Appendix 1—figure 1. Variable prediction accuracy within an ancestry group.

This figure extends Figure 1 of the main text, showing prediction accuracies based on large-scale diverse GWAS that are the union of all strata matching the number of individuals in each stratum. The numbers in parentheses show GWAS sample sizes (see Materials and methods for details). Each box and whiskers plot was computed based on 20 iterations of resampling estimation and prediction sets. Thick horizontal lines denote the medians. The polygenic scores were estimated in samples of unrelated WB individuals. Phenotypes were then predicted in distinct samples of unrelated WB individuals, stratified by sex (A), age (B) or Townsend deprivation index, a measure of SES (C). In red and green cases, polygenic scores are based on a GWAS in a sample limited to one sex, age or SES group (a 'stratum’). In black, polygenic scores are based on a diverse GWAS in a pooled sample of all strata. In blue, polygenic scores are based on a diverse GWAS in a pooled sample of all strata but downsampled to match the size of the stratified GWAS.