489). In addition, the expression of DPYD was
significantly reduced in individuals possessing the -131
C>A CC genotype compared to those with -131C>A AC
genotype (196.32 ± 16.39 units, 320.05 ± 87.23 units,
P=0.0409).
Conclusion: Analysis of the correlation between each
SNP and enzyme activity showed that two novel SNPs in
the promoter region, -832G>A and -131C>A, were
associated with enzyme activity, while known core
markers do not significantly affect enzyme
activity. Although further studies should be conducted to
confirm these findings, this study could make a valuable
contribution to further research, especially in the area of
personalized medicine.
References: 1) Weng L, Zhang L, Peng Y and Huang RS
Pharmacogenetics and pharmacogenomics: a bridge to
individualized cancer therapy Pharmacogenomics.
2013;14:315-324.
Disclosure of Interest: None Declared
Objectives: The goal of this study was to determine the
frequency of SNPs rs910080, rs1997794 and rs1022563
of PDYN gene among Malaysians and study their
association with the phenotype of opioid dependent.
Methods: A total of 338 opioid dependents and 461 male
volunteer subjects for SNP rs910080, 451 Opioid
dependents and 515 male volunteers for rs1997794 and
finally 459 opioid dependents and 463 male volunteers
for rs1022563 were included in this study. SNPs were
genotyped using Taqman SNP genotyping assay. The
results obtained were analyzed for allele and genotype
frequencies. An association between genotypes and the
opioid dependence phenotype was also performed using
Haploview 4.2.
Results: All the three markers genotyped for both cases
and randomly ascertained controls were in HardyWeinberg equilibrium. A significant association was
observed in opiate dependent subjects for allele A for
SNP rs910080 (p= 0.0081) odds ratio1.465; 95% Cl
(1.1017- 1.9491) compared to allele G. However, there
were no significant association between opiate
dependent and volunteers for SNP rs1997794 and
rs1022563.
Conclusion: This study suggests that variant A allele of
rs910080 may contribute to vulnerability to opiate
dependence among Malaysian population and this
finding may guide future studies to identify genetic risk
factors for opioid dependence
Disclosure of Interest: D. Nagaya Grant/Research
support
from:
1001/PSK/8620013
and
1001/PSK/8620014 , Z. Zahari: None Declared, M. Salem:
None Declared, B. Yahaya: None Declared, T. Choon
Grant/Research support from: 1001/PSK/8620013 and
1001/PSK/8620014 , R. Ismail: None Declared, N. Mohd
Yusoff: None Declared
P132
ASSOCIATION STUDY BETWEEN THE DPYD GENETIC
VARIANTS AND DPYD ENZYME ACTIVITY
IN KOREAN POPULATION
1,*
2
3
1
J.-G. Shin , T. S. Kang , H. S. Cheong , H. D. Shin , M.
2
W. Chung
1
Department of Life science, Sogang University, Seoul,
2
Toxicological Evaluation and Research Department,
National Institute of Food and Drug Safety Evaluation,
3
Osong, Department of Genetic Epidemiology, SNP
Genetics, Seoul, Korea, Republic Of
P133
THE PREVALENCE OF CYP2D6 GENE POLYMORPHISMS
AMONG FILIPINOS AND THEIR USE AS BIOMARKERS
FOR CANCER RISK AMONG THOSE WITH LUNG CANCER
1,*
2
3
R. J. B. Luna , E. M. C. de la Paz , J. Nevado Jr. , C. L.
3
3
4
4
Silao , C. Ngelangel , A. D. Wang , R. H. Sebastian , R.
4
4
4
4
Ceniza , L. L. P. Simpao , L. F. Beratio , E. Dominguez ,
4
A. Albay
1
Microarray Core Laboratory, Institute of Human
Genetics, National Institutes of Health, UP Manila,
2
National Institutes of Health, University of the
3
Philippines Manila, Institute of Human Genetics,
Objectives: Combining the genetic and clinical
information in individuals is important for personalized
medicine to discover genetic factor. Variance in drug’s
effect and toxicity can be caused by differences in
126
4
National Institutes of Health, UP Manila, Section of
Pulmonology, Department of Medicine, University of the
Philippines - Philippine General Hospital, Manila,
Philippines
Methods: A total of 344 methadone maintenance
treatment (MMT) patients had been genomewide
genotyped and the quality control steps were
genomewide performed. The pathway-based association
analyses were conducted by the gene sets in pathways
based on a gene-based association method, which
aggregates gene-based p-values into a pathway-based pvalue. A total of 31 single nucleotide polymorphisms
(SNPs) were located within the CDH2 genetic encoding
region in this pathway. These SNPs were further analyzed
using general linear model (GLM) with methadone
treatment responses screening. The significant results
were further corrected for multiple comparisons using
the false discovery rate (FDR) analyses.
Results: Among the pathways, the adherens junctions
interactions pathway showed the most significantly
association with methadone dose (Pathway-based
P=0.0008). The CDH2 gene with 31 SNPs within this
pathway were significantly associated with methadone
dose (Gene-based P=0.009). The genotypes of SNPs
rs528438, rs8094439, and rs17446819 located at intron2
were significantly associated with both systolic blood
pressure (SBP; in mm-Hg) (GLM p≦0.008, FDR≦0.043)
and diastolic blood pressure (DBP; in mm-Hg) (GLM
p≦0.003, FDR=0.028), but less significant with
methadone dose (GLM p≦0.045, FDR=0.099). The major
allele type carrier had higher methadone dose, but lower
SBP and DBP than the minor allele carriers.
Conclusion: In summary, further verification in the
significant association candidate gene is essential
in pathway-based association analyses.
Disclosure of Interest: None Declared
Objectives: This study aims to determine the prevalence
of CYP2D6 polymorphisms among Filipinos. It also aims
to determine if such variants are associated with the
occurrence of lung cancer, as tobacco-derived
procarcinogens are metabolized by CYP2D6 to their
carcinogenic derivatives.
Methods: Utilizing a candidate gene approach, 47 single
nucleotide polymorphisms (SNPs) of the CYP2D6 gene
were genotyped from DNA samples of 115 cases with
lung cancer and age- and sex-matched 115 controls. The
samples were genotyped using the Illumina GoldenGate
Genotyping assay.
Results: Results show that 18 out of 47 polymorphisms
have significant genotypic variability (>1% for at least 2
genotypes). No variant is associated with lung
cancer. However, rs1135840, rs16947 and rs28360521,
were found to be highly variable among Filipinos and
these findings may have clinical implications. Both
rs1135840 and rs16947 are associated with cancer;
rs16947 with timolol-induced bradycardia; and
rs28360521 with lose-dose aspirin-induced lower
gastrointestinal bleed.
Conclusion: This study demonstrates that CYP2D6
polymorphisms are present among Filipinos, which,
although not found to be associated with lung cancer,
can be useful biomarkers for future pharmacogenetic
studies.
Disclosure of Interest: None Declared
P136
CYP2D6 GENE POLYMORPHISMS AND COLD PRESSOR
PAIN SENSITIVITY: LACK OF ASSOCIATION AMONG
HEALTHY MALAY MALES
1 2,*
3
4
2
Z. Zahari
, L. Chee Siong , M. A. Ibrahim , N. Musa ,
5
6
2
M. A. Mohd Yasin , L. Yeong Yeh , T. Soo Choon , N.
7
8
Mohamad , R. Ismail
1
Department of Pharmacy, Hospital Universiti Sains
2
Malaysia, Pharmacogenetics and Novel Therapeutics
Cluster, Institute for Research in Molecular Medicine
3
(INFORMM) , Department of Emergency Medicine,
School of Medical Sciences, Universiti Sains Malaysia,
4
Kota Bharu, Malaysia, Department of Pharmacology and
Toxicology, College of Pharmacy, Hawler Medical
5
University, Hawler, Iraq, Department of Psychiatry,
6
School of Medical Sciences, , School of Medical Sciences,
7
Universiti Sains Malaysia, Kota Bharu, Faculty of
Medicine & Health Sciences, Universiti Sultan Zainal
8
Abidin, Kuala Terengganu, Centre of Excellence for
Research in AIDS (CERiA), University of Malaya, Kuala
Lumpur, Malaysia
P135
PATHWAY-BASED METHADONE DOSE ASSOCIATION
ANALYSES
DISCOVERED
CDH2
GENETIC
POLYMORPHISMS
ASSOCIATION
WITH
BLOOD
PRESSURE
1 2,*
3
1
1
Y.-L. Liu
, R.-H. Chung , S.-W. Liu , S.-C. Wang , H.-W.
1
4
25
Kuo , H.-C. Yang , I.-K. Ho
1
Center for Neuropsychiatric Research, National Health
2
Research Institutes, Miaoli County, Graduate Institute of
Clinical Medical Science, China Medical University,
3
Taichung, Division of Biostatistics and Bioinformatics,
Institute of Population Health Sciences, NATIONAL
4
HEALTH RESEARCH INSTITUTES, Miaoli County, Institute
5
of Statistical Science, Academia Sinica, Taipei, Center for
Drug Abuse and Addiction, China Medical University
Hospital, Taichung, Taiwan, Province of China
Objectives: In an attempt to identify pathway-based
association with methadone dose, the Cadherin 2, type
1, N-cadherin (neuronal) (CDH2) of a calcium dependent
cell-cell adhesion glycoprotein encoding genetic region
showed significantly association. In the further treatment
responses association analyses, the CDH2 genetic
polymorphisms were mainly associated with blood
pressure.
Objectives: Endogenous morphine contributes to the
modulation of nociception. Cytochrome P450, Family 2,
Subfamily D, Polypeptide (CYP2D6) enzyme acts at
critical steps in the endogenous morphine synthesis
127
pathway. We investigated the influence of CYP2D6 gene
polymorphisms on cold pressor pain sensitivity among
healthy Malay males.
Methods: After obtaining an informed-consent, we
determined ten CYP2D6 alleles among 152 healthy Malay
males (18- 63 years old) using nested allele-specific
multiplex polymerase chain reaction (PCR) methods.
Excluded were individuals with a positive result of urine
screening for drug test, chronic or ongoing acute pain,
and other conditions that may affect pain or cold pressor
test (CPT). Cold pressor pain sensitivity (pain threshold,
pain tolerance and pain intensity) were assessed six
times over a 24 hour period. RM-ANOVA between group
analysis was applied to compare cold pressor pain
characteristics with different CYP2D6 alleles, genotypes
and predicted phenotypes.
Results: Mean pain threshold, pain tolerance and pain
intensity scores showed no significant difference with
CYP2D6 polymorphisms.
Conclusion: CYP2D6 polymorphisms play no role in the
inter-individual variability in cold pressor pain threshold,
pain tolerance and pain intensity among healthy Malay
males.
