EUR+AFR+ANC compared to EUR+AFR; we note a modest correlation between each prediction method and the proportion of European-related ancestry (Reich et al., 2009) within African samples (see S19 Table). We repeated our analyses using stratified 10-fold cross-validation to estimate mixing weights (see Methods). We observed that methods that use two training populations continued to substantially outperform PRS using a single training population despite a decrease in prediction adjusted R2 (vs. Table 5) for each method, consistent with the limited sample size for estimating mixing weights (S20 Table).
