To assess the utility of analyzing a much larger brain dataset, we compared previously reported DLPFC eQTLs to CMC-derived eQTL, estimating the proportion of non-null hypotheses (π1) in CMC and the number of additional eQTL found in CMC that were not detected in the other studies. GTEx v6 is the largest public dataset of eQTLs from DLPFC tissue (n = 92) assayed by RNA-seq; its replication in CMC is π1 = 0.98. Considering microarray-based eQTLs from the Harvard Brain Bank 15, BrainCloud16, NIH17, and the UK Brain Expression Consortium (UKBEC)18, we estimated π1 to be 0.75, 0.70, 0.79, and 0.93, respectively, indicating that our results captured most eQTLs found in other independent samples. Replication was somewhat lower for a recent meta-analysis that included a mix of several distinct brain regions19 (π1 = 0.62), and for eQTLs detected in blood (π1 = 0.54)20. We also derived eQTL for 279 DLPFC samples as part of the NIMH Human Brain Collection Core (HBCC) microarray data and found replication π1 = 0.77. Moreover, concordance of the direction of allelic effect was high, with 93%
