Lecture 20 association tests
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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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Lecture 20 association tests

Lecture 20 - Association Tests

  • Gibson and Muse, Chapt. 3, 2nd Ed.


Association populations

Association Populations

  • Case-Control - unstructured populations

  • Family-Based - structured populations

  • Continuous variable - structured and/or unstructured


Pitfalls of association tests

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


Genomewide association model free unbiased

Genomewide AssociationModel-Free & Unbiased

cases

controls

M1

M4

M5

M2

M3

M4

M1

M2

M3

M5

causal mutation


Lecture 20 association tests

Pug Dog Encephalitis

A canine model of Multiple Sclerosis?

  • CNS Inflammation & Necrosis

  • Early Onset = 1.5 yrs

  • Fatal = 3 weeks

  • Complex Inheritance


Lecture 20 association tests

Pug Dog Encephalitis

A canine model of Multiple Sclerosis?

cases

controls

M1

M2

M3

M4

M5

M1

M2

M3

M4

M5


A review

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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