The VTSABD and MTFS were analyzed together as a mega-analysis to increase power and ensure that the same variants were used to form each set. An indicator variable that identified which study a subject originated from was included as a covariate to address any potential study-related effects. Sex, age and 10 PCs were also included as covariates in this analysis. We tested the combined effects of common and rare variation in SKAT as described in Ionita-Lanza et al. (2013). Briefly, the effect of common and rare variants are assessed separately and then the corresponding test statistics are combined using weights such that common and rare variants contribute equally to the overall test statistic. We required that all variants be polymorphic in both the VTSABD and MTFS to avoid singleton or rare variants in one data set overly influencing the results. In total, 1,312 sets were tested for association with AD.
