We identified 413 genome-wide significant associations, representing 256 genes in 13 tissues (Figure 2a). The largest number of associations was detected in the CMC-DLPFC GREX data (Figure 2c; 49 genes outside the MHC, 69 genes overall). We sought replication of our CMC DLPFC SCZ-associations in an independent dataset of 4,133 cases and 24,788 controls in collaboration with the iPSYCH-GEMS SCZ working group (Supplementary Figure 4b). We tested for replication of all Bonferroni-significant genes identified in our CMC-DLPFC analysis. Twelve out of 100 genes replicated in the iPSYCH-GEMS data, significantly more than expected by chance (binomial test, p = 0.0043). Notably, 11/12 replicating loci are previous GWAS loci, compared to 38/88 non-replicating loci. There was significant concordance between our discovery (PGC+CLOZUK2) and replication (iPSYCH-GEMS) samples; 72/100 genes have consistent direction of effect, including all 12 replicating genes (binomial p = 1.258 × 10−5), and we found significant correlation of effect sizes (p = 1.784 × 10−4; rho = 0.036) and –log10 p-values (p = 1.073 × 10−5; rho = 0.043).
