Supplementary Material for: Analysis of Gene-Gene Interactions Using Gene-Trait Similarity Regression

<b><i>Objective:</i></b> Gene-gene interactions (G×G) are important to study because of their extensiveness in biological systems and their potential in explaining missing heritability of complex traits. In this work, we propose a new similarity-based test to assess G×G at the gene level, which permits the study of epistasis at biologically functional units with amplified interaction signals. <b><i>Methods:</i></b> Under the framework of gene-trait similarity regression (SimReg), we propose a gene-based test for detecting G×G. SimReg uses a regression model to correlate trait similarity with genotypic similarity across a gene. Unlike existing gene-level methods based on leading principal components (PCs), SimReg summarizes all information on genotypic variation within a gene and can be used to assess the joint/interactive effects of two genes as well as the effect of one gene conditional on another. <b><i>Results:</i></b> Using simulations and a real data application to the Warfarin study, we show that the SimReg G×G tests have satisfactory power and robustness under different genetic architecture when compared to existing gene-based interaction tests such as PC analysis or partial least squares. A genome-wide association study with approx. 20,000 genes may be completed on a parallel computing system in 2 weeks.