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Analyzing Phenotypic Variations and Polymorphism

Analyzing Phenotypic Variations and Polymorphism. Phillip Tao Advisor: Professor Eleazar Eskin Grad Student: Emrah Kostem. Polymorphism and SNP. Polymorphism is a variation between the genome of two individuals or chromosomes Many types: Deletion * Duplication * Inversion *

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Analyzing Phenotypic Variations and Polymorphism

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  1. Analyzing Phenotypic Variations and Polymorphism Phillip Tao Advisor: Professor EleazarEskin Grad Student: Emrah Kostem

  2. 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

  3. 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]

  4. Past Methods and My Idea • Polymorphism has been used to try to find causes for diseases such as cancer, etc. [5][6][7]. • 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

  5. 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)

  6. 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

  7. 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

  8. Resources • http://www.usatoday.com/news/health/2005-02-17-gene-map_x.htm • http://www.nature.com/nature/journal/v448/n7157/full/nature06067.html • http://www.nature.com/ng/journal/v29/n3/full/ng753.html • http://en.wikipedia.org/wiki/Chromosome_abnormalities • http://circ.ahajournals.org/cgi/content/abstract/circulationaha;102/2/197 • http://jmd.amjpathol.org/cgi/content/full/8/4/499 • http://atvb.ahajournals.org/cgi/content/full/atvbaha;16/2/304

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