OFFICE FOR HEALTH AND MEDICAL RESEARCH
EXPRESSION OF INTEREST (EOI) FORM
SYDNEY GENOMICS COLLABORATIVE GRANTS PROGRAM
2015-16
DEADLINE 5pm, Monday 12th October 2015
SECTION A – ADMINISTRATIVE SUMMARY
A.1
Application Title
Provide a short descriptive title (maximum 200 characters including spaces).
A.2
Administering Institution
Administering Institution Details
Institute Name
A.3
Administering Institution Contact
Select a Title: Choose a Title
Family Name:
Given Name:
Postal Address:
Telephone:
Mobile:
Email:
NSW Genomics Collaborative Grants Program 2015-16
A.4
Chief Investigator A (1st Chief Investigator) Details
Select a Title: Choose a Title
Family Name:
Given Name:
Postal Address:
Telephone:
Mobile:
Email:
Are you an Australian Citizen/ Permanent Resident?
Are you located in New South Wales?
YES
YES
☐
☐
NO
NO
☐
☐
YES
YES
☐
☐
NO
NO
☐
☐
A.5
Chief Investigator B
Select a Title: Choose a Title
Family Name:
Given Name:
Postal Address:
Telephone:
Mobile:
Email:
Are you an Australian Citizen/ Permanent Resident?
Are you located in New South Wales?
[Instruction – please add more Chief Investigators as required]
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SECTION B – PROJECT PROPOSAL
B.1
Lay Project Summary
In lay terms summarise the application referring to aims, significance and expected outcomes
suitable for NSW Health website and media releases (maximum 2500 characters including spaces).
B.2
Short Form Proposal
Summarise the application referring to aims, significance and expected outcomes. Please include how
the project meets the aims and use the guidelines under each heading (maximum 500 words each):
1.
Objectives, design and expected outputs and outcomes (50%)
This should include an outline of the study design under the following headings: Aims and
Objectives, Background, Research Plan, Analysis, Specific Outputs, Expected Outcomes.
Responses should correspond with the Eligibility and Assessment Criteria. It should include
a description of the nature and number of bio-specimen samples to be sequenced, any
tests already done, patient information linkages, subject selection criteria and any other
relevant information.
Short Form Proposal (500 Word Cap):
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NSW Genomics Collaborative Grants Program 2015-16
2.
Significance of the Expected Outcomes and/or Innovation of the Concept (25%)
Outline the clinical relevance of the project and the likely impact it will have on clinical
practice in NSW, Australia and the world. Proposals should focus on areas of substantial
research need and benefit, where the outcomes are anticipated to be feasible for
adoption into the health system. Briefly outline how the proposal will sit in the ‘bench to
bedside’ continuum for research translation. Provide a brief analysis as to how the
impacts of the project as described will deliver ‘value for money’ in the health system. This
section should also address the Eligibility and Assessment criteria, where appropriate,
especially around delineation of a likely outcome for a defined patient group.
Short Form Proposal (500 Word Cap):
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NSW Genomics Collaborative Grants Program 2015-16
3.
Team Quality and Capability, relative to opportunity (25%)
The expertise and experience of the research team relevant to the project, their
collaborative potential and potential collaborators and success in obtaining and delivering
past grant funding. An overview of previous achievements of the team and/or of
collaborative effort of team members should be provided.
Short Form Proposal (500 Word Cap):
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NSW Genomics Collaborative Grants Program 2015-16
SECTION C – BIOINFORMATICS AND GENOME SEQUENCES
C.1
Requested Bioinformatics Services and Genome Sequence amounts.
ITEM
DETAILS
NUMBER OF
SEQUENCES
COMMENTS
DETAILS
SERVICE
SOURCE
COMMENTS
Whole Genome
Sequencing at the
Garvan Institute
REFER TO APPENDIX
AND ENSURE THAT THE
SEQUENCING CAN BE
UNDERTAKEN ON THE
ILLUMINA HI SEQ X TEN
ITEM
Bioinformatics services
(indicate if sourced from
the Garvan or elsewhere)
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NSW Genomics Collaborative Grants Program 2015-16
SECTION D – ETHICS AND CONSENT
D.1
Ethics
Please outline whether ethics approval has been obtained;
If yes – Please include which ethics committees have approved the project, If there are any
conditions attached to the approval, please outline these as well.
