Bootstrapped confidence intervals were calculated by drawing, with replacement, a sample of equal size to the prediction sample, and then calculating the incremental R2 for the GWAS-based polygenic score, the MTAG-based polygenic score, and the difference between them. Our pooled results were obtained as a sample-size-weighted sum of HRS and Add Health results. As the bounds of the 95%-confidence intervals, we use the 2.5th- and 97.5th-percentile values of the incremental R2’s across 1000 bootstrap draws. Incremental R2 estimates and their confidence intervals for the prediction analyses are in Supplementary Tables 17 to 20 and Supplementary Figure 8.
