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A partition-based approach to identify gene-environment interactions in genome wide association studies.


ABSTRACT: It is believed that almost all common diseases are the consequence of complex interactions between genetic markers and environmental factors. However, few such interactions have been documented to date. Conventional statistical methods for detecting gene and environmental interactions are often based on the linear regression model, which assumes a linear interaction effect. In this study, we propose a nonparametric partition-based approach that is able to capture complex interaction patterns. We apply this method to the real data set of hypertension provided by Genetic Analysis Workshop 18. Compared with the linear regression model, the proposed approach is able to identify many additional variants with significant gene-environmental interaction effects. We further investigate one single-nucleotide polymorphism identified by our method and show that its gene-environmental interaction effect is, indeed, nonlinear. To adjust for the family dependence of phenotypes, we apply different permutation strategies and investigate their effects on the outcomes.

SUBMITTER: Fan R 

PROVIDER: S-EPMC4143762 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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A partition-based approach to identify gene-environment interactions in genome wide association studies.

Fan Ruixue R   Huang Chien-Hsun CH   Hu Inchi I   Wang Haitian H   Zheng Tian T   Lo Shaw-Hwa SH  

BMC proceedings 20140617 Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo


It is believed that almost all common diseases are the consequence of complex interactions between genetic markers and environmental factors. However, few such interactions have been documented to date. Conventional statistical methods for detecting gene and environmental interactions are often based on the linear regression model, which assumes a linear interaction effect. In this study, we propose a nonparametric partition-based approach that is able to capture complex interaction patterns. We  ...[more]

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