Disclosure of Interest: Z. Zahari Grant/Research support
from: Grant No.1001.PSK.8620014, L. Chee Siong: None
Declared, M. A. Ibrahim: None Declared, N. Musa
Grant/Research
support
from:
Grant
No.1001.PSK.8620014, M. A. Mohd Yasin Grant/Research
support from: Grant No.1001.PSK.8620014, L. Yeong Yeh:
None Declared, T. Soo Choon Grant/Research support
from: Grant No.1001.PSK.8620014, N. Mohamad: None
Declared, R. Ismail: None Declared
diphenyltetrazoliumbromide (MTT) assay. The frequency
of chromosome aberration (CA) was determined
according to standard procedures. Expression of cellular
surface antigen for HSCs (Sca-1) was confirmed by flow
cytometer. Myelotoxicity of HQ was studied using the
colony-forming unit (CFU) assay for the following
myeloid
progenitors:
CFUgranulocyte/erythrocyte/macrophage/megakaryocyte
(CFU-GEMM), CFU-granulocyte/macrophage (CFU-GM),
CFU-granulocyte (CFU-G), CFU-macrophage (CFU-M),
CFU-erythroid (CFU-E) and Burst-forming unit erythroid
(BFU-E).
Results: HQ reduced (p<0.05) viability of BMCs at 25 µM
and 50 µM, and the IC10, IC25, and IC50 were 17 µM, 23
µM and 35 µM, respectively. Increased (p<0.05)
frequency of CA was observed in HQ-treated bone
marrow cells as compared to control. Reduced (p<0.05)
Sca-1 expression at 17 µM, 23 µM and 35 µM indicates
cytotoxic effect of HQ on cultured mouse hematopoietic
progenitors and stem cells. Myeloid clonogenic assay
revealed reduced (p<0.05) total colony numbers in the
presence of HQ at 6.25 µM and a complete inhibition in
colony growth at higher concentrations (12.5 µM to 35
µM). HQ reduced (p<0.05) the growth of CFU-GEMM,
CFU-GM and CFU-G at 6.25 µM, while the growth of CFUM, CFU-E and BFU-E were not remarkably affected at its
lower concentrations (1.56 µM and 6.25 µM).
Conclusion: In conclusion, HQ exposure induces
chromosomal instability of exposed bone marrow cells
and its myelotoxicity effect could be dependent through
a lineage-mediated response which may be responsible
for in vivo hematological troubles. Further in vivo study is
warranted to confirm this hypothesis.
Disclosure of Interest: None Declared
P137
LINEAGE-MEDIATED MYELOTOXICITY AND
CHROMOSOME ABERRATION STATUS OF
HYDROQUINONE-EXPOSED MURINE BONE MARROW
DERIVED-HEMATOPOIETIC STEM AND MYELOID
PROGENITOR CELLS
1,*
1
POPULATIONS GENETICS
P138
LRRK2 N551K AND R1398H VARIANTS: A GENETIC AND
FUNCTIONAL STUDY
1,*
2
3
4
3
A. Gopalai , S.-Y. Lim , L. L. Chua , Y. Zhao , E.-K. Tan ,
1
A. Ahmad-Annuar
1
2
biomedical science, Medicine, University Malaya, Kuala
3
Lumpur, Malaysia, Neurology, National Neuroscience
4
Institute, Clinical Research, Singapore General Hospital,
Singapore, Singapore
1
Z. Abdul Hamid , C. Paik Wah , N. Khen Eng , J. Mohd
1
Idris
1
Biomedical Science, Universiti Kebangsaan Malaysia,
Kuala Lumpur, Malaysia
Objectives: Benzene exposure has been linked to
hematotoxicity and leukemogenicity. The impact of
benzene exposure on complex microenvironment of
Hematopoetic Stem Cells (HSCs) niche, comprising of
bone marrow cells, HSCs and lineage-specific progenitors
remains elusive. This study aims to evaluate the effect of
a benzene metabolite, Hydroquinone (HQ) on the
chromosomal stability of exposed bone marrow cells,
survivability HSCs and to compare its myelotoxicity effect
on different lineages of myeloid-committed progenitors.
Methods: HQ was added at varying concentrations (0 –
50 µM) for 24 hours to the murine bone marrow cells
(BMCs) cultures. Viability of HQ-treated BMCs were
determined by using 3-(4,5-dimetylthiazol-2-yl)- 2,5-
Objectives: We investigated the frequency of the N551K
and R1398H LRRK2 variants in our PD population and
assessed the possible functional effect conferred by
these variants on PD pathogenicity.
Methods: Parkinson's disease patients were diagnosed
based on the UK PD Brain Bank Criteria, and healthy
individuals with no history of neurological conditions
were recruited as controls. Written consent was
obtained from these individuals. Samples were
genotyped through Taqman® allelic discrimination assay.
Functional assays including aspects such as cell viability
and mitochondria health were carried out on transfected
128
cells carrying the variants. Transfected cells were
exposed to oxidative stress to assess the possible
protective effect in cells carrying the N551K and R1398H
variants.
Results: The rs7308720 (C>A, p.N551K) and rs7133914
(G>A, p.R1398H) variants in our cohort suggested
protective effect with an odds ratio of 0.6 (p=0.007) for
N551K and 0.7 (p=0.041) for R1398H respectively. The
minor alleles for both these variants are present at a
frequency of approximately two-folds higher in the
control than in the patients.
Conclusion: The N551K and R1398H variants were found
to be protective in our population. These findings are
coherent with what have been found in both the Asian
and Caucasian population (Tan et al., 2010; Chen et al.,
2011; Ross et al., 2011). We are currently exploring the
functional effect of these variants on the cell.
Disclosure of Interest: None Declared
(49.02%) and control groups (63.27%). Statistical
analysis, however, showed no significant difference. The
percentage of distribution of AG, AA and GG was similar
among CRSwNP and CRSsNP. The wild-type allele (A) and
mutant-allele (G) showed similar frequencies between
CRS and healthy controls and also among CRSwNP and
CRSsNP. Statistical analysis was not significant.
Conclusion: This study was unable demonstrate the
association of genotype and allele frequencies for both
TNFa -1031 and TNFb +252 gene polymorphisms
between CRS participants and healthy controls as well as
between CRSwNP and CRSsNP. Although TNFa -1031 and
TNFb +252 genes do not play major role in the
pathogenesis of CRS among our subjects, the
identification of susceptible SNPs in the development of
CRS merits further investigations with improve sample
sizes.
Disclsure of Interest: None Declared
P139
TUMOUR NECROSIS FACTOR GENE POLYMORPHISM
AMONG CHRONIC RHINOSINUSITIS PATIENTS WITH OR
WITHOUT NASAL POLYPS OF HOSPITAL USM
1 2,*
3
3
A. Ahmad
, K. Misron , S. Sheikh Abdul Hamid , R. R.
3
Ramli
1
Basic Science and Oral Biology Unit, School of Dental
2
Sciences, Human Genome Center, School of Medical
3
Sciences, Department of Otorhinolaryngology-Head &
Neck Surgery, School of Medical Sciences, UNIVERSITI
SAINS MALAYSIA, Kubang Kerian, Malaysia
P140
VARIATION AND MUTATION DATABASE OF MALAYSIAN
NODE OF HUMAN VARIOME PROJECT: AN UPDATE
1 2,*
2
1
B. H. Halim-Fikri
, B. Atif Amin , A. Nurul Fatihah , W.
1
1
3
J. Wan Khairunnisa , A. Mia Yang , H. Sarifah , A. R. Nur3
3
4
Shafawati , W. I. Hatin , B. Rosnah , J. Muhammad Farid
4
4
1
2
, A. W. Zaidah , B. A. Zilfalil , A. L. Ahmad Zubaidi
1
Department of Paediatric, Universiti Sains Malaysia,
2
Kota Bharu, Faculty of Medicine & Health Sciences,
Universiti Sultan Zainal Abidin (UniSZA), Kuala
3
4
Terengganu, Human Genome Centre, Department of
Hematology, Universiti Sains Malaysia, Kota Bharu,
Malaysia
Objectives: The purpose of this study is to determine the
distribution of tumour necrosis factor (TNF) genes; TNFa
-1031 and TNFb +252 gene polymorphisms among
chronic rhinosinusitis (CRS), chronic rhinosinusitis with
nasal polyp (CRSwNP) and chronic rhinosinusitis without
nasal polyp (CRSsNP).
Methods: Fifty-one CRS participants; 25 CRSwNP and 26
CRSsNP participants and 49 healthy controls were
enrolled in this case control study. All DNA samples were
extracted from the collected buccal swaps and
genotyped for TNFa -1031 and TNFb +252 genes by mean
of RFLP technique.
Results: For TNFa -1031, the homozygous wild-type (TT)
and heterozygous mutant-type (TC) showed almost equal
distribution among CRS and healthy controls. TT
genotype was 58.82% in CRS while 69.39% in controls.
Similar distribution was observed in CRSwNP and
CRSsNP, where both showed 29.41% distribution for TT,
while for TC; 19.69% was CRSwNP and 21.57% was
CRSsNP. No homozygous mutant genotype (CC) was
identified. Statistical analysis showed no significant
difference. Similarly, the wild-type allele (T) and mutantallele (C) between CRS and healthy controls, and
between CRSwNP and CRSsNP were equally distributed
and showed no significant difference. As for TNFb +252,
the heterozygous mutant genotype (AG) was found to be
more prevalent as compared to homozygous wild-type
(AA) and homozygous mutant-type (GG) in both CRS
Objectives: The Malaysian Node of Human Variome
Project Database (MyHVPDb) is a country specific
database of human variant and gene mutation that was
established in 2011. MyHVPDb was created to collect,
collate and curate genetics data of all the Malaysian
ethnic groups which include SNPs, mutations and other
variants. This ethnic specific mutation and variation
databases are being continuously updated, recording
extensive information over the genetic heterogeneity of
the Malaysian ethnic groups.
Methods: The collection of data for this database is from
two main sources: by direct submission (laboratory
analysis); by extraction from published data in journals
and other databases (e.g., Online Mendelian Inheritance
in
Man
(OMIM,
http://omim.org/),
dbSNP
(http://www.ncbi.nlm.nih.gov/projects/SNP/),
Human
Gene
Mutation
Database
(HGMD,
http://www.hgmd.org/). These collected data was
curated, interpreted and make available on information
on variations within a single gene or a group of gene
associated with a specific disease.
Results: The database comprises of SNP Database and
Mutation Database. The SNP database has stored 291718
SNPs that was obtained by genotyping the SNPs of 103
healthy individuals from six Malay sub-ethnic groups. The
129
Mutation Database is a database comprising of
mutations of genes that are related to diseases common
in Malaysia. It now contains over 150 mutations from 20
genes from various ethnic groups in Malaysia. These data
on mutations were collected from results published in
journals.
