Generally, the loss of genetic signal from down-sampling will only exacerbate the problem of measurement error in PGSs constructed with finite-sample estimates as weights (Becker et al. 2021). As one of the most common third-party applications of publicly available GWAS summary statistics, we strongly encourage researchers to evaluate the loss of explanatory power in their main PGS analysis before they share down-sampled summary statistics with other users. This loss can be evaluated (i) across traits, as indicated by the overall reduction in variance explained (R2/pseudo-R2) and (ii) with the rank correlation of point estimates to evaluate the comparability of the overall pattern of polygenic score associations.
