We used PRS-CS60 to adjust original GWAS beta weights for linkage disequilibrium and Plink261 to construct each PGS from these weights. We evaluated the incremental R2/pseudo-R2 (ΔR2) attained by adding the polygenic score to a regression with baseline covariates (e.g., age, sex, and ancestry PCs). We used least squares regression for continuous outcomes and logistic regression for categorical ones and adjusted the standard errors in COGA to account for the family structure. Regression models were estimated using the estimatr package in R62. We estimated 95% CIs for ΔR2 using bootstrapping (1,000 iterations) in the boot R package 63.
