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Correcting for population structure in GxE GWAS

Our paper on correcting for population structure in gene-by-environment (GxE) GWAS has just been published in PLoS Genetics! Here is a link to the paper.

One of the important factors that explain phenotypic variance of traits is gene-by-environment interactions (GEIs). Several GxE GWAS have been performed to identify GEIs associated with traits. However, association studies like GWAS are susceptible to false positives due to population structure, but the impact of population structure on GxE GWAS has not been investigated thoroughly.

In this paper, we showed for the first time that population structure can cause spurious gene-by-environment interactions both analytically and empirically. We used simulations based on 1000 Genomes Project and two real GxE GWAS datasets to show our finding. We also developed the “two RE” approach that utilizes two kinship matrices to correct for population structure in GxE GWAS. We showed that our method effectively removes the effect of population structure on GEI statistics.

Here is a full citation to the paper.

Sul JH, Bilow M, Yang WY, Kostem E, Furlotte N, et al. (2016) Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models. PLoS Genet 12(3): e1005849. doi: 10.1371/journal.pgen.1005849

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