Next-Generation Sequencing

1. Next-Generation Sequencing Eric Jorgenson Epidemiology 217 2/28/12

2. Outline Overview of Sequencing Example Next Generation Sequencing Study: Whole Genome, Exome, Families (IBD), Cancer PTC Taste Sensitivity

3. Links to videos and articles http://www.bloomberg.com/video/84364498/ http://www.bloomberg.com/video/84364540/ http://www.bloomberg.com/video/86406762/ http://www.bloomberg.com/news/2012-01-17/search-genome-as-tennis-thrice-weekly-no-barrier-to-decoded-dna.html http://www.bloomberg.com/news/2012-02-15/harvard-mapping-my-dna-turns-scary-as-threatening-gene-emerges.html

4. Huntington’s Disease Testing Almqvist AJHG 1999

5. Number of Genetic Markers for Genetic Studies Genome-wide Linkage Studies 300-400 Microsatellite Markers Genome-wide Association Studies 100,000-2,500,000 SNPs Exome Sequencing Studies 30,000,000 Basepairs Gene-based Studies 22,000 Genes Whole Genome Sequencing Studies 3,200,000,000 Basepairs

6. Variant detection through next generation sequencing Meyerson et al. NRG 2010

7. ANNOVAR: Using Annotation to Narrow the Search Space openbioinformatics.org/annovar

8. Outline Overview of Sequencing Example Next Generation Sequencing Study: Whole Genome, Exome, Families (IBD), Cancer PTC Taste Sensitivity

9. Sequencing of a Single Individual with Family Data Lupski et al. NEJM 2010

10. CMT Subtypes: Many Genes

11. Phenotypes in Unsequenced Family Members

12. SNP Distribution in Proband

13. The First 8 Human Genomes

14. Nonsynonymous SNPs in Known Disease Genes

15. Family Pedigree

16. Putative Causal Variant at a Conserved Amino Acid

17. Exome Sequencing Identifies a Tibetan Adaptation Yi et al. Science 2010

18. Family Sequencing for Rare Diseases Roach et al. Science 2010

19. Sequence Data Improves Identity By Descent Resolution Su and Jorgenson under review

20. Cancer: Tumor vs. Normal Lee et al. Nature 2010

21. Nonsynonymous Somatic Mutations in Neuroblastoma Molenaar et al. Nature 2012

22. Mutation count associated with age, stage, and survival Molenaar et al. Nature 2012

23. Outline Overview of Sequencing Example Next Generation Sequencing Study: Whole Genome, Exome, Families (IBD), Cancer PTC Taste Sensitivity

24. Distribution of PTC Phenotype Number of Subjects PTC Score

25. TAS2R38 Receptor Structure Kim et al. J Dent Res 2004

26. 3 SNPs Form 3 Haplotypes P A V Taster Non-taster A V I Rare A A V

27. PTC Phenotype by TAS2R38 Diplotype Number of Subjects PTC Score

28. Outliers After Adjusting for TAS2R38 Diplotype Number of Subjects PTC Score

29. Unusual PTC Phenotypes (AVI Homozygotes in Green) 11 8 9 3 8 10 12 9 9 9

30. Unusual PTC Phenotypes (AVI Homozygotes in Green) 11 14 10 10 9 2 4 11 11

31. 10 Genomes, 5 Hard Drives

32. Summary of Variation

33. Quality Control:99.8% Concordance

34. Variant Distribution in Utah

35. Variant Distribution in Utah

36. Using Relatedness 11 8 9 3 8 10 12 9 9 9

37. Identity By Descent

38. Identity By Descent

39. Nonsynonymous Variants

40. How can whole genome sequence influence treatment? • Identify Genes with Protein Altering Mutations • Determine Variation in Specific Genes

41. Genes with Protein Altering Variants

42. ABO Blood Group

43. Determination of ABO Type

44. Appendix: Study Design Considerations in Sequencing • Extreme Sampling • Families

45. Sampling from the Extremes of a Quantitative Distribution Su and Jorgenson under revision

46. Relative Power of Sampling from Various Phenotype Deciles Su and Jorgenson under revision

47. Families can reduce error rates Roach et al. Science 2010

48. Families can reduce error rates Roach et al. Science 2010