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BaDGE (Bayesian model for Detecting Gene Environment interaction)

This is a R package implementing the Bayeisan model for detecting gene environment interaction described in the following manucript. An important follow-up step after genetic markers are found to be associated with a disease outcome is a more detailed analysis investigating how the associated gene or a chromosomal region and an established environment risk factor interact to influence the disease risk. The standard approach to this study of gene-environment interaction considers one genetic marker at a time, and therefore could misrepresent and underestimate the genetic contribution to the joint effect when one or more functional loci, some of which might not be genotyped, exist in the region and interact with the environment risk factor in a complex way. We develop a more global approach based on a Bayesian model that uses a latent genetic profile variable to capture all of the genetic variation in the entire targeted region and allows the environment effect to vary across different genetic profile categories.

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Reference:

  • Yu K , Wacholder S , Wheeler W , Wang Z , Caporaso N , et al. 2012 A Flexible Bayesian Model for Studying Gene–Environment Interaction. PLoS Genet 8(1): e1002482.