• Special Designs
• 46 min
  1. Family-based association tests: introduction

  • Dr. Christoph Lange
• 29 min
  2. Family-based association tests: FBAT testing strategies for large-scale association studies

  • Dr. Christoph Lange
• 37 min
  3. Two-stage genome-wide association designs

  • Dr. Andrew Skol
• Special Populations
• 40 min
  4. Admixture mapping

  • Dr. Paul McKeigue
• Whole-Genome Studies: Types of Data
• 34 min
  5. QTL association mapping

  • Prof. Bruce Weir
• 50 min
  6. Adjusting for population structure in genetic association studies

  • Prof. David Balding
• Whole-Genome Studies 2: Methods
• 47 min
  7. Whole-genome association studies: practical advice and considerations

  • Dr. Mike Weale
• Archived Lectures *These may not cover the latest advances in the field
• 49 min
  8. Family-based association tests: FBATs for various data types

  • Dr. Christoph Lange
• 44 min
  9. Choosing between family-based and population-based association designs

  • Dr. Ren-Hua Chung
• 54 min
  10. Use of isolated populations: pitfalls and potential

  • Dr. Leena Peltonen
• 40 min
  11. Information on untyped variation in genome-wide association studies

  • Dr. Dan Nicolae
• 37 min
  12. Detecting multiple associations in genome-wide studies

  • Prof. Frank Dudbridge
• 30 min
  13. Genome scanning by composite likelihood

  • Dr. Andrew Collins
• 41 min
  14. Multistage sampling for genetic studies

  • Prof. Robert Elston
• 39 min
  15. Screening large-scale association study data: exploiting multi-gene interactions with random forests

  • Dr. Kathryn Lunetta
• 43 min
  16. A survey of multi-locus methods for analysis of large SNP datasets

  • Mr. A. Geert Heidema
• 34 min
  17. Sequential analysis methods in genomic scans

  • Prof. Michael Province

Printable Handouts

PDF

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

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.