DNA Sequence Data Applications
Disease Tracking, Treatment and Prevention
Hotspots of Genetic Diversity
• DNA profiling is based on the concept that
every genome is unique
• DNA consists of paired nucleotides, which
members of the same species share
approximately 99% commonality
• Almost all genetic diversity exists in small
polymorphic regions
DNA Polymorphisms
• Single-nucleotide polymorphisms (SNP –
pronounced snips)
• Short tandem repeats (STR)
• Variable number of tandem repeats (VNTR)
• DNA profiling relies on these regions
known as molecular markers
DNA Profiling in Fighting Disease
• Identifying markers like SNPs help medical
researchers to distinguish different types of
disease causing agents
• Cataloging the appropriate genetic markers
is called scoring a gene
• Until recently it took 3 months to score a
gene
• Now it it possible to score thousands in a
single day
New DNA Profiling Applications
• Protecting against threats to food supply
• Connecting strains of pathogens to the
disease they cause
• Determining the appropriate course of
treatment for different genetic variations of
cancer
DNA Sequencing
• DNA fingerprinting is helpful when
comparing variable sections of similar
genomes within the same species
• When a scientist is identifying an unknown
pathogen, a different technique is used
• Technicians use sections of genome that are
distinct for different species of bacteria
Fusariam Infection: A Case Study in
Using DNA to Guard Against a Plant
Epidemic
How new technology is being used to
blockade an ancient fungal disease that
threatens the world’s food supply
Guarding Against a Plant Epidemic
• The Fusarium toxin causes a disease in
barley and wheat called ‘head blight’ (or
scab) and ‘stalk rot’ in corn
• Human exposure to these toxins in infected
grain results in a variety of symptoms
including acute dermatitis, diarrhea, and
hemorrhaging
A Fungal Toxin in Action
• A healthy wheat head (left)
stands in contrast to one
inoculated with Fusarium
graminearum showing
symptoms of head blight
disease (right)
• This illustrated damage
causes $3 billion in the
U.S. alone
O’Donnell, 2000
One Disease – Eight Causes
• In the past, all scab epidemics
worldwide were thought to be
caused by a single pathogen
• The scab species could not be
distinguished from the toxins
they produced
• DNA profiling revealed that at
least eight genetically distinct
scab pathogens exist
O’Donnell, 2000
How Profiling Helps
• Based on DNA profiling, scientists created a
DNA-based diagnostic procedure
• It precisely distinguishes between the eight
species allowing technicians to determine the
pathogen's origin
• By determining which plants from various
parts of the world harbor the pathogens,
officials are able to prevent them from
spreading epidemics to the U.S.
O’Donnell, 2000
Lung Cancer : A Case Study in DNA
Analysis to Treat Genetic Diseases
• Approximately 20% of lung cancer are
classified as small-cell carcinomas
• The rest are classified as non-small-cell
carcinoma (NSCLC), for which therapies
often lead to unpredictable results
• Until DNA profiling, there was no way to
predict NSCLC’s response to therapy
Medical News Today, 2009
Non-Small-Cell Carcinoma
• Using DNA microarray analysis researchers
discovered that NSCLCs have genetic
patterns that predetermine their behavior
• Some are genetically disposed to spread
aggressively, and to metastasize early
• Others are likely to be easily treated
Medical News Today, 2009
Tumor Subtypes Detected
• Bronchoid
– Associated with the likelihood of improved
survival in early-stage disease
– Tumors that are least likely to respond to
chemotherapy because many genes associated
with resistance to chemotherapy agents
• Squamoid
– Associated with better survival in advanced
disease
Medical News Today, 2009
Escherichia coli O157:H7
A Case Study in Identifying the
Evolution of a Pathogen
• E. coli is a waterborne and foodborne bacteria
whose virulence seems to have been increasing
• Recent outbreaks have been marked by greater
hemolytic uremic syndrome (HUS)
• DNA profiling was used to prove newly evolved
strains are increasingly deadly
Manning, 2008
E. coli O157:H7 virulence
• Novel avenues of infection with new
animals and produce have resulted in
‘relentless evolution’
• O157 strains have increased geographically
and in diversity
– Viruses are responsible for insertions into the
bacterial DNA adding toxins that cause HUS
– The 2006 spinach outbreak is an example – it
demonstrated that the pathogen could subsist on
produce as well as meat
Manning, 2008
E. coli Evolution
Changing patterns revealed through
DNA profiling
DNA sequences have been
used to trace:
– the decline in one strain
of hemolytic E. Coli
(Clade 2)
– while another becomes
more prevalent (Clade 8)
– DNA collected during
outbreak proved new
clade increased 500%
Manning, 2008
E. coli Evolution (continued)
• Distribution of Shiga
toxin variants
among O157 strains
by clade
• As clades vary by
toxin, profiling the
DNA of the
pathogen is critical
to save lives with
prompt identification
of the appropriate
toxins
Manning, 2008
Training Exercise
• Pathologists use techniques like DNA
fingerprinting and sequence analysis to
identify pathogens or their specific strain
• In this lab, you will act as a pathologist at a
well-equipped research hospital. Your task
is to identify a bacterial sample received
from a clinician at the site of a mysterious
outbreak through sequence analysis
Virtual Lab: Identify a Pathogen
• You will follow a multi-step process to identify
potential bacterial pathogens by collecting and
searching for its DNA sequence
• Pay close attention – the public is anxious about
reports of an unidentified outbreak and the news
media is going to be asking questions when you
finish
• To begin visit:
http://www.hhmi.org/biointeractive/vlabs/bacterial
_id/index.html and click on ‘enter the lab’
HHMI, 2008
News Conference
• After completing your research, the news media
expects answers to questions based on your
findings.