Conclusion: This database also will complement other
databases in South East Asia (SEA) such as Thailand and
Singapore Variant and Mutation databases to provide
crucial information on the genetic background of the
population in the SEA as well as the pattern of disease at
the molecular level. Hence, MyHVPDb will be useful not
only for researchers in Malaysia but also for those in
countries with similar ethnic background throughout the
world.
Disclosure of Interest: None Declared
indigenous populations, subsequently identified their
signatures of positive natural selections.
Methods: 64 subjects from Negrito, Senoi (Che Wong)
and Proto Malay (Jakun) were genotyped with Illumina
Omni2.5 SNP-array. Analyses of positive natural
selections were carried out using 3 metrics namely, FST,
iHS and XP-EHH. Malays from Singapore Genome
Variation Project (SGVP) were used as an outgroup for
comparison.
Results: Analyses revealed genes underlied the regions
of positive natural selection were enriched in immune
response system, as well as amino acid and sugar
metabolism. These included PRKAA2 (FST p-value =
4.39E-08; iHS p-value = 3.30E-03); DAB1 (FST p value =
2.43E-08; iHS p-value = 9.90E-03; XP-EHH), HIF1A (iHS pvalue = 9.01E-03) and CDH13 (FST p-value = 1.06E-08).
Conclusion: The search for genomic signatures of
positive selection yielded differential evidence of local
adaptation even within a small geographical region in
Peninsular Malaysia. This could possibly be attributed to
their different population histories, presumably the
adaptations occurred after the population splits.
Disclosure of Interest: None Declared
P141
IDENTIFICATION OF SIGNATURE OF POSITIVE NATURAL
SELECTION AMONG THE INDIGENOUS POPULATIONS
FROM PENINSULAR MALAYSIA
1
2
3
4
5
Y. Yunus , X. Liu , D. Lu , F. Aghakhanian , W.-Y. Saw ,
3
5
6
7
L. Deng , M. Ali , X. Wang , F. Mohd Nor , T. Abdul
7
8
9
4
Rahman , S. A. Shaari , M. Z. Salleh , P. Maude , R. T.10
3
6
1,*
H. Ong , S. Xu , Y.-Y. Teo , B. P. Hoh
1
IMMB, Fac Medicine, Universiti Teknologi MARA, Sungai
2
Buloh, Malaysia, NUS Graduate School for Integrative
Science and Engineering, National University of
Singapore, Singapore 117456, Singapore, Singapore,
3
Max Planck Independent Research Group on Population
Genomics, Chinese Academy of Sciences and Max Planck
Society Partner Institute for Computational Biology,
Shanghai Institutes for Biological Sciences, Chinese
4
Academy of Sciences Shanghai, Shanghai, China, Jeffrey
Cheah School of Medicine and Health Sciences, Monash
University Sunway Campus, Selangor, Selangor,
5
Malaysia, Life Sciences Institute, National University of
6
Singapore, Singapore, Saw Swee Hock School of Public
Health, National University of Singapore, Singapore
7
117597, Singapore, Singapore, Clinical Pathology
Diagnostic Centre Research Laboratory, Faculty of
Medicine, Universiti Teknologi MARA, Sungai Buloh
8
Campus, Selangor, Malaysia,
Clinical Pathology
Diagnostic Centre Research Laboratory, Faculty of
Medicine, Universiti Teknologi MARA, Sungai Buloh
9
Campus,
Selangor,
Singapore,
Integrative
Pharmacogenomics Institute, Universiti Teknologi MARA,
10
42300 Puncak Alam, Selangor, Saw Swee Hock School of
Public Health, National University of Singapore,
Singapore 117597, Singapore, Malaysia
P142
POPULATION STRUCTURE OF FIVE INDIGENOUS ETHNIC
GROUPS IN SABAH, NORTH BORNEO, AND THEIR
HISTORICAL MIGRATION RELATIONSHIPS TO SOUTHERN
CHINA AND
SOUTHEAST ASIAN POPULATIONS
1,*
2
3
C. W. Yew , M. Z. Hoque , J. Pugh-Kitingan , C. L. Y. Voo
1
4
1
5
5
, J. Ransangan , S. T. Y. Lau , X. Wang , W. Y. Saw , T.
5
5
6
7
8
H. Ong , Y. Y. Teo , S. H. Xu , B. P. Hoh , M. E. Phipps , S.
1
V. Kumar
1
2
Biotechnology Research Institute, Faculty of Medicine
3
and Health Sciences, Faculty of Humanities, Arts and
4
Heritage, Borneo Marine Research Institute, Universiti
5
Malaysia Sabah, Kota Kinabalu, Malaysia, Department
of Statistics and Applied Probability, National University
6
of Singapore, Singapore, Singapore, CAS-MPG Partner
Institute for Computational Biology, Shanghai Institutes
7
for Biological Sciences, Shanghai, China, Institute for
Molecular Medical Biotechnology, Universiti Teknologi
8
MARA, Sungai Buloh, Jeffrey Cheah School of Medicine
and Health Sciences, Monash University, Bandar Sunway,
Malaysia
Objectives: This study aims to unravel and compare the
population structure and genetic relationships of the
Northern Borneo ethnic groups against Southern China
and Southeast Asian populations, for subsequent
inference of their migration history.
Methods: Ethical clearance was obtained and blood
samples were collected from healthy individuals. A total
of 98 individuals representing five indigenous ethnic
groups i.e. Dusun, Rungus, Sonsogon, Sungai-Lingkabau
and Murut-Paluan were genotyped with ~2.4 millions
genome-wide SNP markers. It was then merged with the
Objectives: Indigenous populations, locally known as
Orang Asli, are officially classified into 3 main ethnolinguistic groups namely, Negrito, Senoi and Proto-Malay.
They are believed to have experienced long period of
isolation and local adaptation to multiple environmental
stresses, including malnutrition and persistent exposure
to various infectious diseases. In this study, we
performed a high-density genotyping on the 3
130
Pan-Asian SNP Consortium (PASNP) data to form a
comprehensive set of 60 populations. The genetic
relationships were inferred by principal component
analysis, categorization and quantification of ancestrycomponent, phylogenetic ancestry-component tree and
estimation of migration direction.
Results: It was found that the five ethnic groups of Sabah
form a distinct cluster that is close to the Filipino
Austronesians and Taiwan natives. The Sabah natives
form a unique genetic ancestry, denoted as 'NorthBorneo'. The Sonsogon has an average of 95% 'NorthBorneo' ancestry, inferring putative population
differentiation. The 'North-Borneo' and 'Taiwan-Natives'
share a direct common ancestor, who are clustered with
Southern China populations. Importantly, it was
estimated that there was no migration from Taiwan
towards North Borneo. This findings corroborate with
the suggestion that the proto-Austronesian originated
from Southern China. As such, we now hypothesize that
the native populations of Sabah are the direct
descendants of the proto-Austronesian, instead of the
Taiwan natives as originally believed. Bayesian analysis is
underway to test this hypothesis.
Conclusion: The findings indicate that Sabah's indigenous
population has a unique pool of genetic variants.
Disclosure of Interest: None Declared
however, Senois and Proto-Malays are admixed between
Negritos and East Asians (EA). Formal admixture tests
also show Negrito gene flow into SEA and some EA
population such as Lahu and Dai suggesting Negritos
genetic component contribution in mainland SEA. We
also find that these populations have greater
homozygosity compared to the neighboring SEA and EA
populations which resulted from their isolation or
bottleneck they experienced. Divergence time estimation
also reveals Negritos are the first group among others
that separated from EA approximately 14 KYBP followed
by Senois and Proto-Malays.
Conclusion: The results suggest that although indigenous
Malaysians are genetically closest to EA than other
populations worldwide, they are substantially distinct. It
also indicates several waves of human dispersal into SEA.
Disclosure of Interest: None Declared
P144
ASSOCIATION
OF
SINGLE
NUCLEOTIDE
POLYMORPHISMS (SNP) IN PCSK9 GENE WITH LIPID
ANALYSIS AMONG IBAN AND BIDAYUH ETHNIC GROUPS
IN SARAWAK POPULATION
1,*
1
1
2
H. H. Hood , Y. T. Siaw , S. P. Sim , H. Helmy , M. M.
3
Aminudin
1
Paraclinical Sciences, Universiti Malaysia Sarawak,
2
Kuching, Community Medicine and Public Health,
3
Centre for Pre- University Studies, Universiti Malaysia
Sarawak, Kota Samarahan, Malaysia
P143
ANALYSIS OF GENETIC STRUCTURE IN INDIGENOUS
POPULATIONS OF PENINSULAR MALAYSIA
1,*
2
3
4
F. Aghakhanian , Y. Yunus , T. Jinam , A. Manica , R.
1
2
1
Naidu , B. P. Hoh , M. E. Phipps
1
Jeffrey Cheah School of Medicine and Health Sciences,
2
Monash University Malaysia, Institute of Medical
Molecular Biotechnology, Universiti Teknologi MARA,
3
Selangor, Malaysia, Division of Population Genetics,
National Institute of Genetics, Mishima, Japan,
4
Evolutionary Ecology Group, Department of Zoology,
University of Cambridge, Cambridge, United Kingdom
Objectives: Proprotein convertase subtilisin/kexin type 9
(PCSK9) gene (MIM: 603776) encoded protein that
facilitates cholesterol level in blood. Known mutation in
the PCSK9 gene would indicate hypercholesterolemia
through gain of function resulting in Familial
Hypercholesterolemia Type 3. The increased risk genetic
variant: rs 12084215 of FH (Say et al, 2013) were used to
indicate any correlation with performed lipid analysis
with untested indigenous population in Sarawak. We are
conducting a study to determine the polymorphic
genotype frequencies among 2 indigenous populations,
the Iban and the Bidayuh in Sarawak, thus elucidating
any association with lipid analysis.
Methods: Blood samples from study subjects were
collected for both genotypes and lipid profile. Peripheral
blood samples were collected, genomic DNA extracted
and genotyped employing Allele Specific-PCR. Genotypes
were categorized into homozygous wild type,
heterozygous and homozygous variants. The lipid profile
consists of total cholesterol, high density lipoprotein, low
density lipoprotein, and triglycerides. Statistical analyses
were done to determine the genotype frequencies and
association with polymorphic genotypes with lipid
analysis.
Results: Total of 112 candidates were assessed to be 92
(82.1%) homozygous wildtype and 20 (17.9%)
heterozygous SNP. There were no significant association
between the genotypes and lipid profiles. The intronic
genetic variant may not affected the gene expression
Objectives: The indigenous populations of peninsular
Malaysia known as Orang Asli (OA) are putative isolated
populations in Southeast Asia (SEA). They have been
divided into three main groups including Negritos, Senois
and Proto-Malays based on their anthropological and
linguistic differences. Despite the huge morphological,
anthropological and linguistic diversity, the genetic
structure of these populations is unknown. The objective
of this research is to study the population genetic
structure of OAs using high-density SNP genotyping
methods.
