The recommendations of this manuscript extend to future genome-wide interaction studies as well. For such studies, it is not sufficient to control for stratification, site, platform, and plate effects as is done in traditional (main effect) genome-wide studies. Rather, all relevant covariate-by-gene and covariate-by-environment interactions must also be included in the model to eliminate artifactual genome-wide signals that may otherwise swamp what are likely to be small true G×E signals.