• For every question, click on the correct answer. If
you make a mistake you will be returned to the
question to correct your statement.
• Good luck.
Software courtesy Russell, W
What technology did your sequencing use?
• A – Polymerization
• B – Polymeric Imaging
• C – Polymeric Systems
• D – Polymerase Chain Reaction
Sorry
That was the wrong answer
Correct !
Congratulations
What do proteolytic enzymes accomplish
when preparing samples?
• A – Energizes the cell wall to activate DNA
• B – Digests the cell wall to make access to DNA
possible
• C – Strengthens cell wall to protect DNA
• D – Denatures the cell wall to inactivate DNA
Sorry
That was the wrong answer
Correct !
Congratulations
Why is the 16S rRNA Gene Chosen to
Identify Unknown Bacteria ?
• A – Its DNA sequences are completely distinct for every
species, making identification simple
•
B – The gene is so common that it is economical to process
•
C – Its gene sequences are all shared (conserved) by most
bacteria so it is a good candidate for a universal primer
needed to copy the DNA
•
D – Its sequences are mostly conserved making it easy to
bind with primers while distinct regions help with
identification
Sorry
That was the wrong answer
Correct !
Congratulations
What is the name of the pathogen you
identified?
• A – Escherichia coli
• B – Salmonella typhimurium
• C – Bartonella henselae
• D – Brucella canis
Sorry
That was the wrong answer
Correct !
Congratulations
If sandflies are common at the site of the outbreak,
what disease will the pathogen likely cause?
• A – Lyme Disease
• B – Yellow Fever
• C – Oroya Fever
• D – Angiomatosis
Sorry
That was the wrong answer
Correct !
Congratulations
How do BLAST searches work?
• A – A sample is compared to the GenBank public
DNA sequence database available through the
National Library of Medicine
• B – BLAST assigns a numerical value to the
degree of similarity between two DNA
sequences
• C – BLAST returns a numerical score based
on a set formula (algorithm). The higher
the score, the better is the match
• D – All of the above
Sorry
That was the wrong answer
Correct !
Congratulations
What is the name of the process by which PCR quickly
multiplies the number of DNA copies?
•
•
•
•
A – Amplification
B – Compensation
C – Stratification
D – Expansion
Sorry
That was the wrong answer
Correct !
Congratulations
Works Cited
• Howard Hughes Medical Institute. 2008 Virtual Bacterial ID Lab.
http://www.hhmi.org/biointeractive/vlabs/bacterial_id/index.html.
Accessed 2009 May 10.
• Russell W. How to use PowerPoint: multiple choice quizzes.
http://presentationsoft.about.com/. Accessed 2009 May 10.
• Manning SD et al. 2008 Variation in virulence among clades of
Escherichia coli O157:H7 associated with disease outbreaks. PNAS.
105(12): 4868-4873.
• Medical News Today. DNA Profiling Study Identifies Three New
Lung Tumor Subtypes.
http://www.medicalnewstoday.com/articles/55446.php. Accessed
2009 May 4.
• O’Donnell KL, Ward. DNA Profiling: Guarding against a plant disease
epidemic. August 2000: 4-7.