We carried out analyses for polygenic scoring of schizophrenia risk using the largest available schizophrenia association dataset3 as the “discovery” set. Quantitative scores were computed for each subject in this paper based on the set of SNPs with P values less than predefined P value thresholds (pT) in the discovery data set: pT < 0.0001, pT < 0.001, pT < 0.01, pT < 0.05, pT < 0.1, pT < 0.2, pT < 0.3, pT < 0.5, and pT < 1. For each SNP set defined by pT, we calculated the proportion of variance explained (Nagelkerke’s r2, Supplementary Fig. 1D). Throughout this work, we refer to the scores defined at pT < 0.5 simply as “polygenic risk scores” (PRS).
