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1. Introduction
2. Structure of presentation
3. What are whole-genome association studies?
4. Why do whole-genome association studies?
5. Steps in WGA study
6. Example: HIV setpoint
7. Phenotype definition
8. Natural history of HIV disease
9. Setpoint: the real world
10. How to define the setpoint?
11. Whole genome genotyping panels (1)
12. Whole genome genotyping panels (2)
13. PLINK
14. QC of genotype data
15. QC of genotype/phenotype match
16. Stratification can lead to false positives
17. Implications of differences in disease rates
18. PCA method can reveal hidden groups
19. PCA for SNP data ("EIGENSTRAT")
20. PCA properties
21. Modified EIGENSTRAT procedure
22. SNP-by-SNP analysis
23. X chromosome SNP-by-SNP analysis
24. Options for modeling the X
25. Multiple testing approaches
26. Bonferroni method
27. Q-Q (quantile-quantile) plot
28. HIV setpoint illustrating usefulness of Q-Q plot
29. False discovery rate
30. Permutation
31. Why is the dependence of tests not too crucial?
32. "Outright hits" is not huge gain in power (1)
33. "Outright hits" is not huge gain in power (2)
34. FDR is unaffected for large pools (1)
35. FDR is unaffected for large pools (2)
36. Variance of FDR is affected
37. Bayesian alternatives
38. Bayes factor
39. Bayesian false discovery probability (BFDP)
40. Genomewide-significant SNPs in HLA region
41. HLA-C effect is mediated via expression
42. Additional topics
43. Acknowledgements
44. References (1)
45. References (2)
46. References (3)
47. References (4)

Topics Covered

• What are whole-genome (genome-wide) association studies and why do them?
• Steps in WGA study
• HIV setpoint
• Phenotype definition
• Setpoint
• Whole genome genotyping panels
• PLINK
• Cryptic population stratification
• PCA and EIGENSTRAT
• SNP-by-SNP analysis
• Multiple testing approaches
• Bonferroni method
• Q-Q (quantile-quantile) plot
• False discovery rate
• Permutation
• Outright hits
• Pool of hits
• Bayesian alternatives
• Bayes factor
• Bayesian false discovery probability (BFDP)

Links

Series:

• Genetic Epidemiology II

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Weale, M. (2007, October 1). Whole-genome association studies: practical advice and considerations [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved April 20, 2024, from https://hstalks.com/bs/611/.
Export Citation (RIS)

Publication History

• Published on October 1, 2007

Financial Disclosures

• Dr. Mike Weale has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.