al., 2008)) to estimate proportions of local ancestry at each region and those estimates used to account for stratification based on those mixing proportions in subsequent tests in specific candidate regions. Importantly, Keller (Keller, 2014), suggests that although including these marker-based variables in linear models examining moderation of specific genetic associations (e.g., gene-by-intervention effects) effectively removes the confounding influence of population stratification, this is only true with respect to main effects. Thus, fully accounting for the effect of population stratification on an interaction requires the inclusion of all stratification related product terms (e.g., gene-by-stratification and intervention-by-stratification effects).
