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Population Substructure and Control Selection in Genome-Wide Association Studies

Author

Listed:
  • Kai Yu
  • Zhaoming Wang
  • Qizhai Li
  • Sholom Wacholder
  • David J Hunter
  • Robert N Hoover
  • Stephen Chanock
  • Gilles Thomas

Abstract

Determination of the relevance of both demanding classical epidemiologic criteria for control selection and robust handling of population stratification (PS) represents a major challenge in the design and analysis of genome-wide association studies (GWAS). Empirical data from two GWAS in European Americans of the Cancer Genetic Markers of Susceptibility (CGEMS) project were used to evaluate the impact of PS in studies with different control selection strategies. In each of the two original case-control studies nested in corresponding prospective cohorts, a minor confounding effect due to PS (inflation factor λ of 1.025 and 1.005) was observed. In contrast, when the control groups were exchanged to mimic a cost-effective but theoretically less desirable control selection strategy, the confounding effects were larger (λ of 1.090 and 1.062). A panel of 12,898 autosomal SNPs common to both the Illumina and Affymetrix commercial platforms and with low local background linkage disequilibrium (pair-wise r2

Suggested Citation

  • Kai Yu & Zhaoming Wang & Qizhai Li & Sholom Wacholder & David J Hunter & Robert N Hoover & Stephen Chanock & Gilles Thomas, 2008. "Population Substructure and Control Selection in Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 3(7), pages 1-14, July.
    • Handle: RePEc:plo:pone00:0002551
    DOI: 10.1371/journal.pone.0002551
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    References listed on IDEAS

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    1. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    2. B. Devlin & Kathryn Roeder, 1999. "Genomic Control for Association Studies," Biometrics, The International Biometric Society, vol. 55(4), pages 997-1004, December.
    3. Chao Tian & Robert M Plenge & Michael Ransom & Annette Lee & Pablo Villoslada & Carlo Selmi & Lars Klareskog & Ann E Pulver & Lihong Qi & Peter K Gregersen & Michael F Seldin, 2008. "Analysis and Application of European Genetic Substructure Using 300 K SNP Information," PLOS Genetics, Public Library of Science, vol. 4(1), pages 1-11, January.
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    Cited by:

    1. Jianzhong Ma & Christopher I Amos, 2012. "Principal Components Analysis of Population Admixture," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-12, July.
    2. Zhaoming Wang & Allan Hildesheim & Sophia S Wang & Rolando Herrero & Paula Gonzalez & Laurie Burdette & Amy Hutchinson & Gilles Thomas & Stephen J Chanock & Kai Yu, 2010. "Genetic Admixture and Population Substructure in Guanacaste Costa Rica," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-10, October.
    3. Wang, Linglu & Li, Qizhai & Li, Zhaohai & Zheng, Gang, 2011. "Bayes factors in the presence of population stratification," Statistics & Probability Letters, Elsevier, vol. 81(7), pages 836-841, July.

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