V=∑t=1nAtσgt2+Iσe2 where n is the number of subsets from any non-overlapping partitioning of SNPs; n = 22 for the joint analysis by chromosome, n = 5 for the analysis by MAF bin and n = 3 for the analysis of SNP by gene annotation in which SNPs were classed as CNS+ genes (2,725 genes representing 547 Mb), SNPs in other genes (14,804 genes representing 1,069 Mb) and the remaining SNPs not in genes. Gene boundaries were set at ± 50 kb from the 5′ and 3′ UTRs of each gene, and CNS+ genes were the four sets identified by Raychaudhuri et al.34 (one set comprised genes expressed preferentially in the brain compared to other tissues, and the other three sets comprised genes annotated to be involved in neuronal activity, learning and synapses). The CNS+ set was found to explain more of the SNP-based heritability than expected by chance for schizophrenia35. All methods have been implemented into the freely available GCTA software65.