Methods: We genotyped 169 individuals from three
main Malaysian indigenous groups using Illumina
HumanOmni2.5 SNP array. We compared our data with
datasets from Human Genome Diversity Panel (HGDP)
and Malays from Singapore Genome variation Project
(SGVP).
Results: Structural analyses indicate that Negritos are
substantially distinct from other SEA populations;
131
thus explained why the lipid profiles of tested population
lies within the optimal classification provided by ATP III
guidelines. The guidelines give information for global risk
assessment in coronary heart diseases (CHD) and other
lipid related disorders.
Conclusion: Study present limited information to
associate the polymorphic genotype frequencies with
lipid profiles. Thus, more samples and SNPs in PCSK9
genes as well as other lipid related gene are required to
provide sufficient data for the analysis. Besides that,
more works should be done to elucidate the genes
responsible for lipid abnormality.
Disclosure of Interest: None Declared
P146
POLYMORPHISMS AND HAPLOTYPES OF INTERFERONGAMMA RECEPTOR GENES ARE ASSOCIATED WITH THE
ISK OF PULMONARY TUBERCULOSIS
1,*
2
1
3
J.-G. Shin , B. L. Park , L. H. Kim , C. S. Park , H. D. Shin
1
1
2
Department of Life science, Sogang University, SNP
3
Genetics, Seoul, Department of Internal Medicine,
Soonchunhyang University Bucheon Hospital, Bucheon,
Korea, Republic Of
Objectives: Tuberculosis (TB) is an infectious disease
caused by mycobacterium, which most commonly affects
the lungs. Immune responses of TB patients were mainly
regulated by T helper 1 cell which secrets the interferongamma (IFN-γ). IFN-γ mediated immune responses are
regulated by interacting with its receptor composed of
two subunits, IFN-γ receptor (IFNGR) 1 and 2 that encode
the ligand-biding chain (alpha-chain) and non-ligand
binding chain, respectively. In this study, we investigated
the possible associations between single nucleotide
polymorphisms (SNP) in IFNGR1 and IFNGR2 with the risk
of TB in Korean population.
Methods: In the current study, a total of twenty-two
genetic variants (11 in IFNGR1 and 11 in IFNGR2) were
genotyped using a TaqMan assay on the ABI prism
7900HT (Applied Biosystems, Foster City, CA, USA) in 673
patients and 592 normal controls to investigate the
association between IFNGR1 and IFNGR2 polymorphisms
and the risk of TB. Logistic analyses between the TB and
SNPs were conducted using Haploview v4.2 software,
PHASE software, and SAS, version 9.4 (SAS Inc., Cary, NC,
USA).
Results: The case-control analysis of the association
showed that four genetic variants in IFNGR1 (rs9376269,
rs9376268, rs9376267, rs56251346) were marginally
associated with the risk of TB (OR=1.18-1.40 and P=0.020.04), while other SNPs in IFNGR1 failed to show any
associations. For the haplotype analysis, five and four
major haplotypes are obtained from each LD block in
IFNGR1 and IFGNR2. In the haplotype analysis,
IFNGR1_ht2 showed marginal association with the risk of
TB (OR=1.26 and P=0.04). However, no genetic
polymorphisms and haplotypes in IFNGR2 showed
significant associations with the risk of TB.
Conclusion:
An
association
analysis
between
polymorphisms in IFNGR genes and the risk of TB showed
that four SNPs, rs9376269, rs9376268, rs9376267,
rs56251346, were marginally associated with the
development of TB. Our association analyses
demonstrated that genetic variants in IFNGR1 might
affect the IFN-γ pathway. The current study is likely the
first to report the importance of IFNGR1 and IFNGR2 as a
genetic factor in mycobacterium infectious disease,
which may prove useful for identifying the etiology of TB
in Korean population.
References: 1) O'Garra A, Redford PS, McNab FW, Bloom
CI, Wilkinson RJ, Berry MP. The immune response in
tuberculosis. Annu Rev Immunol. 2013;31:475-527.
Disclosure of Interest: None Declared
P145
MITOCHONDRIAL HAPLOGROUP M9A1A1C1B IS
ASSOCIATED WITH HYPOXIC ADAPTION IN TIBETAN
1
1
1
1
1
1,*
Q. Li , H. Sun , K. Lin , X. Huang , Z. Yang , J. Chu
1
Medical Genetic, Institute of Medical Biology, Kunming,
China
Objectives: To investigate the association between
mitochondrial DNA diversity and hypoxic adaption in
Tibetan living in different altitude.
Methods: Genomic DNA of 144 unrelated Tibetans living
in different altitudes and 47 unrelated Han Chinese were
collected. mtDNA haplogroup classification and mtDNA
mutation genotyping were carried out by DNA
sequencing.
Results: The frequencies of mitochondrial haplogroup B
and haplogroup M7 in the high-altitude population were
significantly lower than those in the low-altitude
population, while the frequencies of haplogroup G and
haplogroup M9a1a1c1b in the high-altitude population
were significantly higher than those in the low-altitude
population(p<0.05). The frequencies of 3394C and 7697A
which were the division site of haplogroup M9a1a1c1b in
the high-altitude population were significantly higher
than those in the low-altitude population(p<0.05)
Conclusion: Our results suggested that mitochondria
DNA Haplogroup G and M9a1a1c1b may be associated
with hypoxic adaptation. In particular, for haplogroup
M9a1a1c1b, its 3394C and 7697A mutations may be the
primary cause of adaptation to hypoxia.
References: 1..Beall CM (2007)Two routes to functional
adaptation: Tibetan and Andean high-altitude natives.
Proc Natl Acad Sci U S A 104 Suppl 1: 8655-8660.
2.Ji F, Sharpley MS, Derbeneva O, Alves LS, Qian P, et al.
(2012) Mitochondrial DNA variant associated with Leber
hereditary optic neuropathy and high-altitude Tibetans.
Proc Natl Acad Sci U S A 109: 7391-7396.
3.Gu M, Dong X, Shi L, Lin K, Huang X, et al. (2012)
Differences in mtDNA whole sequence between Tibetan
and Han populations suggesting adaptive selection to
high altitude. Gene 496: 37-44.
Disclosure of Interest: None Declared
132
P147
GENE GEOGRAPHY OF KAZAKH POPULATIONS FROM
THE Y-CHROMOSOMAL DATA
1,*
2
3
M. Zhabagin , O. Balanovsky , Z. Sabitov , I.
4
1
5
Tazhigulova , A. Askapuli , K. Dibirova , M. Chukhryaeva
2
2
2
6
7
, A. Agdzhoyan , N. Markina , Y. Yusupov , P. Tarlykov ,
7
1
8
E. Zholdybaeva , A. Akilzhanova , Z. Zhumadilov , E.
5
Balanovska
1
Department of Genomic and Personalized Medicine,
Center for Life Sciences of Nazarbayev University, Astana,
2
Kazakhstan, Laboratory of Genogeography , Vavilov
Institute of General Genetics, Moscow, Russian
3
Federation, Gumilov Eurasian National University,
4
Forensic science centre of the Ministry of Justice of the
5
Republic of Kazakhstan, Astana, Kazakhstan, Laboratory
of Human Population Genetics , Research Centre for
6
Medical Genetics, Moscow, Institute of Humanitarian
Research of the Republic of Bashkortostan, Ufa, Russian
7
Federation, National Center for Biotechnology of the
8
Republic of Kazakhstan, Center for Life Sciences of
Nazarbayev University, Astana, Kazakhstan
P148
PARP15 POLYMORPHISMS ASSOCIATED WITH FIRST
INDUCTION CHEMOTHERAPY IN ACUTE MYELOID
LEUKEMIA
1,*
2
1
3
M. K. Lee , H. S. Cheong , H. D. Shin , S.-S. Yoon
1
2
Life Science, Sogang University, Genetic Epidemiology,
3
SNP Genetics, Seoul National University Hospital, Seoul,
Korea, Republic Of
Objectives: Poly ADP-ribose polymerases (PARPs)
catalyze ADP-ribosylation, a type of post-translational
modification. PARPs are involved in a wide range of
cellular processes including DNA repair, apoptosis and
transcriptional regulation. Some members of the PARP
gene family, most notably PARP1 gene, have been
actively studied in genome-wide association studies for
acute myeloid leukemia (AML). Among these PARP
genes, Poly ADP-ribose polymerase family, member 15
(PARP15) is also a potential candidate gene for cancer
development due to the role of transcriptional repressor
with poly ADP-ribose polymerase activity. In order to
verify our hypothesis that PARP15 might be related to
AML, this study investigated the possible association
between PARP15 single nucleotide polymorphisms
(SNPs) and the risk of AML. Furthermore, we analyzed
the genetic effects of PARP15 on the clinical phenotypes
based on cytosine arabinose (AraC) chemotherapy in
AML patients.
Methods: In the present study, ten PARP15
polymorphisms were genotyped using a TaqMan assay in
a total of 344 Korean subjects including 103 AML
patients and 241 normal controls. The genetic effects of
the polymorphisms on the risk of AML and the outcome
of chemotherapy were analyzed using SAS software.
Results: The PARP15 polymorphisms were not associated
corr
with the risk of AML (P
> 0.05). However, logistic
regression analysis revealed that two polymorphisms,
corr
rs7612991 (P
= 0.047 and odd ratio = 3.18) and
corr
rs12489170 (P
= 0.044 and odd ratio = 0.32), were
significantly associated with the outcome of first
induction chemotherapy in AML patients. For the
haplotype analysis, a total of 11 haplotypes were
obtained from two LD blocks (7 from block1 and 4 from
block2), and two common haplotypes (Block2haplotype1 and Block2_haplotype2) were also related to
corr
AML chemotherapy outcome (P = 0.034, odd ratio =
corr
3.13 for Block2-haplotype1 and P = 0.044, odd ratio =
0.32 for Block2_haplotype2).
Conclusion: Our results showed that two SNPs and two
haplotypes (rs7612991, rs12489170, Block2-haplotype1,
Block2_haplotype2) were associated with outcome for
fist induction chemotherapy in AML patients. This
suggests that the PARP15 polymorphisms might be
potential therapeutic targets and/or prognostic markers
for identifying patients more likely to respond to
chemotherapy in the Korean population.
Disclosure of Interest: None Declared
Objectives: This study aims to analyze patterns of
genetic variation in Kazakhstan which was a crossroad for
multiple waves a migration in the historical past.
Methods: We have genotyped 1,800 samples by 45
phylogenetically informative SNP markers on the Ychromosome. These samples represent all major tribal
(clan) groups of Kazakhs and cover regularly the area of
the ninth largest country in the world.
Results: We have created the gene geographic Atlas of
Kazakhstan gene pool. First part of the Atlas includes
spatial distribution maps of the Y-chromosomal
haplogroups in the present-day populations. The second
part includes reconstruction of the gene pool in XIX
century, based on the archive census information about
spatial distribution of clans and – extrapolated from
present day data – haplogroup frequencies in these
clans. Thus, the Atlas allows trace genetic variation both
in space and time.
