We applied the CMC-DLPFC and GTEx-derived prediction models to schizophrenia cases and controls from the PGC2 and CLOZUK2 collections, constituting a large transcriptomic analysis of schizophrenia. Predicted gene expression levels were calculated for 19,661 unique genes across brain regions (Figure 1c) and tested for association with SCZ case-control status. We identified 413 significant associations, constituting 67 independent associations. We found significant replication of our CMC DLPFC associations in a large independent replication cohort, in collaboration with the iPSYCH-GEMS consortium. Our prediXcan results were significantly correlated with co-localization estimates (“PP4”) from COLOC. Importantly, GWAS loci with no significant prediXcan associations also had no evidence for co-localization with eQTLs. Together, these results imply that our prediXcan associations identify genes with good evidence for colocalization between GWAS and eQTL architecture, and are not contaminated by linkage disequilibrium (LD). One caveat is that four of our associations (SNX19, NAGA, TYW5, and GNL3) have no evidence for colocalization in COLOC results, or following visual inspection of local GWAS and eQTL architecture, and may be false positives.
