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1. Introduction
2. Genes underlying complex phenotypes
3. Phenotype - genotype association
4. SNP association with disease allele
5. LD maps and allelic association
6. How does LD occur?
7. LD through the generations
8. Decay of LD
9. Decay of LD with physical distance
10. Variability in LD overwhelms the mean
11. The role of LD in facilitating allelic association
12. LD patterns and allelic association
13. What is a haplotype?
14. Haplotype vs. single-locus analyses
15. Illustration of phase
16. Haplotypes
17. Single or multiple locus approach
18. The importance of haplotypes
19. Haplotype tagging for efficient genotyping
20. Block definition is non-trivial
21. Ambiguity phase (haplotype) information problem
22. Haplotype determination options
23. Dealing with ambiguous phase
24. Types of statistical estimation
25. Statistical estimation - EM algorithm
26. Haplotype frequency estimation via EM
27. Steps of haplotype frequency estimation via EM
28. Graphic representation of the steps
29. Framework of haplotype-based genetic studies
30. APOE c19 region
31. APOE SNPs: single-locus frequency comparisons
32. APOE region: 4-locus estimated frequencies
33. LRT results for APOE and control regions
34. Statistical challenge - sparse data
35. Empirical null distribution estimation
36. Haplotype estimation and permutation testing
37. Empirical null distributions from permutation tests
38. LRT results for APOE and control regions
39. Example for distribution of LRT values
40. Statistical challenge - multiple tests
41. Correction for multiple tests
42. Haplotype-phenotype association
43. Available software
44. Some software packages

Topics Covered

• Phenotype-genotype association
• Linkage disequilibrium maps and allelic association
• What is linkage disequilibrium?
• The role of linkage disequilibrium in facilitating allelic association
• What is a haplotype?
• The importance of haplotypes
• Haplotype tagging
• The missing phase information problem
• Haplotype determination options
• Statistical estimation of haplotypes
• General framework for case-control studies using haplotypes
• Haplotype estimation and permutation testing
• Statistical challenges
• Software packages

Links

Series:

• Gene-Environment Interactions

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Publication History

• Published on October 1, 2007
• Archived on May 28, 2025

Financial Disclosures

• Prof. Lyle Palmer has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.