We also run the Mantel test to compare genetic,
geographic and ‘quasigenetic’ distances between
regional Kazakh populations, where quasigenetic
distances were obtained by comparing frequencies of
different clans in the 18 sampled geographic locations.
The significant correlation (r1 = 0.50; p <0.001) between
genetic and quasigenetic matrices indicates important
role which the tribal-clan structure plays in structuring
the gene pool. The weaker correlation between genetic
and geographic matrices (r2 = 0.31; p <0.05) might reflect
a moderate migration activity between the studied
geographical populations. It is worth noting that
quasigenetic diversity in Kazakhstan itself is closely linked
to geography (r3 = 0.53; p <0.001).
Conclusion: Based on these results we conclude that
patronymic organization of society was a major factor
shaped the structure of the modern Kazakh gene pool.
This work was supported by Nazarbayev University and
by Russian Foundation for Basic Research grant 13-0600670. Disclosure of Interest: None Declared
133
P149
ASSOCIATION BETWEEN DEPRESSION AND 5,10METHYLENETETRAHYDROFOLATE REDUCTASE (MTHFR)
GENE
POLYMORPHISMS IN THE TUNISIAN
POPULATION.
1 2,*
3
1 2
M. A. S. Sayadi
, O. ACHOUR , A. Ezzaher , A.
3
1
3
2
Omezzine , W. Douki , A. Bousslama , L. Gaha , M. F.
1
Najjar
1
2
Laboratory of Biochemistry-Toxicology,
Research
Laboratory “Vulnerability to Psychotic disorders LR 05 ES
10”, Department of Psychiatry, Monastir University
3
Hospital, Monastir, LR 12 SP 11, Biochemistry
Department, Sahloul Sousse University Hospital, Sousse,
Tunisia
Health Science, Universiti Sains Malaysia, Kubang Kerian,
Malaysia
Objectives: To study the genetic relationship among the
Orang Asli individuals in Peninsular Malaysia.
Methods: After obtaining approval and consent from the
participants, blood samples of unrelated individuals from
3 Orang Asli tribes comprising 33 Semang (Bateq,
Mendriq, Kintaq, Kensiu and Jahai), 7 Proto Malays
(Jakun and Semelai) and 16 Senoi (Semai and Semaq
Beri) were collected. Genotyping of the 56 individuals
was performed with the Affymetrix Genome-Wide
Human SNP 6.0 Array. The SNPs genotype data were
then exported to PLINK and the analysis of
multidimensional scaling (MDS) of identity by state (IBS)
distance was performed. R software was used to display
the multidimensional plot.
Results: The data analysis based on the multidimensional plot showed that individuals belong to
Semang tribe was separated from Senois’ and Proto
Malays’ individuals. All individuals of five sub-tribes of
Semang were seen scattered closely to each other except
for Bateq sub-tribe which was separated far from the
other individuals. The Senoi and Proto Malay tribes were
placed together on the second dimension of the MDS
plot. The Semai sub-tribe seems to be scattered closer to
Jakun whereas all individuals of Semaq Beri seems
scattered randomly. However, Semelai sub-tribe appears
to be an outlier.
Conclusion: The MDS analysis shows that most of the
individuals of Orang Asli residing in Peninsular Malaysia
tend to be clustered together within their sub-tribes.
Further studies with additional sub-tribes and more
number of individuals will help in defining the population
structure and genetic relationship of Orang Asli in
Malaysia.
Disclosure of Interest: None Declared
Objectives: The aim of this work was to study the
association between the polymorphism of 5,10methylenetetrahydrofolate reductase (MTHFR) gene and
depression in Tunisian patients and to explore their
relation to clinical and therapeutic characteristics of this
disease.
Methods: Our study included 208 depressive patients
and 187 controls aged 44.1±13.5 and 38.9±13.2 years,
respectively. MTHFR gene polymorphism were
determined by PCR-RFLP (Polymerase Chain Reaction Restriction fragment length polymorphism).
Results: No significant difference was detected in the
distribution of the genotype frequencies of MTHFR
C677T polymorphisms (χ²=5.443, df=2, p=0.066) between
patients and controls. We showed significant association
between depression and CC genotype (OR= 1.526, CI
95%= 1.005–2.315, p=0.047). TT Genotype was more
frequent in patient compared to controls but it may be
protect from depression in our population (OR= 0.524, CI
95%= 0.253–1.085, p=0.079). There was no significant
association between gender and the clinical and
therapeutic characteristics of this population and this
polymorphism.
Conclusion: Depression was significantly associated with
CC genotype of MTHFR C677T polymorphism, suggesting
that this genotype may be implicated in the installation
of depression. Further studies are required to clarify the
implication of MTHFR C677T polymorphism in the
pathophysiology of depression.
Disclosure of Interest: None Declared
P151
POPULATION GENETIC STRUCTURE OF THE EIGHT
MALAY SUB-ETHNIC GROUPS IN PENINSULAR
MALAYSIA
1,*
1
1
1
P. B. Yahya , N.-S. Ab Rajab , H. Wan Isa , S. Sulong ,
1
1
A. Harun , Z. Bin-Alwi
1
SCHOOL OF MEDICAL SCIENCES, UNIVERSITI SAINS
MALAYSIA, Kota Bharu, Malaysia
P150
THE MULTI-DIMENSIONAL SCALE ANALYSIS OF THE
ORANG ASLI INDIVIDUALS IN PENINSULAR MALAYSIA
1,*
1
1
2
N. Mohd Nasir , W. I. Hatin , P. Yahya , S. Mat Yasin ,
3
4
1
E. Ismail , N. N. Nik Hassan , B. A. Zilfalil
1
Department of Pediatrics, School of Medical Sciences,
2
Universiti Sains Malaysia, Kubang Kerian, Department of
Zoology, Faculty of Resource Science and Technology,
Universiti Malaysia Sarawak, Kota Samarahan,
3
Department of Genetics, School of Bioscience and
Technology, Faculty of Science and Technology, Universiti
4
Kebangsaan Malaysia, Bandar Baru Bangi, School of
Objectives: Our previous study has shown the genetic
structure of six Malay sub-ethnic groups from peninsular
Malaysia namely Melayu Kelantan, Melayu Minang,
Melayu Jawa, Melayu Bugis, Melayu Kedah and Melayu
Pattani which resembled Indonesian population with
significant mixture of Chinese and Indian genetic
component. The aim of this current study is to
investigate the pattern of the Malay population genetic
structure by including two additional sub-ethnic groups
namely Melayu Banjar and Melayu Champa.
Methods: A total number of 130 healthy and unrelated
individuals who were randomly chosen from the eight
134
sub-ethnic groups of Malay population residing in Johor,
Kelantan, Kedah, Negeri Sembilan, Perak, and Narathiwat
were SNPs genotyped using Affymetrix GeneChip
Mapping Xba 50 K Array. After strict screening criteria, 54
794 autosomal SNPs (for all eight sub-ethnic groups
except for Melayu Banjar and Melayu Champa which
were 52 501 SNPs and 53 700 SNPs respectively) from
each individual were used for further analysis. The
genotype data were compiled with 11 other populations’
genotype data from Indonesia, China, India, Africa and
indigenous populations in Peninsular Malaysia obtained
from the Pan-Asian SNP database. The genetic structure
analysis was carried out using PEAS and STRUCTURE
software program
Results: Genetic structure of Melayu Champa, Melayu
Minang, Melayu Kelantan, Melayu Kedah, and Melayu
Pattani shows consistent admixture of genetic
component from Indonesia, India and China. Melayu
Banjar and Melayu Bugis genetic structure resembled
the Indonesia Toraja and Indonesia Melayu whereas
Melayu Jawa is more similar to Indonesia Java with
slightly proportion of Chinese genetic component seen in
all the three Malay sub-ethnic groups.
Conclusion: All eight Malay sub-ethnic groups in
peninsular Malaysia have a very close genetic
relationship with Indonesia populations with a significant
proportion of genetic component from both India and
China especially in Melayu Kedah, Melayu Pattani,
Melayu Kelantan, Melayu Champa and Melayu Minang.
Disclosure of Interest: None Declared
clustering analyses were conducted on frequency data
obtained from the STR study. On the other hand, control
region of the mitochondrial DNA (HV1, HV2, and HV3)
was examined with a PCR-resequencing approach. The
9-bp deletion in the region V was typed with a direct PCR
method. Various statistical analyses, including haplotype
analysis, phylogetics, and Bayesian estimation were
conducted on the resulted mitochondrial data.
Results: Based on the diversity indices of both STR
markers and mitochondrial DNA, the Bajau population
was shown to harbour higher diversity than the KadazanDusun and Rungus populations. Among them, higher
genetic similarity was observed between the KadazanDusun and Rungus, than with the Bajau. From the
clustering analyses, the Bajau was found to group closer
to other Southeast Asian populations, whereas the
Kadazan-Dusun and Rungus clustered among the
Taiwanese aboriginal groups. Mitochondrial data reveals
genetic fractions of different ages in the examined
indigenous populations, which may represent evidence
of multiple independent episodes of migration waves
into the island of Borneo.
Conclusion: The differences of genetic fractions in the
indigenous populations in our study imply separate origin
of populations in Borneo, whereby their entry into the
island of Borneo may have happened at different
timeframes and directions.
Disclosure of Interest: None Declared
P153
A NOVEL STATISTICAL APPROACH TO SELECT
APPROPRIATE SUSCEPTIBILITY GENES AND IMPROVE
PREDICTIVE ABILITY OF DISEASES
1
1
1
S. Balan , A. Sunder , L. Musmade , H. Pallikarana
1
1,*
1
Tirumala , S. Mohammed , P. Mankad
1
Xcode Life Sciences, Chennai, India
P152
GENETIC STRUCTURE AND DIVERSITY OF INDIGENOUS
POPULATIONS IN SABAH, EAST MALAYSIA
1
1
1
2
B. P. Kee , L. H. Lian , K. H. Chua , E. T. J. Chong , P. C.
2,*
Lee
1
Department of Biomedical Science, University of Malaya,
2
Kuala Lumpur, Faculty of Science and Natural Resources,
Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
Objectives: The island of Borneo is located at the centre
of Southeast Asia and it could be an important station to
facilitate human migration in this region. The peopling
pattern of Borneo is believed to be shaped by both
ancient (50,000 years ago) and recent (5,000 years ago)
migration waves. We aimed to evaluate the genetic
structure of indigenous populations residing in Borneo
and relate them to other populations in the neighbouring
regions.
