We conducted a multi-trait analysis of EduYears and our supplementary phenotypes to improve polygenic prediction accuracy. These phenotypes are well suited to joint analysis because their pairwise genetic correlations are high, in all cases exceeding 0.5 (Supplementary Table 14). We applied a recently developed method, Multi-Trait Analysis of GWAS, or MTAG11, to summary statistics for the four phenotypes from meta-analyses that exclude the prediction cohorts. For all four phenotypes, MTAG increases the number of lead SNPs identified at genome-wide significance (Supplementary Figures 17–20, Supplementary Table 15). Fig. 4C shows the incremental R2 for the polygenic scores based on GWAS and MTAG association statistics (but otherwise constructed using identical methods) when the target phenotype is either EduYears (left panel) or Cognitive Performance (right panel).
