Biostatistics 666: Association Tests in Structured Populations

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Overview

This lecture introduces the problem of population stratification in the context of genetic association studies. It also discusses introduces several possible strategies for detecting and handling population structure, specifically:

  • Q-Q plots as a diagnostic tool in genetic association studies.
  • Using family based association tests, such as the TDT, to avoid spurious association even when a single marker is tested.
  • Using the genomic control method to controling the overall inflation of test statistics, when many markers are tested.
  • Using genotype based matching approaches to model population structure more explicitly.

Lecture Notes

Slides in PDF Format

Recommended Reading

  • Genomic Control for Association Studies
    • Devlin and Roeder (1999) Biometrics 55:997-1004
    • Pritchard and Rosenberg (1999) Am J Hum Genet 65:220-228
  • Methods for Inferring Population Structure
    • Pritchard, Stephens and Donnelly, 2000. Genetics 155: 945-959
  • Principal Components Analysis
    • Price et al (2006) Nature Genetics 38:904-909
  • Transmission Disequilibrium Tests
    • Spielman et al (1993) Am J Hum Genet 52:506-16 (trios)
    • Curtis (1997) Ann Hum Genet 61:319-33 (sibling pairs)