Methods: A total of 639 volunteers from three of the
largest indigenous populations in the state of Sabah,
Malaysia (i.e., Kadazan-Dusun, Bajau, and Rungus) were
recruited in the study. Genomic DNA was extracted from
venous blood or buccal samples using a conventional
phenol-chloroform extraction method. We examined
genetic markers in both autosomal and mitochondrial
genomes. A total of 15 Short Tandem Repeat (STR)
markers were amplified using Powerplex 16 system
(Promega, USA) and analyzed with fragment analysis
mode on a genetic analyzer. Diversity indices and
Objectives: Genetic risk prediction is a nascent scientific
concept in India compared to the Western world.
Therefore our greatest challenge is estimating ethnicityspecific frequencies of the polymorphisms and to keep
research in this arena ongoing, using available HapMap
data is a norm. Still, a noteworthy anticipation is that
allele frequencies (AF) in Asian Indians could differ from
HapMap Caucasian population (CEU). Therefore we
investigated the discriminative accuracy of testing
multiple susceptibility genes (their most relevant single
nucleotide polymorphisms/SNPs) for chronic, lifestylerelated diseases. We also studied the ethnicity-specific
differences in risk allele frequencies (RAF) and predictive
ability of disease-associated SNPs comparing Asian
Indians with Caucasians.
Methods: We compared predictive ability of genetic
testing offered by 4 leading companies including Xcode
Life Sciences, based on HapMap data considering a
simulated population of 100,000 individuals. Predictive
ability of genetic risk models was quantified by the area
under receiver operating characteristic curve (AUC)
which depends on the selected SNPs, their AFs and the
135
average population risk. In a random sample of 176
individuals of Asian Indian ethnicity we studied the AFs of
384 SNPs related to chronic, lifestyle-related diseases
and compared it with the data reported in HapMap
CEU population (n=112). All the SNPs were well
evidenced in GWAS for disease risk. DNA was extracted
from saliva samples and genotyping was performed using
®
Illumina GoldenGate assay. AFs were determined by
direct gene count method. Among the 384 SNPs, 46 were
not in Hardy-Weinberg equilibrium and for 12, data were
unavailable in HapMap. We compared the predictive
ability by quantifying the AUC for calculated RAFs (Asian
Indian) with HapMap CEU RAFs.
Results: The AUC values for Type 2 diabetes (T2D) were
significantly higher for Xcode (0.73) compared to the
other companies (0.59, 0.64 and 0.63). A statistically
significant difference (p<0.05) from CEU population was
observed in 43% of these 326 SNPs. For T2D the
predictive ability in terms of AUC values showed an
improvement of 0.74 (calculated RAF) compared to 0.73
(HapMap CEU RAF).
Conclusion: There is a significant difference between the
RAFs of Asian Indians and Caucasians. Hence novel
statistical
approaches
employing
appropriate
susceptibility genes improve predictive ability for
diseases.
Disclosure of Interest: None Declared
the haplotype analysis, no significant associations were
observed (P > 0.05).
Conclusion: Although there are study limitations, such as
no functional evaluations and insufficient sample size of
TCA subgroup due to its rareness condition, our findings
suggest that genetic variants of TRA2B might be
associated with the risk of TCA subtype of HSCR and/or
the mechanisms related to ENS development.
References: Kim JH, Cheong HS, Sul JH, et al. (2012) A
genome-wide association study identifies potential
susceptibility Loci for hirschsprung disease. PloS one.
9:e110292.
Roberts JM, Ennajdaoui H, Edmondson C, Wirth B,
Sanford JR, Chen B. (2014) Splicing factor TRA2B is
required for neural progenitor survival. J Comp Neurol
522:372-92
Storbeck M, Hupperich K, Gaspar JA, Meganathan K,
Martínez Carrera L, Wirth R, Sachinidis A, Wirth B. (2014)
Neuronal-specific deficiency of the splicing factor Tra2b
causes apoptosis in neurogenic areas of the developing
mouse brain. PLoS One 9:e89020.
Disclosure of Interest: None Declared
P155
TARGETED EXOMING IN SEARCH OF HUMAN NEURAL
TUBE DEFECTS GENE(S)
1,*
2
3
S. W. Mohd-Zin , A. Ahmad-Annuar , M.-K. Thong , Y.
4
5
1
Osman , L. Niswander , N. M. Abdul-Aziz
1
Department of Parasitology, Faculty of Medicine,
2
Department of Biomedical Science, Faculty of Medicine,
3
Department of Paediatrics, Faculty of Medicine,
4
University of Malaya, Kuala Lumpur, Klinik Yasmin,
5
Lumut, Perak, Malaysia, Department of Pediatrics,
University of Colorado Anschutz Medical Campus,
Children's Hospital Colorado, Aurora, United States
P154
POTENTIAL
ASSOCIATION
BETWEEN
TRA2B
POLYMORPHISMS
AND
TOTAL
COLONIC
AGANGLIONOSIS OF HIRSCHSPRUNG DISEASE
1,*
2
12
S.-G. Lee , J.-H. Kim , H. D. Shin
1
2
Life Science, Research Institute for Basic Science,
Sogang University, Seoul, Korea, Republic Of
Objectives: Hirschsprung disease (HSCR) is characterized
by absence of ganglion cells in gastrointestinal tract, and
divided into three subgroups of short-segment, longsegment, and total colonic aganglionosis (TCA)
depending on phenotypic variability. In our previous
genome-wide association study, a variant (rs2551372) of
transformer 2 beta homolog (TRA2B) was found to be a
potential site for the risk of TCA among HSCR subgroups.
Since TRA2B is known for the functions in neuronal cell
viability during mammalian development and postnatal
up-regulation in the small intestine, we further carried
out an extend replication study for the association
between TRA2B genetic variants and HSCR.
Methods: A total of 12 common single nucleotide
polymorphisms (SNPs) of TRA2B were genotyped in a
larger cohort of 187 HSCR patients and 283 unaffected
controls.
Results: Although no significant associations in the casecontrol analysis adjusting sex as a covariate were
observed, two SNPs (rs2251407 and rs2247622) revealed
increased associations with TCA subgroup (P = 0.01 and
0.007, respectively) compared to unaffected controls. In
Objectives: Neural tube defects (NTDs) are a group of
malformations of the central nervous system that
originate at various times during neurulation. NTDs are
divided into two groups; open and close NTDs. Spina
bifida occulta (SBO) is thought to arise from secondary
neurulation. However, as observed in our cohort, the
neurological deficits and level of lesions in SBO are
almost similar to spina bifida aperta (SBA) that arises
from primary neurulation. This study investigates
whether there may be a genetic aetiology behind
susceptibility to NTDs and whether there may be a
genetic link between the aperta and occulta forms of
NTDs.
Methods: Four probands with SBO, one SBA and one
cranial meningocele (close cranial NTD) were sent for
whole exome sequencing. Thus far, three results of SBO
were obtained and analysed. Non-synonymous single
nucleotide variants (SNVs), indels (insertion or deletion),
or frameshift mutations with minor allele frequency
(MAF)<0.01 were shortlisted. Genes related to previous
human or mouse NTDs studies and the putative
functional pathways associated with NTDs developments
were used for SNVs filtering and then analysed for
136
novelty and protein functional prediction. Further PCR
validations were tested in other probands and controls
to get MAF case-control comparison and to test the level
of penetrant alleles in the affected triads.
Results: To date, 12-potential SNVs in ADAM19, SOX30,
LAMP1, CECR2, CUBN, LAMA5, and NUP188, have been
identified. Four SNVs shared between the three SBO
probands were identified from ADAM19, SOX30 and
LAMP1. Interestingly, co-variants in CECR2 and CUBN
were present in two of our Malaysian probands.
Furthermore, co-variants in LAMA5 and NUP188 were
also found in one Malaysian proband (SB3A).
Conclusion: This is the first study that investigates
possible candidate genes for NTDs in an occulta cohort.
As the SNVs have a high match with previously published
data in both human and mouse neural tube defects, our
study raises interesting questions whether SBO samples
with neurological deficits are relevant in the search for
the human NTDs gene.
Disclosure of Interest: S. Mohd-Zin Grant/Research
support from: High Impact Research (HIR) Grant
UM.C/625/1/HIR/148/2 from the University of Malaya,
A. Ahmad-Annuar Grant/Research support from: High
Impact Research (HIR) Grant UM.C/625/1/HIR/062 and
UM.C/625/1/HIR/148/2 from the University of Malaya
and HIR Grant UM.C/625/1/HIR/MOHE/MED/08 from
the Ministry of Higher Education Malaysia, M.-K. Thong
Grant/Research support from: High Impact Research
(HIR)
Grant
UM.C/625/1/HIR/062
and
UM.C/625/1/HIR/148/2 from the University of Malaya
and HIR Grant UM.C/625/1/HIR/MOHE/MED/08 from
the Ministry of Higher Education Malaysia, Y. Osman:
None Declared, L. Niswander: None Declared, N. AbdulAziz Grant/Research support from: High Impact Research
(HIR)
Grant
UM.C/625/1/HIR/062
and
UM.C/625/1/HIR/148/2 from the University of Malaya
and HIR Grant UM.C/625/1/HIR/MOHE/MED/08 from
the Ministry of Higher Education Malaysia
Methods: We determined approximately 800,000
genome-wide SNP in four Philippine Negritos (Aeta, Agta,
Mamanwa, Batak) and one Malaysian Negrito (Jehai)
group using Affmetrix 6.0 genechip. We compared the
SNP data with other neighboring groups including
Andamanese Negritos and Papuans. Relationships were
inferred using PCA, ADMIXTURE, and phylogenetic trees
and networks.
Results: Phylogenetic tree analysis showed that the
Andamanese and Papuans are basal to other Negritos in
Southeast Asia whereas PCA and ADMIXTURE results
showed extensive signs of admixture between the
Malaysian and Philippine Negritos with their non-Negrito
neighbors. However, NeighborNet networks show
reticulation between Philippine, Malaysian and
Andamanese Negritos, suggesting a common link
between these groups. We also found signals of
Denisovan admixture in the Philippine Negritos,
particularly in the Aeta.
Conclusion: These results suggest that while Negrito
groups can be genetically differentiated, they also appear
to share a common link. They also display signs of recent
admixture with their neighboring non-Negrito
populations and in the case of Philippine Negritos, with
archaic humans as well.
