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Navigable Slide Index

1. Introduction
2. Talk outline
3. Introduction to genotyping issues
4. A good SNP from the Affy 500K
5. PTPN22 in the WTCCC
6. A difficult Affy 500K SNP
7. Effect of copy number variation
8. Another platform: ParAllele biosciences
9. An overview of the data
10. We need an automated calling algorithm
11. Statistical framework
12. Small versus large batches
13. Bayesian prior distributions
14. Fitting a mixture model to the data
15. Calling strategies
16. One or two dimensional clustering
17. An example of definition for contrasts
18. What do contrasts look like?
19. A variation on the contrast definition
20. Estimation techniques
21. Expectation Maximization (EM) algorithm
22. Bayesian techniques
23. Additional refinements
24. Incorporating Hardy-Weinberg equilibrium (1)
25. Incorporating Hardy-Weinberg equilibrium (2)
26. Moving away from Gaussian assumptions (1)
27. Moving away from Gaussian assumptions (2)
28. ''Christmas tree'' (1)
29. ''Christmas tree'' (2)
30. Typing on the X chromosome (1)
31. Typing on the X chromosome (2)
32. Typing on the X chromosome (3)
33. Differential bias, informative missingness
34. Differential bias (1)
35. Differential bias (2)
36. Differential bias (3)
37. A new statistical model
38. Extended statistical model
39. Informative missingness (1)
40. Informative missingness (2)
41. Informative missingness (3)
42. Overview of scoring algorithms
43. DM, RLMM and BRLMM
44. BRLMM (1)
45. Birdseed (1)
46. Birdseed (2)
47. Chiamo++ (1)
48. Chiamo++ (2)
49. Illuminus
50. JAPL (1)
51. JAPL (2)
52. Conclusion

Topics Covered

• Genome wide association studies
• Genotyping
• Mixture models
• Affymetrix 500K
• Differential bias and informative missingness

Links

Series:

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

Categories:

• Genetics & Epigenetics
• Methods

Talk Citation

Plagnol, V. (2008, June 4). Genotyping algorithms for 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/PBTH9085.
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Publication History

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

Financial Disclosures

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