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GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data

By Jisu Shin, Sang Hong Lee

Posted 01 Jun 2020
bioRxiv DOI: 10.1101/2020.05.31.122549

Genetic variation in response to the environment is fundamental in the biology of complex traits and diseases, i.e. genotype-by-environment interaction (GxE). However, existing methods are computationally demanding and infeasible to handle biobank-scale data. Here we introduce GxEsum, a method for estimating the phenotypic variance explained by genome-wide GxE based on GWAS summary statistics. Through comprehensive simulations and analysis of UK Biobank with 288,837 individuals, we show that GxEsum can handle a large-scale biobank dataset with controlled type I error rates and unbiased GxE estimates, and its computational efficiency can be hundreds of times higher than existing GxE methods.

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