Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

GWAS have identified 108 schizophrenia risk loci, but risk mechanisms for individual loci are largely unknown. Using developmental, genetic, and illness-based RNA sequencing expression analysis in human brain, we characterized the human brain transcriptome around these loci and found enrichment for developmentally regulated genes with novel examples of shifting isoform usage across pre- and post-natal life. Across the genome, we found widespread expression quantitative trait loci (eQTLs), including many with transcript specificity and previously unannotated sequence that were independently replicated. We leveraged this general eQTL database to show that 48.1% of risk variants for schizophrenia associated with nearby expression. We lastly found 237 genes significantly differentially expressed between patients and controls which replicated in an independent dataset, implicated synaptic processes and were strongly regulated in early development. These findings together offer genetic- and diagnosis-related targets for better modeling schizophrenia risk. This publicly-available resource is available at: http://eqtl.brainseq.org/phase1