The full genotypes from the PGC2 cohorts that were used as test sets underwent stringent QC and only comprised 458,744–860,576 SNPs for schizophrenia and 556,278–859,034 SNPs for bipolar disorder. We refrained from using the intersection between all these cohorts to not reduce the number of SNPs used in prediction by too much. This meant that different iterations in the cross-validations were based on predictions using a different number of SNPs. However, each comparison between a single-trait predictor and a multi-trait predictor is based on the same number of SNPs.