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Lecture 20 - Association Tests

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

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Lecture 20 - Association Tests

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  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 h2 • 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

  4. Genomewide AssociationModel-Free & Unbiased cases controls M1 M4 M5 M2 M3 M4 M1 M2 M3 M5 causal mutation

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

  6. Pug Dog Encephalitis A canine model of Multiple Sclerosis? cases controls M1 M2 M3 M4 M5 M1 M2 M3 M4 M5

  7. 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

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