Our measure of prediction accuracy is the incremental R2. To calculate this value, we first regress a phenotype on our set of controls without the polygenic score. Next, we re-run the same regression but with the score included as a regressor. For quantitative phenotypes, our measure of predictive power is the change in R2. For binary outcomes, we calculated the incremental pseudo-R2 from a Probit regression. To obtain 95% confidence intervals, we bootstrapped the incremental R2’s with 1000 repetitions (Supplementary Table 38 and Supplementary Figures 13, 26, 27 and 28.
