Supplementary Figure 14: Comparison of AA meta-analysis results by number of PCA covariates.
QQ plots for association with AD in effective sample size weighted meta-analysis of all AA cohorts (ncase=3,335, ncontrol=2,945) (A) controlling for a full 5 principle components (PCs) in each cohort based on sample size, or (B) controlling for 1-5 PCs in each cohort, restricting to PCs that are associated with variants genome-wide rather than specific genomic regions. Compared to the basic analysis in Panel A, Panel B shows little evidence that the reduced number of PC covariates yields inflation from population stratification. The meta-analysis of AA cohorts reflected in Panel B is used as the primary analysis for the current paper.
