Printable Handouts

PDF

Navigable Slide Index

1. Introduction
2. Outline
3. What is population structure?
4. The problem of structure in association studies
5. The problem can be worse
6. Detecting unknown structure
7. Detecting unknown structure: mixture modelling
8. Structure: no-admixture model
9. Structure: admixture model
10. Example of admixture model
11. Principal components analysis
12. Example of PCA
13. Detecting unknown structure using PCA: summary
14. PCA example: East Asia
15. PCA example: Europe
16. Ancestry informative markers (AIMs)
17. Unknown strucrure
18. Is there a problem? (1)
19. Is there a problem? (2)
20. A priori known structure
21. Sample matching (1)
22. Sample matching (2)
23. Stratified testing
24. Limitations of stratified testing
25. Controlling for unknown structure
26. Genomic control
27. Advantages and disadvantages of genomic control
28. Use inferred structure
29. Regression modelling
30. Structured association (1)
31. Structured association (2)
32. Structured association: STRAT
33. Controlling for unknown structure: PCA
34. EIGENSTRAT: simulation study (1)
35. EIGENSTRAT: simulation study (2)
36. EIGENSTRAT: simulation study (3)
37. Simulation study: differentiated SNPs (1)
38. Simulation study: differentiated SNPs (2)
39. Summary
40. Software
41. References

Topics Covered

• What is population structure?
• The problem of structure in association studies
• Detecting unknown structure
• Mixture modelling, principal components analysis
• Is there a problem?
• Controlling for known structure: matching, family-based designs, stratified testing
• Controlling for unknown structure: genomic control, mixture modelling, principal components, regression modelling

Links

Series:

• Statistical Methods for the Analysis of Genome-Wide Association Studies

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Davison, D. (2008, June 4). Population structure in genome-wide association studies [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved April 15, 2025, from https://doi.org/10.69645/OMKW2854.
Export Citation (RIS)

Publication History

• Published on June 4, 2008
• Archived on February 6, 2025

Financial Disclosures

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