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

Among those significant eQTL SNP-feature pairs that were well-imputed, polymorphic and expressed in the replication dataset (~84% of pairs, ~95% of eFeatures, see Methods , Figure S6 ), >94% had consistent directionality in the two datasets, between 75.7% (eTxns) and 81.5% (eJxns) were directionally consistent and marginally significant (at p < 0.01), and just over half (52.1%−57.0%) were directionally consistent and FDR-corrected significant (published set, p<10 −5 ).

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Interestingly, adjusting for observed factors related to RNA quality that characterize all earlier studies of gene expression in schizophrenic brain, including an earlier report using CMC data 19 , the proportion of genes with differentially expressed features at genome wide significant FDR < 5% that replicate (with directionality and marginal significance at p<0.05) in the CMC dataset was very small (11.0%).

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