We report the first genome-wide association study of a joint analysis using 795 Han Chinese individuals with treatment-refractory schizophrenia (TRS) and 806 controls. Three loci showed suggestive significant association with TRS were identified. These loci include: rs10218843 ( P = 3.04×10 −7 ) and rs11265461 ( P = 1.94×10 −7 ) are adjacent to signaling lymphocytic activation molecule family member 1 ( SLAMF1 ); rs4699030 ( P = 1.94×10 −6 ) and rs230529 ( P = 1.74×10 −7 ) are located in the gene nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 ( NFKB1 ); and rs13049286 ( P = 3.05×10 −5 ) and rs3827219 ( P = 1.66×10 −5 ) fall in receptor-interacting serine/threonine-protein kinase 4 ( RIPK4 ). One isolated single nucleotide polymorphism (SNP), rs739617 ( P = 3.87×10 −5 ) was also identified to be associated with TRS. The -94delATTG allele (rs28362691) located in the promoter region of NFKB1 was identified by resequencing and was found to associate with TRS ( P = 4.85×10 −6 ). The promoter assay demonstrated that the -94delATTG allele had a significant lower promoter activity than the -94insATTG allele in the SH-SY5Y cells. This study suggests that rs28362691 in NFKB1 might be involved in the development of TRS.

BackgroundThe human genome contains millions of single nucleotide polymorphisms (SNPs); many of these SNPs are intronic and have unknown functional significance. SNPs occurring within intron branchpoint sites, especially at the adenine (A), would presumably affect splicing; however, this has not been systematically studied. We employed a splicing prediction tool to identify human intron branchpoint sites and screened dbSNP for identifying SNPs located in the predicted sites to generate a genome-wide branchpoint site SNP database.ResultsWe identified 600 SNPs located within branchpoint sites; among which, 216 showed a change in A. After scoring the SNPs by counting the As in the ± 10 nucleotide region, only four SNPs were identified without additional As (rs13296170, rs12769205, rs75434223, and rs67785924). Using minigene constructs, we examined the effects of these SNPs on splicing. The three SNPs (rs13296170, rs12769205, and rs75434223) with nucleotide substitution at the A position resulted in abnormal splicing (exon skipping and/or intron inclusion). However, rs67785924, a 5-bp deletion that abolished the branchpoint A nucleotide, exhibited normal RNA splicing pattern, presumably using two of the downstream As as alternative branchpoints. The influence of additional As on splicing was further confirmed by studying rs2733532, which contains three additional As in the ± 10 nucleotide region.ConclusionsWe generated a high-confidence genome-wide branchpoint site SNP database, experimentally verified the importance of A in the branchpoint, and suggested that other nearby As can protect branchpoint A substitution from abnormal splicing.Electronic supplementary materialThe online version of this article (10.1186/s40246-017-0122-6) contains supplementary material, which is available to authorized users.

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