Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits

Abstract

The genetic basis of complex traits involves the function of many genes with small effects as well as complex gene-gene and gene-environment interactions. As one of the major players in complex diseases, the role of gene-environment interactions has been increasingly recognized. Motivated by epidemiology studies to evaluate the joint effect of environmental mixtures, we developed a functional varying-index coefficient model (FVICM) to assess the combined effect of environmental mixtures and their interactions with genes, under a longitudinal design with quantitative traits. Built upon the previous work, we extend the FVICM model to accommodate binary longitudinal traits through the development of a generalized functional varying-index coefficient model (gFVICM). This model examines how the genetic effects on a disease trait are nonlinearly influenced by a combination of environmental factors. We derive an estimation procedure for the varying-index coefficient functions using quadratic inference functions combined with penalized splines. A hypothesis testing procedure is proposed to evaluate the significance of the nonparametric index functions. Extensive Monte Carlo simulations are conducted to evaluate the performance of the method under finite samples. The utility of the method is further demonstrated through a case study with a pain sensitivity dataset. SNPs were found to have their effects on blood pressure nonlinearly influenced by a combination of environmental factors.