1. CSE 182 Project

2. 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

3. DNA sequence reads

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

5. 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

6. 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

7. dbSNP

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

9. OMIM

10. OMIM

11. 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!