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Unpublished Paper
A penalized robust semiparametric approach for gene-environment interactions
(2015)
  • Shuangge Ma, Yale University
Abstract

In genetic and genomic studies, gene-environment (G*E) interactions have important implications. Some of the existing G$\times$E interaction methods are limited by analyzing a small number of G factors at a time, by assuming linear effects of E factors, by assuming no data contamination, and by adopting ineffective selection techniques. In this study, we propose a new approach for identifying important G*E interactions. It jointly models the effects of all E and G factors and their interactions. A partially linear varying coefficient model (PLVCM) is adopted to accommodate possible nonlinear effects of E factors. A rank-based loss function is used to accommodate possible data contamination. Penalization, which has been extensively used with high-dimensional data, is adopted for selection. The proposed penalized estimation approach can automatically determine if a G factor has an interaction with an E factor, main effect but not interaction, or no effect at all. The proposed approach can be effectively realized using a coordinate descent algorithm. Simulation shows that it has satisfactory performance and outperforms several competing alternatives. The proposed approach is used to analyze a lung cancer study with gene expression measurements and clinical variables.

Keywords
  • Gene-environment interactions; Robustness; Partially linear varying coefficient model; Penalized selection
Publication Date
2015
Citation Information
Shuangge Ma. "A penalized robust semiparametric approach for gene-environment interactions" (2015)
Available at: http://works.bepress.com/shuangge/50/