Effects of gene-environment and gene-gene interactions in case-control studies: a novel Bayesian semiparametric approach

DOI10.1214/18-BJPS413zbMATH Open1439.92124arXiv1601.03519OpenAlexW3004471812MaRDI QIDQ2180259FDOQ2180259

Authors: Durba Bhattacharya, Sourabh Bhattacharya 

Publication date: 13 May 2020

Published in: Brazilian Journal of Probability and Statistics (Search for Journal in Brave)

Abstract: Cognizance of gene-environment interactions may help prevent or detain the onset of complex diseases like cardiovascular disease, cancer, type2 diabetes, autism or asthma by adjustments to lifestyle. In this regard, we extend the Bayesian semiparametric gene-gene interaction model of Bhattacharya & Bhattacharya (2015) to include the possibility of influencing gene-gene interactions by environmental variables and possible mutations caused by the environment. Our model accounts for the unknown number of genetic sub-populations via finite mixtures composed of Dirichlet processes, which are related to each other through a hierarchical matrix normal structure responsible for inducing gene-gene interactions and possible mutations in association with environmental variables. We also extend the Bayesian hypotheses testing procedures of Bhattacharya & Bhattacharya (2015) to detect the roles of genes and their interactions, environment and the influence of environment on gene-gene interactions, in case-control studies. We develop an effective parallel computing methodology, which harnesses the power of parallel processing technology to the efficiencies of our conditionally independent Gibbs sampling and Transformation based MCMC (TMCMC) methods.Applications of our model and methods to simulation studies with biologically realistic case-control genotype datasets obtained under five distinct set-ups yield encouraging results in each case. We followed these up by application of our ideas to a real, case-control based genotype dataset on early onset of myocardial infarction. Beside being in broad agreement with the reported literature on this dataset, the results obtained give some interesting insights to the differential effect of gender on MI.

Full work available at URL: https://arxiv.org/abs/1601.03519

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zbMATH Keywords

case-control studyDirichlet processparallel processingmatrix normalgene-gene and gene-environment interactiontransformation based MCMC

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Pathology, pathophysiology (92C32)

Cites Work

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• Effects of gene-environment and gene-gene interactions in case-control studies: a novel Bayesian semiparametric approach
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Cited In (12)

• A semiparametric efficient estimator in case-control studies for gene-environment independent models
• New perspective on the benefits of the gene–environment independence in case–control studies
• Title not available (Why is that?)
• Genotype-based Bayesian analysis of gene-environment interactions with multiple genetic markers and misclassification in environmental factors
• Robust Bayesian Variable Selection for Gene–Environment Interactions
• Jackknife empirical likelihood method for case-control studies with gene-environment independence on controls
• Genotype-based association models of complex diseases to detect gene-gene and gene-environment interactions
• Case–control genome-wide joint association study using semiparametric empirical model and approximate Bayes factor
• Case-Control Inference of Interaction between Genetic and Nongenetic Risk Factors under Assumptions on Their Distribution
• Bayesian semiparametric analysis for two-phase studies of gene-environment interaction
• Effects of gene-environment and gene-gene interactions in case-control studies: a novel Bayesian semiparametric approach
• A Bayesian semiparametric approach to learning about gene-gene interactions in case-control studies

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