Our analysis has focused on the confounding effect of PS on single-marker association analyses. While there is an increasing emphasis on detecting interactions between genes and between genes and the environment, Wang et al. [34] recently evaluated the bias resulting from the confounding effect of PS in studies of gene-gene or gene-environment interactions. Based on simulation studies, they showed that bias due to PS could be large for studies of interactions, especially when strong correlation between genes (or between genetic and environmental factors) takes place. Using data generated from the CGEMS project and tools developed in this paper, we can empirically evaluate the impact of PS on the study of gene-gene interaction under different control selection strategies. However, valid assessment of effect of PS on gene-environment interaction may require additional assumptions depending on the control selection procedure chosen.