If no – Please outline your plan for ethics approval.
D.2
Patient Consent
Please outline whether patient consent has been obtained;
If yes – for what components of the project and in what capacity.
If no – Please outline your plan for gaining patient consent and what it will cover.
SECTION E – PROJECT FUNDING
E.1
Does the project have funding secured?
If yes – list sources
If no – Please outline how will funding be secured for the remainder of the project?
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APPENDIX – SPECIFICATIONS
Sydney Genomics Collaborative
NSW Genomics Collaborative Grants Program
Technical Information – Whole Human Genome Sequencing
The Kinghorn Centre for Clinical Genomics (KCCG) at the Garvan Institute of Medical Research is the provider
of whole human genome sequencing for the NSW Genomics Collaborative Grants Program. KCCG is equipped
with the Illumina HiSeq X Ten platform, which has the capacity to sequence up to 350 human genomes per
week.
Sequencing service specification
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Sequencing services are for research purposes only.
Sequencing is for whole human genomes only (transcriptomic and epigenomic sequencing is not
permitted; non-human derived DNA is not permitted)
Applicants should budget $1,750+GST per DNA sample.
Genomes will be sequenced to a minimum mean coverage of 30X (minimum 100 Gbases, 2x150bp paired
end reads, >75% of bases with Q score > 30) in line with Illumina’s ‘Sequencing Coverage Calculation
Methods for Human Whole-Genome Sequencing’ documentation (http://tinyurl.com/o9bkmy7).
DNA extraction and quantification
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DNA should be extracted using Qiagen DNeasy Blood / Tissue Extraction Kits or similar. Please contact
KCCG prior to extraction to ensure compatibility and suitability of the extraction protocol.
DNA should be suspended in Qiagen Elution Buffer (EB - 10 mM Tris-Cl, pH 8.5) or Illumina Suspension
Buffer (RSB).
Fluorometric-based methods for quantification including Qubit or PicoGreen are recommended to provide
accurate quantification of dsDNA. Spectrophotometry is not a recommended quantification method for
whole genome sequencing.
DNA samples must meet the following specifications;
Protocol
Vol. (uL)
Conc. (ng/uL)
A260:280
Total
WGS v2.1 (TruSeq PCR-Free)
>50
50 - 100
>1.8
>2,500 ng
WGS v2.0 (TruSeq Nano)
>50
20 - 100
>1.8
>1,000 ng
DNA samples must not be amplified (i.e. DNA should not have been subjected to PCR, WGA, MDA) or
reverse transcribed from RNA.
DNA samples must be free of contaminating nucleic acids.
DNA samples cannot be derived from FFPE material.
DNA samples should not be modified prior to shipping (e.g. bisulphite conversion).
DNA samples must be pure, intact and of high molecular weight.
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Samples submitted failing to meet any of the above criteria will be removed from further processing and the
submitter notified.
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Shipping instructions
Samples must be submitted in FluidX 2D Barcoded tubes associated with online submission forms
(provided by KCCG).
Online sample submission must be completed and submitted for validation prior to samples shipping.
Samples should be shipped Frozen on Dry Ice and tracking number provided to KCCG.
Ethics and consent
 DNA can only be accepted from studies governed by a recognised Human Research Ethics Committee
(HREC).
 DNA can only be accepted from individuals that have undergone informed consent for genetic testing.
 Study approval and consent will be required to be in place before sequencing commences for submissions
to be considered in the funding round.
Turnaround time and data delivery
 On sample acceptance following internal QC, data will be returned within 6 weeks (subject to capacity).
 Data will be supplied as FASTQ data files. Bioinformatic analysis (i.e. alignment and variant calling –BAM
and VCF files) can be performed at the KCCG at an additional cost of $250+GST per genome.
 Data will be made available via DNAnexus or shipped on external hard drive (additional charges will
apply).
Terms and conditions
 Each project will need to agree to KCCG Terms and Conditions (attached).
Contact

For further information, contact:
Kinghorn Centre for Clinical Genomics
Sequencing Facility,
Garvan Institute of Medical Research
P: (02) 9355 5846
E: kccgseq@garvan.org.au
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