Bayesian variable selection for hierarchical gene-environment and gene-gene interactions.

Abstract:

:We propose a Bayesian hierarchical mixture model framework that allows us to investigate the genetic and environmental effects, gene by gene interactions and gene by environment interactions in the same model. Our approach incorporates the natural hierarchical structure between the main effects and interaction effects into a mixture model, such that our methods tend to remove the irrelevant interaction effects more effectively, resulting in more robust and parsimonious models. We consider both strong and weak hierarchical models. For a strong hierarchical model, both the main effects between interacting factors must be present for the interactions to be considered in the model development, while for a weak hierarchical model, only one of the two main effects is required to be present for the interaction to be evaluated. Our simulation results show that the proposed strong and weak hierarchical mixture models work well in controlling false-positive rates and provide a powerful approach for identifying the predisposing effects and interactions in gene-environment interaction studies, in comparison with the naive model that does not impose this hierarchical constraint in most of the scenarios simulated. We illustrate our approach using data for lung cancer and cutaneous melanoma.

journal_name

Hum Genet

journal_title

Human genetics

authors

Liu C,Ma J,Amos CI

doi

10.1007/s00439-014-1478-5

subject

Has Abstract

pub_date

2015-01-01 00:00:00

pages

23-36

issue

1

eissn

0340-6717

issn

1432-1203

journal_volume

134

pub_type

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