Disclosure of Interest: None Declared
P157
DISTRIBUTION OF MC1R ARG163GLN VARIANT IN
MODERN JAPANESE, RECENT AINU AND JOMON
INDIVIDUALS
1,*
2
3
T. Motokawa , N. Adachi , H. Kanzawa-Kiriyama , K.-I.
3
Shinoda
1
Skin Research Department, POLA Chemical Industries,
2
INC., Yokohama, Department of Legal Medicine,
lnterdisciplinary Graduate School of Medicine and
Engineering, University of Yamanashi, Yamanashi,
3
Department of Anthropology, National Museum of
Nature and Science, Ibaraki, Japan
P156
TRACING LINKS BETWEEN NEGRITOS IN SOUTHEAST
ASIA USING GENOME-WIDE SNPS
1,*
2
1
T. Jinam , M. Phipps , S. Naruya
1
Division of Population Genetics, NATIONAL INSTITUTE OF
2
GENETICS, Mishima, Japan, Jeffrey Cheah School of
Medicine and Health Sciences, Monash University
(Sunway Campus), Selangor, Malaysia
Objectives: Melanocortin receptor 1 (MC1R), a Gprotein-coupled receptor on melanocytes, plays an
important role in melanogenesis. Agonist binding induces
biosynthesis of eumelanin. MC1R is highly polymorphic,
and some variants are related to melanogenic
phenotypes. Furthermore, a few variants are also
regional, and are thought to offer important markers in
discussing population movements. We have previously
found relationships between the Arg163Gln variant and
pigmented spots in Japanese individuals, and shown the
possibility of unique regional distributions in Japanese
(HGM2005). The present study analyzed the distribution
pattern of the allele in modern Japanese, Jomon (one of
ancestral groups of Japanese), and Ainu (descendants of
Hokkaido Jomon), and discuss how these distribution
patterns arose in Japan.
Methods: Modern Japanese: Genomic DNA was isolated
from eyebrow hairs collected from randomly selected
Japanese subjects, and the Arg163Gln allele was
Objectives: The Southeast Asian region is widely viewed
as a corridor for early human migrations. The Negritos
are thought to be remnants of this early migration and
currently inhabit the Andaman islands, Philippines and
the Malay Peninsula. They are phenotypically unique
from their neighbors and are traditionally associated
with darker skin, frizzy hair, short stature and a huntergathering lifestyle. We seek to infer the relationship
between the various Negrito groups and to ascertain
whether they share a common ancestry tracing back to
the earliest settlers.
137
sequenced. Subject hometowns were collected by
questionnaire and divided into three areas of Japan
(central, north peripheral, and south peripheral).
Ainu: The Arg163Gln allele was analyzed by TaqMan SNP
Genotyping Assays using genomic DNA. Ainu DNA was
collected from skeletons unearthed in Hokkaido.
Jomon: Allele data were extracted from DNA sequence
data of a Jomon individual, and analyzed using a nextgeneration sequencer. The Jomon DNA sample was
collected from teeth (date of burial estimated as about
2000 BCE) unearthed in Shitsukari-Abe.
Results: The percentage of subjects carrying homozygous
163Arg alleles was significantly higher in Japanese from
peripheral areas (n=31) than in Japanese from the central
area (n=244). The percentage was significantly higher in
Ainu (n=29) than in modern Japanese (n=244). The
Jomon sample (n=1) was homozygous for 163Arg.
Conclusion: A dual structure model has been widely
accepted for the formation of the modern Japanese
population. In this model, the Japanese derive from
indigenous Jomon and Yayoi immigrants, with mixtures
of these populations spreading into Japan, but
populations with relatively greater Jomon genetic
background remaining in peripheral areas of Japan. Ainu
have been regarded as direct descendants of Jomon. Our
results show that the percentage of the 163Arg allele
increases with proximity of the population to Jomon,
implying that the 163Arg allele in modern Japanese
might indicate descent from Jomon.
Disclosure of Interest: None Declared
absolute latitude. These SNPs are located in regions of
about 450 genes. Analysis of association spectra of these
top SNPs and corresponding genes in Genetic Association
Database (GAD) reveals that major associated
phenotypes are metabolic traits, immune and infectious
diseases, neuro-psychiatric disorders, behavioral traits,
response to xenobiotics, and chemo-dependency traits.
Key biological processes involving these genes include
regulation of metabolism, signal transduction, response
to exogenous stimuli, regulation of neural system. Some
of top genomic regions were found under positive or
balancing selection in Africans or European/Asian
populations according to hyaplotype homozigozyty (EHH,
XP-EHH) and Tajima tests. Examples of regions subjected
to selective pressure during human migrations include
UDP-Glucuronosyltransferase-2B7 (UGT2B7, metabolism
of xenobiotics), uncoupling proteins (UCP2-3,
thermoregulation), and interferon lambda (IFNL4,
modulation of immune response) genes.
Conclusion: We suppose that genetic diversity in the
substantial part of the human genome were shaped by
adaptation to new environment during early human
migrations. This pattern of genetic diversity may
contribute to common diseases in modern populations,
and may be explained by the hypothesis of
canalization/decanalzation of genotype-environment
relationships under the pressure of natural selection.
Disclosure of Interest: None Declared
P159
GENOMIC REGIONS INVOLVED IN THE DETECTION OF
DIFFERENT PATHOGENS REQUIRES ACCUMULATION OF
RARE VARIANTS
1
1
1
I. Uktverytė , I. Domarkienė , L. Ambrozaitytė , V.
1,*
Kučinskas
1
Department of Human and Medical Genetics, Vilnius
University, Vilnius, Lithuania
P158
GENOME-WIDE SEARCH FOR SIGNALS OF HUMAN
ADAPTATION TO CLIMATE
1 2,*
2
2
V. Stepanov
, V. Kharkov , A. Markov , A.
2
2
2
Cherednichenko , K. Vagaitseva , E. Trifonova
1
2
Tomsk State Univeraity, Institute for Medical Genetics,
Tomsk, Russian Federation
Objectives: Determine genomic regions with the greatest
number of rare variants in the Lithuanian population.
Methods: Unrelated individuals who indicated at least
three generations of Lithuanian ethnicity formed the
sample set of 52 samples. Next-generation exome
sequencing after in-solution capture enrichment
(TargetSeq™, SureSelect) with an average of a 40-fold
coverage was performed using 5500 SOLiD™ Sequencer
at the Vilnius University. Sequence alignment, secondary
and tertiary analysis performed using LifeScope™
Genomic Analysis Software v2.5. Data management of
exome annotated variants was performed using
PostgreSQL v.9.2.3. Linear regression model was
constructed using R v3.0.3 (Ade4, Rcmdr) [1].
Results: A linear regression of rare exome variants (MAF
< 5%) to total variants per gene in the Lithuanian
population was performed. Analysis showed that the
outlying genes in the Lithuanian population were MUC4,
MUC5B, TTN, which had the greatest number of rare
variants per total number of variants as compared to the
other genes. The MUC gene family members (MUC4,
Objectives: Adaptation to new environment during early
human migrations played the substantial role in shaping
the genetic structure of modern human populations. We
have investigated the distribution of genome-wide SNPs,
correlated with climatic and geographic parameters, in
worldwide human populations.
Methods: Our data on genome-wide SNPs frequencies in
30 Eurasian populations were pooled with the data on 49
worldwide populations from Human Genome Diversity
Project (HGDP) and HapMap III. Overlapping set of about
200K SNPs in 79 populations was analyzed by means of
positional search of association of allele frequencies with
climatic and geographic parameters and search for
signals of natural selection. Top signals were subjected
to bioinformatic analysis of disease association spectra,
biological processes, pathways, and molecular functions
of corresponding genes using GAD, DAVID, KEGG and
STRING resources.
Results: About 1000 top SNPs were found very
significantly correlated with key climatic parameters and
138
MUC5B) encode secreted or cell-associated glycoproteins
of epithelial cells. Proteins of these genes play a role in
cellular interaction and protecting from extracellular
pathogens. Titin (TTN) is the gene with the largest cDNA.
Moreover, analysis showed that MUC16, ZNF717, HLADRB1, PKD1L2, MAP2K3, DYNC2H1 genes had the least
number of rare variants per total number of variants.
HLA-DRB1 gene product is part of the immune system.
The ZNF717 gene product is a transcription factor. The
PKD1L2 gene product is a component of cation channel
pores. The MAP2K3 gene product participates in the
MAP kinase-mediated signaling cascade. The DYNC2H1
gene product is involved in retrograde transport in the
cilium and has a role in intraflagellar transport.
Conclusion: A large number of rare variants in MUC4,
MUC5B, TTN genes could be due to the specificity of
these genes and/or to the physical length of a gene. A
larger number of common variants (MAF > 5%) in these
genes may be due to the effect of natural selection on
the gene products that interact with a large number of
other gene products or participate in the general cell
functions.
Acknowledgment: LITGEN project (VP1-3.1-ŠMM-07-K01-013) is funded by the European Social Fund under the
Global Grant measure.
References: [1] Raska P., Zhu X. Rare variant density
across the genome and across populations. BMC
Proceedings 2011, 5(Suppl 9):S39.
Disclosure of Interest: None Declared
Methods: A total of 110 Iban and Bidayuh were
recruited. Physical assessments were performed and two
blood tubes were withdrawn. Subjects’ clinical blood
lipid parameters were analyzed and DNA was extracted.
Allele Specific-PCR of LDLR gene for two polymorphisms
(c. 1060+7 T>C & c. 1706-55A>C) were categorized into
homozygous wild, heterozygous and homozygous SNP.
Agarose gel electrophoresis was performed and the data
were analysed using SPSS.
Results: Preliminary data shows that 99.1% have
homozygous SNP and 0.9% have homozygous wild in c.
1060+7 T>C, while in c. 1706-55A>C: 66.4% have
heterozygous SNP, 21.8% have homozygous SNP and
11.8% have homozygous wild. So far there is no
significant association between SNPs and lipid profiles
level among Iban and Bidayuh population in Sarawak. We
also found out that the level of LDL mean is
approximately and within the border line for all the
categories of genotypes. The mean (SD) of LDL
cholesterol level for c. 1060+7 T>C homozygous wild,
homozygous SNP is 3.4 (0.00) and 3.2 (1.09) respectively
while for c. 1706-55A>C heterozygous SNP, homozygous
wild and homozygous SNP is 3.2 (1.05), 3.4 (1.03) and 3.3
(1.25) respectively. This might be due to the combined
genotypes of variants within LDLR gene were detected.
Conclusion: Preliminary findings from this ongoing
research show that SNPs of the LDLR gene are present in
the Iban and Bidayuh. Further works is needed to
determine the linkage disequilibrium among variants of
LDLR gene.
Disclosure of Interest: None Declared
P160
SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) OF LOWDENSITY LIPOPROTEIN RECEPTOR GENE (LDLR) IN LIPID
RELATED
GENE-ASSOCIATED
FAMILIAL
HYPERCHOLESTEROLAEMIA
AMONG
IBAN
AND
BIDAYUH
ETHNIC
GROUPS
IN
SARAWAKIAN
POPULATION: PRELIMINARY DATA ANALYSIS
1,*
1
1
2
Y. Siaw , H. Hood , S. P. Sim , H. Helmy , M. M.
3
Aminudin
1
2
Paraclinical Science, Community Medicine and Public
3
Health, Centre for Pre-University Studies, Universiti
Malaysia Sarawak, Kuching, Malaysia
RNA BIOLOGY
P161
DIFFERENTIAL EXPRESSION OF MICRO-RNA’S AND
MRNA’S IN PBMCS OF SPINOCEREBELLAR ATAXIA1
PATIENTS
1,*
1
D. Kumaran , G. Hasan
1
National Centre for Biological Sciences, Bangalore, India
Objectives: Spinocerebellar ataxia1 or SCA1 is an
autosomal dominant neurodegenerative disorder
characterized by loss of balance and motor coordination
due to primary dysfunction of the cerebellum and is
caused by CAG repeat expansion in ATAXIN1. Ataxin1 is
known to play a role in transcription and RNA
metabolism. Transcriptional deregulation is an early
occurrence in the pathogenesis of the disease.The aim of
my work is to understand if alterations in miRNA and
mRNA expression occur during the progression of the
disease and to understand if these changes can be
captured in Peripheral Blood Mononuclear Cells (PBMCs)
of patients.
