schizophrenia4, as has been shown for other complex traits3,26–28. Some of these additional risk loci are likely contained near the most highly significant results of our stage 1 analysis. Supporting this hypothesis, of the top loci that did not reach genome-wide significance in the combined stage 1 and 2 analysis, a sign test (P < 10−4) and a Fisher’s combined test (P < 10−5) both showed an excess of same-direction allelic association (41 of 51 non-MHC SNPs) in the discovery and replication datasets.
