Behavior of QQ-Plots and Genomic Control in Studies of Gene-Environment Interaction

Arend Voorman, Thomas Lumley, Barbara McKnight and Kenneth Rice

PLOS ONE, 2011, vol. 6, issue 5, 1-7

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 GE 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 GE GWAS, and how this differs from main-effects analyses. We also explain how simple adjustments to standard regression-based methods used in GE GWAS can alleviate this problem.

Date: 2011
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0019416

DOI: 10.1371/journal.pone.0019416

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