Methods: Presymptomatic and symptomatic patients
and normal individuals living in the same geographic
location and having common genetic founders were
selected. Small RNA sequencing was conducted in 8
patients (4 presymptomatic and 4 severe) and 8 normal
Objectives: Familial Hypercholesterolaemia (FH) is a
genetic disease caused by defects in a number of
variants, including low-density lipoprotein receptor gene
(LDLR)
that
regulate
plasma
LDL-cholesterol
concentrations. FH typically passed down through
families in an autosomal dominant manner. That means
one only needs to acquire the abnormal gene from one
parent in order to be affected by the disease. FH has a
worldwide prevalence of 0.2%, however it is considerably
higher in some population because of a founder effect.
This study was initiated as there is no FH data available in
Sarawak. We aimed to determine the frequencies lipid
related gene polymorphisms in Iban and Bidayuh ethnic
groups in Sarawak, and its associations with lipid
profiles.
139
individuals. Subsequently RNA sequencing was done in a
subset of these patients and correlation of miRNA-mRNA
was carried out using Ingenuity Pathway analysis tool. An
in-depth analysis of the RNA sequencing data in terms of
pathways, affected networks and validation by QPCR was
also carried out. Differential expression was analyzed
using edgeR.
Results: Co-expressed miRNA clusters were observed in
SCA1 patients. Significant miRNA and mRNA expression
differences were obtained between the presymptomatic
and symptomatic SCA1 patients when compared to
normal individuals. Over-expression of three miRNAs
observed in the symptomatic SCA1 patients specifically
targets the expression of 86 mRNA’s, which are down
regulated. Together, these data indicate that several
important pathways leading to neurodegeneration and
activation of microglial components are affected in the
PBMCs of SCA1 patients.
Conclusion: Differentially expressed miRNAs and mRNAs
in SCA1 were captured in PBMCs of SCA1 patients
indicating the reliability of using blood for the study of
neurodegenerative progression in SCA1.
Disclosure of Interest: None Declared
IC50 (0.9 uM), through its low fluorescent signal (2.32).
Reference minigene representing skipping even showed
high signal (39.36). This was validated using RT-PCR
showing discreet and single 1032 bp of PCR product of
exon 53 minigene following exposure with Isodiospyrin.
Direct sequencing further validated the non-skipping
event.
Conclusion: Isodiospyrin with IC50 (0.9uM) failed to
inhibit ESE in exon 53 minigene. This is may be due to
overlapping of various ESEs occuring in exon 53 of
Dystrophin gene. We are currently awaiting results of
Isodiospyrin activity against ESE-specific minigene.
Disclosure of Interest: None Declared
P162
ISODIOSPYRIN DOES NOT ALTER SPLICING ACTIVITY OF
DYSTROPHIN GENE EXON 53
1,*
2
3
R. Rashid , M. Mustapha , Z. A. Mohd Hussin , H. Abdul
4
1
Wahab , T. H. Sasongko
1
2
Human Genome Centre, Department of Neurosciences,
3
Department of Paediatrics, Universiti Sains Malaysia,
4
Kubang Kerian, School of Pharmaceutical Sciences,
Universiti Sains Malaysia, Penang, Malaysia
Objectives: To determine the effects of vitamin E in
regulating myogenic regulatory factors (MRFs) at early
stage of myogenic differentiation in senescent human
myoblasts.
Methods: Primary human myoblasts were cultured into
young and senescent. Cells were treated with
tocotrienol-rich fraction (TRF) and alpha-tocopherol
(ATF) for 24 hours. All groups of myoblasts were induced
to differentiate into myotubes and the MRFs (MYF5,
MYOD1 and MYOG) mRNA expressions were determined
while fusion index analysis was carried out after 9 days of
differentiation induction. Comparison between two
treatment groups was carried out using independent Ttest, while ANOVA test was used to analyse differences
between multiple treatment groups.
Results: Our data showed that replicative aging affects
the normal myogenic differentiation programs of
myoblasts. Induction of MYOD1 and MYOG mRNA
expression was delayed, but MYF5 mRNA was normal in
senescent myoblasts. The transcription level of MYOD1
mRNA in young cells increased 2-fold after one day of
induction, but a significantly lower expression of MYOD1
mRNA was shown in senescent myoblasts (p<0.05). A
similar pattern of expression was observed for MYOG
mRNA. About 4-fold increment of MYOG mRNA after two
days of differentiation in young cells was observed while
only 2-fold increment was seen in senescent cells. TRF
treatment promotes myogenic differentiation by upregulating MYOD1 and MYOG mRNA in senescent cells.
The impaired expression of MYOD1 and MYOG mRNA
during replicative senescence was significantly recovered
with TRF treatment (p<0.05). ATF however only
increased the MYOD1 mRNAs expression in senescent
myoblasts as compared to untreated control (p<0.05).
Moreover, both MYOD1 and MYOG mRNA expression
P163
DYNAMICS OF MYOGENIC REGULATORY FACTORS
REVEALED THE POTENTIAL IMPLICATION OF VITAMIN E
IN MEDIATING DIFFERENTIATION DURING SKELETAL
MUSCLE AGING
1,*
1
1
S. C. K. Khor , N. Abdul Karim , W. Z. Wan Ngah , S.
1
Makpol
1
Biochemistry, Universiti Kebangsaan Malaysia, Kuala
Lumpur, Malaysia
Objectives: Study focusing on the usage of isodiospryin
as exon skipping inducer in kinetic inhibition against
topoisomerase-I has been successful. This exon skipping
capacity may facilitate search for therapeutic compounds
against Duchenne Muscular Dystrophy (DMD). However,
it is not clear if Isodiospyrin capacity to induce exon
skipping was facilitated through the inhibition of exonic
splicing enhancer (ESE). At the preliminary, we tested
Isodiospyrin against the splicing activity of a minigene
containing a real exon of Dystrophin gene where there
are a number of overlapping ESEs.
To determine the inhibitory effect of isodiospyrin against
exon splicing enhancers of exon 53 minigene in
dystrophin gene.
Methods: Exonic splicing enhancer of exon 53 Dystrophin
gene were identified using ESEfinder 3.0 software. A
group of minigenes for testing splicing activity of
Dystrophin exon 53 minigenes were constructed and
preceded to cloning. They were then validated using
sequencing technique prior to transfection into HEK-293
cell line for splicing assay. The assay was done using
luciferase assay and reverse transcriptase PCR (RT-PCR)
before a final confirmation with direct sequencing.
Results: Luciferase assay showed no skipping event for
exon 53 minigene following exposure with Isodiospyrin
140
level in ATF-treated cells were significant lower
compared to TRF-treated cells (p<0.05), indicating the
superior effect of TRF in regulating MRFs at early stage of
myogenic differentiation in senescent human myoblasts.
Conclusion: Our study demonstrated that deregulation
of myogenic differentiation in senescent myoblasts is
reversible by TRF and ATF, which could be a potential
intervention in restoring regenerative defects during
aging or muscular diseases. The effect of TRF however is
more superior as compared to ATF.
Disclosure of Interest: None Declared
unpaired student T-test with a p-value < 0.01. Pathway
enrichment was also performed with key genes within
these pathways selected for validation with qPCR.
Results: The gene expression profiling indicated that
were a substantial number of genes that were
differentially expressed with more than a 2-fold change
(p < 0.01) between each of the four different conditions.
We selected key genes within significant pathways that
were analyzed through pathway enrichment. These key
genes included regulators of cell proliferation,
transcription factors, cytokines and tumour suppressor
genes. These genes play key roles in signal transduction
pathways including those involved in G protein coupled
receptor signaling, transcription factor regulation,
tumourigenesis and cytokine signaling.
Conclusion: In this study we have shown that key genes
involved in significant and well established pathways, can
be exploited as a potential blood based biomarker to
differentiate between high and low grade gliomas, nongliomas and control samples.
Disclosure of Interest: None Declared
P164
A BLOOD BASED GENE EXPRESSION AND SIGNALING
PATHWAY ANALYSIS TO DIFFERENTIATE BETWEEN HIGH
GRADE AND LOW GRADE GLIOMAS.
1*
1
1
S.N. Ponnampalam , M.F. Zulkifle , N.A. Azami , S.
1
1
1
Ponnusamy , N.R. Kamaluddin , Z. Zakaria
1
Cancer Research Centre, Institute for Medical Research,
Jalan Pahang, 50588 Kuala Lumpur, Malaysia
Introduction: Brain tumours are the 17th most common
cancer worldwide. Gliomas are the most common of the
primary brain tumours and are highly malignant. Several
genetic mutations are associated with gliomas but to
date none have been targeted successfully to confer any
significant therapeutic application.
Objectives: (a) To undertake gene expression profiling of
the blood of glioma patients to determine key genetic
components of signaling pathways
(b) To develop a panel of genes that could be used as a
potential blood based biomarker to differentiate
between high and low grade gliomas, nonglioma and
control samples.
Methods: Blood samples were obtained from glioma
patients, non-glioma and control subjects. Ten samples
each were obtained from patients with high and low
grade tumours respectively, ten samples from nonglioma patients and twenty samples from control
subjects. The tumours included Grades I and II
oligodendroglioma and Grades I to IV astrocytoma
including glioblastoma multiforme. The non-glioma
conditions included hemangioblastoma, inflammatory
pseudotumour,
arteriovenous
malformation,
hemorrhagic stroke and multiple sclerosis. Total RNA was
isolated from each sample after which first and second
strand synthesis was performed. The resulting cRNA was
then hybridized with the Agilent Whole Human Genome
(4x44K) microarray chip according to the manufacturer's
instructions. Universal Human Reference RNA and
samples were labeled with Cy3 CTP and Cy5 CTP
respectively. Four groups of samples were analyzed as
follows: high grade glioma vs control, high grade vs low
grade glioma, low grade glioma vs control and nonglioma vs control. Microarray data were analyzed by
Agilent Gene Spring 12.1V software using stringent
criteria which included at least a 2-fold difference in gene
expression between samples in the four different
conditions. Statistical analysis was performed using the
141