Analyzing Phenotypic Variations and Polymorphism

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Analyzing Phenotypic Variations and Polymorphism

• Phillip Tao
• Advisor Professor Eleazar Eskin
• Grad Student Emrah Kostem

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Polymorphism and SNP

• Polymorphism is a variation between the genome of
  two individuals or chromosomes
• Many types
• Deletion
• Duplication
• Inversion
• Single Nucleotide Polymorphism (SNP)
• These often cause major diseases, such as Cri
  du Chat and Charcot-Marie-Tooth disease, when
  large portions of the genome are affected 4.
  However, their effect on small portions of the
  genome, (especially non-coding portions) have
  been mostly unstudied

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Problem

• Polymorphisms can be used to identify disposition
  toward certain illnesses 1
• Use mouse genome to identify problem causing
  alleles
• A lot of data to analyze, 8.27 million SNP in
  mice 2, estimated 10 million in humans 1
• Very difficult to identify non-SNP polymorphisms
• Can be very long, 1.5 million base pairs 3

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Past Methods and My Idea

• Polymorphism has been used to try to find causes
  for diseases such as cancer, etc. 567.
• They decided on a disease first, found an area of
  a genome they believe might influence the
  disease, then looked for polymorphisms in that
  area
• My way is to map the entire set of polymorphisms
  for a given genome (mouse genome), then look for
  correlations

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Proposal, step 1

• Develop a way to identify non-SNP polymorphisms
• Find start of problem area
• Use marker sequence to find end of problem area
• Identify problem
• Idea borrowed from Restriction Fragment
• Length Polymorphism (RFLP)

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Proposal, step 2

• Use Ruby to develop a tool to easily and flexibly
  model the data
• Develop algorithms to find correlation between
  polymorphisms and trait variations

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Schedule

• A basic but functional version of the Ruby on
  Rails website should be finished, and a working
  but slow and inefficient version of the
  polymorphism finder should be done.
• By the end of Winter Quarter, the final version
  of the polymorphism finder should be finished,
  and a better version of the RoR website should
  also be finished
• By the end of the project, an algorithm should be
  found to analyze correlation between certain
  polymorphisms and trait variations

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Resources

1. http//www.usatoday.com/news/health/2005-02-17-gen
   e-map_x.htm
2. http//www.nature.com/nature/journal/v448/n7157/fu
   ll/nature06067.html
3. http//www.nature.com/ng/journal/v29/n3/full/ng753
   .html
4. http//en.wikipedia.org/wiki/Chromosome_abnormalit
   ies
5. http//circ.ahajournals.org/cgi/content/abstract/c
   irculationaha102/2/197
6. http//jmd.amjpathol.org/cgi/content/full/8/4/499
7. http//atvb.ahajournals.org/cgi/content/full/atvba
   ha16/2/304