Robust Bayesian Variable Selection for Gene–Environment Interactions

DOI10.1111/BIOM.13670MaRDI QIDQ6079754zbMATH OpenFDO

Authors Jie Ren, Fei Zhou, Xiaoxi Li, Shuangge Ma, Yunping Jiang, Cen Wu

Publication date 30 October 2023

Published in Biometrics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2006.05455

zbMATH Keywords

Bayesian variable selectiongene-environment interactionsMarkov chain Monte Carlorobust analysissparse group selection

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10)

Abstract: Gene-environment (G$imes$E) interactions have important implications to elucidate the etiology of complex diseases beyond the main genetic and environmental effects. Outliers and data contamination in disease phenotypes of G$imes$E studies have been commonly encountered, leading to the development of a broad spectrum of robust regularization methods. Nevertheless, within the Bayesian framework, the issue has not been taken care of in existing studies. We develop a fully Bayesian robust variable selection method for G$imes$E interaction studies. The proposed Bayesian method can effectively accommodate heavy-tailed errors and outliers in the response variable while conducting variable selection by accounting for structural sparsity. In particular, for the robust sparse group selection, the spike-and-slab priors have been imposed on both individual and group levels to identify important main and interaction effects robustly. An efficient Gibbs sampler has been developed to facilitate fast computation. Extensive simulation studies and analysis of both the diabetes data with SNP measurements from the Nurses' Health Study and TCGA melanoma data with gene expression measurements demonstrate the superior performance of the proposed method over multiple competing alternatives.

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Cited in

(15)

• Genotype-based Bayesian analysis of gene-environment interactions with multiple genetic markers and misclassification in environmental factors
• Structured gene-environment interaction analysis
• Variable selection in Bayesian generalized linear‐mixed models: An illustration using candidate gene case‐control association studies
• scientific article; zbMATH DE number 6275702 (Why is no real title available?)
• pqrBayes
• Hierarchical false discovery rate control for high-dimensional survival analysis with interactions
• Robust identification of gene-environment interactions under high-dimensional accelerated failure time models
• BHAFT: Bayesian heredity-constrained accelerated failure time models for detecting gene-environment interactions in survival analysis
• The spike-and-slab quantile Lasso for robust variable selection in cancer genomics studies
• Benchmarking sparse variable selection methods for genomic data analyses
• Robust sparse Bayesian regression for longitudinal gene-environment interactions
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• Robust Bayesian variable selection for the quantile varying coefficient model
• Robust Bayesian high-dimensional variable selection and inference with the horseshoe family of priors
• Variable selection and inference with a new robust Bayesian elastic net

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