The optimal PRS weights reflect the true size of association between each SNP in the PRS and the trait. In practice, the size of this association must be estimated. We considered the effect size estimates computed in the EA GWAS (be), which may be very accurate in the EA population but potentially less appropriate in the admixed population. Therefore, we also considered the effect size estimated in a trainig admixed population (ba) and the effect size estimated in fixed effects meta-analysis (bm). We also compared these to PRSs without weights (or αp = 1 ∀p) because unweighted PRSs are often used in practice (Qi et al., 2017; Raffield et al., 2017). We always oriented the alleles to represent trait-increasing alleles.
