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

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Presentation transcript:

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

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

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

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

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

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

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