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Behavior of QQ-plots and genomic control in studies of gene-environment interaction.

ABSTRACT: Genome-wide association studies of gene-environment interaction (GxE GWAS) are becoming popular. As with main effects GWAS, quantile-quantile plots (QQ-plots) and Genomic Control are being used to assess and correct for population substructure. However, in G x E work these approaches can be seriously misleading, as we illustrate; QQ-plots may give strong indications of substructure when absolutely none is present. Using simulation and theory, we show how and why spurious QQ-plot inflation occurs in G x E GWAS, and how this differs from main-effects analyses. We also explain how simple adjustments to standard regression-based methods used in G x E GWAS can alleviate this problem.

SUBMITTER: Voorman A

PROVIDER: S-EPMC3093379 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

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Behavior of QQ-plots and genomic control in studies of gene-environment interaction.

Voorman Arend A Lumley Thomas T McKnight Barbara B Rice Kenneth K

PloS one 20110512 5

Genome-wide association studies of gene-environment interaction (GxE GWAS) are becoming popular. As with main effects GWAS, quantile-quantile plots (QQ-plots) and Genomic Control are being used to assess and correct for population substructure. However, in G x E work these approaches can be seriously misleading, as we illustrate; QQ-plots may give strong indications of substructure when absolutely none is present. Using simulation and theory, we show how and why spurious QQ-plot inflation occurs ...[more]

PMID: 21589913

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