DNA Profiling_1_

							 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
                                     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%
Changing patterns revealed through
DNA profiling
                                                         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
                                of
                 identification Manning, 2008
                 the appropriate
           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.