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. 2020 Nov 30;15(11):e0242927.
doi: 10.1371/journal.pone.0242927. eCollection 2020.

Novel methods for epistasis detection in genome-wide association studies

Lotfi Slim  1   2 , Clément Chatelain  2 , Chloé-Agathe Azencott  1   3 , Jean-Philippe Vert  1   4
Affiliations

Novel methods for epistasis detection in genome-wide association studies

Lotfi Slim et al. PLoS One. .

Abstract

More and more genome-wide association studies are being designed to uncover the full genetic basis of common diseases. Nonetheless, the resulting loci are often insufficient to fully recover the observed heritability. Epistasis, or gene-gene interaction, is one of many hypotheses put forward to explain this missing heritability. In the present work, we propose epiGWAS, a new approach for epistasis detection that identifies interactions between a target SNP and the rest of the genome. This contrasts with the classical strategy of epistasis detection through exhaustive pairwise SNP testing. We draw inspiration from causal inference in randomized clinical trials, which allows us to take into account linkage disequilibrium. EpiGWAS encompasses several methods, which we compare to state-of-the-art techniques for epistasis detection on simulated and real data. The promising results demonstrate empirically the benefits of EpiGWAS to identify pairwise interactions.

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Conflict of interest statement

The commercial affiliations of some of the co-authors do not alter our full adherence to all PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Average ROC (left) and PR (right) curves for the fourth scenario and n = 500.
See this image and copyright information in PMC

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