Genome-wide Association S tudy

1. Genome-wide Association Study • Focus on association between SNPs and traits • Tendency • Larger and larger sample size • Use of more narrowly defined phenotypes(blood lipids, proinsulin or similar biomarkers • Limitations • Sufficient sample size • The massive number of statistical tests performed presents an unprecedented potential for thepositiveresults • Search the entire genome-->not worth the expenditure

2. Advantage of ExomeSequecing • Whole genome sequencing • Redundant raw data(6 Gb in each human diploid genome ) • Exomesequecing(targeted exome capture) • Exons are short and 180,000 exons constitute 1% of the human genome • The goal is to identify the functional variation that is responsible for both mendelian and common diseases

3. Significance • Exomesequencing can be used to identify causal variants of rare disorders • The first reported study that used exome sequencing as an approach to identify an unknown causal gene for a rare mendeliandisorder

4. The Shendure Lab • Next-generation human genetics • A multiplex approach to genome sequencing • Targeted sequence enrichment • Protocols relying on molecular inversion probe • Hybrid capture • Novel analytical strategies to identify the genetic basis of Mendelian disorders by exomesequecing • Autosomal recessive disorders such as Miller syndrome • Autosomal dominant disorders such as Kabuki syndrome

5. Hapmapproject • Focuse on common SNPs(at least 1% of the population) • Samples: 4 populations • (30*3 YRI, 30*3 CEU, 45 JPT, 45 CHB) • Data: • SNP frequencies, genotypes

7. Work flow

8. Target enrichment Methods a. PCR-based approach b. Molecular inversion probe(MIP)-based approach c. Hybrid capture-based approach Mamanova et al. Nat Method 7(2):112-118

9. Mamanova et al. Nat Method 7(2):112-118

10. Figure. ①Probe list of array2 ② Probe list of array1 ③Exome on 1-22, X and Y chromosomes

11. Work flow

12. Coming…

13. Method

14. Method

15. Method 2:MIP and resequencing

16. Method 3: Whole genome sequencing

17. Method 4:

18. Figure. Table of cSNPs of 8 HapMap individuals

19. Figure. Table of Splice Site Variants of 8 HapMap individuals

20. Figure. Table of Coding Indelsof 8 HapMap individuals

21. Figure. Table of coverage of 8 HapMap individuals and 4 FSS individual

22. Figure. Intervals that were exclued….

23. Figure. ①Probe list of array2 ② Probe list of array1 ③Exome on 1-22, X and Y chromosomes

24. YRI: Nigeria - Yoruba people of Ibadan CHB: China - Beijing JPT: Japan - Tokyo CEU: Centre d'Etude du Polymorphisme Humain (CEPH) Eur: European–American ancestry

30. About mendelian disease

31. Traditional situation

32. Current situation

33. Considerations Causal genes may be shared by case group. Control group may not contain that mutation. Common mutation may not be causal. Causal mutation should cause animo acid change.

34. Result

35. Further application Typical single gene disorder. Disorder caused by single but not uniform gene. Multiple gene disorder. Complex disease. Cancer.