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1. Introduction
2. Outline of talk
3. Polymorphisms in the genome
4. Advantages of SNPs
5. Analogy: dealing from deck of cards
6. Recombination
7. Functional vs. non-functional SNPs
8. Causes of disequilibrium
9. Equilibrium vs. disequilibrium conditions
10. Measuring pairwise LD
11. Example: chromosome 22
12. Change in LD across chromosome 22
13. Graphical models
14. Independent random variables
15. First order Markov chain
16. Second order Markov chain
17. Pedigree analysis
18. Contingency tables
19. Pairwise LD table
20. 3-way LD
21. 4-way LD
22. Decomposition of a graphical model
23. Cliques in a graphical model
24. The running intersection property
25. Reducing high dimension to low dimension
26. Worked example
27. Comparing graphical models using likelihoods (1)
28. Comparing graphical models using likelihoods (2)
29. Comparing graphical models using likelihoods (3)
30. Choosing a graphical model
31. Evaluating a graphical model
32. Simulated annealing
33. Example: ELAC2
34. Selecting unrelated individuals
35. Determining haplotypes
36. Utah ELAC2 data subset
37. Java program for graphical modelling of LD
38. Phenotypic associations
39. Java program: LD + phenotype
40. Java program: best solution
41. Testing for disease association (1)
42. Testing for disease association (2)
43. Testing for disease association (3)
44. Testing for disease association: ELAC2
45. Model sampling
46. Java program: model sampling
47. MCMC sample of 1,000,000 p-values
48. Model sampling: ELAC2
49. Java program: reduced SNP set
50. Further developments
51. Genotypic data
52. Familial data
53. Information on physical locations
54. Physical ordering constraints
55. Non-recombining DNA
56. Advantages of graphical modelling
57. Resources (1)
58. Resources (2)

Topics Covered

• Describing linkage disequilibrium
• Visualisation approaches: triangular grid-plots and LD maps
• Graph theory as a useful way of describing complex LD patterns
• Software

Links

Series:

• Genetic Epidemiology I

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Publication History

• Published on September 1, 2004
• Archived on February 25, 2021

Financial Disclosures

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