CSE 182 Project.

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CSE 182 Project

Personalized genomics Very soon, most of you will go to a lab, spit into a test-tube, and get your DNA sequenced. If you don’t believe this, here is a picture of a spitting party from 23 and me April’08 Bafna

DNA sequence reads

Mapping short reads to a reference genome Chromosome 4, Position 42156427 C A A A VCF File Chrom. Pos Ref. Alt. GT 4 42156427 C A C/A

Abstraction of a causal mutation Genome Mutation causes a change in phenotype Gene Some mutations may change the coding part of the gene. Others may be in non-genic region, or not change the code. Coding mutations may be deleterious or benign

Mutations versus polymorphisms Reference Genome Indiv 1 Indiv 2 Polymorphisms are mutations that are ‘common’, or polymorphic in a population. SNPs refer to Single Nucleotide Polymorphisms Indiv 3

dbSNP

VCF file and SNPs Chrom. Pos Ref. Alt. GT rs# 4 42156427 C A C/A

OMIM

OMIM

Project Goal: extract as much information as possible for Individual X Map the variants of the individual to specific OMIM entries. (Extra) If it is not a SNP, identify if it is coding or non-coding, and/or deleterious (Extra) Identify the genealogy of the person. Start early!