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Navigable Slide Index

1. Introduction
2. Genome-wide association studies (GWAS)
3. Testing untyped variation
4. GWAS platforms
5. Coverage measured by r-squared
6. SNP annotation
7. Non-synonymous SNPs coverage
8. Multilocus disequilibrium (MD)
9. Properties of MD
10. Affymetrix 100K coverage
11. Redundant information
12. Pairwise vs. multi-locus LD
13. Pairwise vs. multi-locus LD: example
14. SNP coverage (1)
15. Analytic strategy
16. Interrogating the untyped variation: TUNA
17. Example: rs4654893
18. Inference issues
19. The likelihood
20. Implementation
21. Marker selection
22. Unobserved haplotypes
23. Database construction
24. Accuracy of TUNA
25. SNP coverage (2)
26. Output
27. Alternative approaches
28. Insertions and deletions
29. Indirect methods
30. Information on indels
31. Indel example
32. Summary
33. References

Topics Covered

• Genome-wide association studies
• Methods for testing untyped variation
• Coverage of commonly used platforms
• Multilocus linkage disequilibrium
• TUNA: testing untyped alleles
• Accuracy of imputation
• Indirect methods for structural variation

Links

Series:

• Genetic Epidemiology II

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Nicolae, D. (2007, October 1). Information on untyped variation 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/HDNA7279.
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Publication History

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

Financial Disclosures

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