Allelic imbalance associated with the schizophrenia risk SNP rs1344706 indicates a cis-acting variant in ZNF804A.

There is compelling evidence for association of rs1344706, an intronic SNP within the zinc-finger protein 804A gene (ZNF804A), with schizophrenia (SZ) and bipolar disorder (BD) (O'Donovan et al., 2008; Williams et al., 2011; Zhang et al., 2012). Recently, some of the potential molecular mechanisms underlying the association between rs1344706 and disease risk were published (Girgenti et al., 2012; Hill and Bray, 2012; Hill et al., 2012; Kim et al., 2012; Okada et al., 2012; Umeda-Yano et al., 2013; Wright et al., 2013). Detection of expression quantitative trait loci (eQTL) is an important step in annotation of genomewide association study (GWAS) results that can provide possible functional links to pathophysiology, and putative use in biomarker studies (Vawter et al., 2011). There has been an over-representation of eQTL in the brain with the results of GWAS studies conducted in SZ (Richards et al., 2012). These recent results and prior attempts to find cisand trans-regulatory influences on gene expression in SZ (Vawter et al., 2006; Martin et al., 2009) were motivation to further look for cis-regulatory influences on gene expression for the ZNF804A associated SNP. We provide further independent evidence for the rs1344706 allelic specific expression (ASE) in the dorsolateral prefrontal cortex (DLPFC) of postmortem brains from the Stanley Medical Research Institute (SMRI). The SMRI Array Collection is a collection of postmortem brains from individuals with SZ (n = 35), with BD (n = 34), and psychiatrically normal controls (n = 35). RNA from the DLPFC was available for 99 individuals in the collection. Detailed information about the SMRI Array Collection is available at (http://www.stanleyresearch.org/dnn/ Default.aspx?tabid=197). The ASE published method (Guella et al., 2014) was used for all SMRI Array samples that were heterozygous for the rs12476147 exonic SNP, and normalized to the pooled gDNA assay (Guella et al., 2014). This sensitive method is a specific assay for detection of cis-regulatory effects of variants. The ASE assay detected a significant over-expression of the rs12476147A allele inDLPFC (average 1.12, p-value b 0.0002, 95% confidence interval 1.07–1.17) (Fig. 1) for all 47 subjects pooled. Moreover, cDNA allele ratios were significantly different according to the intronic rs1344706 genotypes (p-value = 0.014), with the SZ risk A allele associated with increased ZNF804A expression (average 1.17, p-value b 0.00002, 95% confidence interval 1.11–1.24) for 27 heterozygous subjects vs. genomic DNA. Further there is a significant difference in cDNA allele ratios between rs1344706 SNP homozygotes (n = 17) and heterozygotes (n = 27) for the expressed A/T allele ratio (p-value = 0.014). This latter result shows that the in phase risk allele for homozygous subjects gives a balanced allelic expression, while heterozygous subjects show an imbalanced expression. Prior studies examined the potential effect of rs1344706 on ASE among SNPs in high LD with rs1344706 (rs12476147 and rs4667001)