Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. Background (1)
3. Background (2)
4. Objectives of stage 1 analysis
5. Typical strategy
6. Problem
7. Case-control study: single SNP power
8. Main effects versus joint and interaction effects
9. Epistasis with no main effects
10. Epistasis with main effect
11. Epistasis main effect
12. Multiplicative models with heterogeneity (1)
13. Multiplicative models with heterogeneity (2)
14. Multiplicative models - two locus example
15. Two locus example - 2+ independent systems
16. Formal definition of the model
17. Example genetic models
18. Random forest analysis
19. Random forest (1)
20. Random forest (2)
21. Random forest variable importance
22. Random forest importance (1)
23. Random forest importance (2)
24. Simulation study
25. Genetic models
26. Genetic models for simulation
27. Simulation study plan (1)
28. Simulation study plan (2)
29. Rank of risk SNPs: N = 100 SNPs (4 risk SNPs)
30. Rank of risk SNPs: N = 1000 SNPs (4 risk SNPs)
31. Rank of risk SNPs: N vs. proportion (1)
32. Rank of risk SNPs: N vs. proportion (2)
33. Simulation study plan (3)
34. Rank of risk SNPs: H8M4 (1)
35. Rank of risk SNPs: H8M4 (2)
36. Conclusions
37. Effects of linkage disequilibrium (1)
38. Effects of linkage disequilibrium: an illustration
39. Effects of linkage disequilibrium (2)
40. Effects of linkage disequilibrium (3)
41. Genome-wide association analysis (1)
42. Genome-wide association analysis (2)
43. GAW 15 simulated 10K data (1)
44. GAW 15 simulated 10K data (2)
45. GAW 15 analysis
46. Variable selection
47. GAW 15 analysis: prediction error
48. GAW 15 analysis results: power
49. Computational issues
50. Summary (1)
51. Summary (2)
52. Random Forest software
53. References
54. Acknowledgments

Topics Covered

• Screening association studies with a two-stage approach
• Multiplicative models with heterogeneity
• Random forest analysis
• Random forest variable importance
• Power
• Effect of linkage disequilibrium
• Genome-wide association studies
• Computational issues

Links

Series:

• Genetic Epidemiology II

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Lunetta, K. (2007, October 1). Screening large-scale association study data: exploiting multi-gene interactions with random forests [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved April 15, 2025, from https://doi.org/10.69645/ETKX5510.
Export Citation (RIS)

Publication History

• Published on October 1, 2007
• Archived on February 25, 2021

Financial Disclosures

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