Efficient gene–environment interaction testing through bootstrap aggregating

Author:

Lau Michael,Kress Sara,Schikowski Tamara,Schwender Holger

Abstract

AbstractGene–environment (GxE) interactions are an important and sophisticated component in the manifestation of complex phenotypes. Simple univariate tests lack statistical power due to the need for multiple testing adjustment and not incorporating potential interplay between several genetic loci. Approaches based on internally constructed genetic risk scores (GRS) require the partitioning of the available sample into training and testing data sets, thus, lowering the effective sample size for testing the GxE interaction itself. To overcome these issues, we propose a statistical test that employs bagging (bootstrap aggregating) in the GRS construction step and utilizes its out-of-bag prediction mechanism. This approach has the key advantage that the full available data set can be used for both constructing the GRS and testing the GxE interaction. To also incorporate interactions between genetic loci, we, furthermore, investigate if using random forests as the GRS construction method in GxE interaction testing further increases the statistical power. In a simulation study, we show that both novel procedures lead to a higher statistical power for detecting GxE interactions, while still controlling the type I error. The random-forests-based test outperforms a bagging-based test that uses the elastic net as its base learner in most scenarios. An application of the testing procedures to a real data set from a German cohort study suggests that there might be a GxE interaction involving exposure to air pollution regarding rheumatoid arthritis.

Funder

Deutsche Forschungsgemeinschaft

Heinrich-Heine-Universität Düsseldorf

Publisher

Springer Science and Business Media LLC

Subject

Multidisciplinary

Cited by 3 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Genetic Epidemiology in the Era of Genomic Medicine;International Encyclopedia of Public Health;2025

2. Gene–environment interactions in human health;Nature Reviews Genetics;2024-05-28

3. GRSxE: Testing Gene-Environment Interactions Through Genetic Risk Scores;CRAN: Contributed Packages;2022-11-11

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