The second evaluation reports the results from the large PGC mega-analysis for schizophrenia. 11 We report results for the same SZGene polymorphisms (if available) plus the smallest P-value in the gene (±25 kb). The PGC and SZGene results agree on the absence of evidence of association for most of these genes (21/25). Four genes (DRD2, GRM3, NOTCH4, and TNF) are genome-wide significant in the PGC analysis, but were not implicated by the SZGene meta-analysis. The lack of association for NOTCH4 and TNF in the candidate gene literature is notable given that these genes are in the major histocompatibility complex (MHC). The MHC contains the most significant association common variant association (P=3.5x10−31) and the second largest OR (1.2) for schizophrenia. 11 Due to extensive linkage disequilibrium, the MHC contains thousands of genome-wide significant associations extending over 7 Mb. Indeed, there are over 60 genome-wide significant associations ±25 kb of NOTCH4 and four ±25 kb of the small TNF gene (2.8 kb). 11
