1. Lecture 20 - Association Tests Gibson and Muse, Chapt. 3, 2nd Ed.

2. Association Populations Case-Control - unstructured populations Family-Based - structured populations Continuous variable - structured and/or unstructured

3. Pitfalls of Association Tests Trait h 2 Number of genes effecting trait Penetrance and expressivity Extent and uniformity of LD Genetic heterogeneity Population stratification Admixture Hidden environmental structure GxE and GxG Incomplete genotyping

5. M4M4 Genomewide Association Model-Free & Unbiased M1M1 M2M2 M3M3 M5M5 cases M1M1 M2M2 M3M3 M5M5 controls M4M4 causal mutation

6. Pug Dog Encephalitis A canine model of Multiple Sclerosis? CNS Inflammation & Necrosis Early Onset = 1.5 yrs Fatal = 3 weeks Complex Inheritance

7. M1M1 M2M2 M3M3 M4M4 M5M5 M1M1 M2M2 M3M3 M4M4 M5M5 casescontrols Pug Dog Encephalitis A canine model of Multiple Sclerosis?

11. A Review Lecture 11 - ESTs Lecture 12 - Genetic markers Lecture 13 - Genetic mapping Lecture 14 - Complex traits Lecture 15 - QTL mapping Lecture 16 - SNP discovery Lecture 17 - Nucleotide diversity and LD Lecture 18 - Tests for selection Lecture 19 - SNP genotyping Lecture 20 - Association mapping