For each of the five diseases, proportion of variance explained was calculated for each disease using the Nagelkerke’s pseudo-R2 metric (Supplementary Table 9). The R2 was calculated for the full model inclusive of the genome-wide polygenic score plus the covariates minus R2 for the covariates alone, thus yielding an estimate of the explained variance. Covariates in the model included age, gender, genotyping array, and the first four principal components of ancestry.
