We next investigated coverage and gene size (using strict gene boundaries, ±0 kb). The 732 hypothesis-driven candidate genes were markedly larger than the remaining 18,891 autosomal RefSeq genes (median 33.5 versus 20.5 kb, Wilcoxon p=4×10−20). Importantly, ISC SNP densities were similar in hypothesis-driven candidate genes in comparison to all other autosomal genes (median 1,360 versus 1,379 bases/SNP, Wilcoxon p=0.25). A sizable fraction of autosomal RefSeq genes had no ISC SNPs within their boundaries (18.7%). As expected, genes with no SNPs were markedly smaller (median 4.1 versus 28.2 kb, Wilcoxon p ≈ 0). As the 732 schizophrenia candidate genes were larger, they were significantly less likely to have no coverage than the remaining RefSeq genes (10.0% versus 19.0%, p=5×10−11). Although this generation of GWAS chips provides partial genomic coverage of common variation, hypothesis-driven candidate genes for schizophrenia had better coverage than other RefSeq genes.
