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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
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

slide6

Pug Dog Encephalitis

A canine model of Multiple Sclerosis?

  • CNS Inflammation & Necrosis
  • Early Onset = 1.5 yrs
  • Fatal = 3 weeks
  • Complex Inheritance
slide7

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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