Using a method that controls for the number of SNPs tested at each locus as well as the number of genes/transcripts assayed [4, 18], we identified high confidence cis-eQTL regulating 1329 genes and 3252 individual transcripts in the human fetal brain. This approximates the number of eGenes identified using the same procedure in adult brain collections of comparable size; for example, in 92 samples from the adult frontal cortex, the GTEx Consortium identified cis-eQTL (FDR < 0.05) for 1588 genes [4]. However, this is likely to constitute only a small percentage of the genes expressed in fetal brain that are subject to variable genetic cis-regulation. Studies in adult human tissues have indicated that a sizeable proportion of expressed genes are variably cis-regulated [4, 50, 51], with eQTL mapping studies showing the expected strong correlation between eQTL discovery and sample size [4]. Larger collections of fetal brain are therefore likely to yield many additional eQTL, with resulting improvements in power to identify gene expression changes relevant to brain-related traits.
