Common PTP4A1-PHF3-EYS variants are specific for alcohol dependence.

We previously reported a novel, functional and replicable risk gene region [i.e., protein tyrosine phosphatase type IVA gene, member 1 - Plant HomeoDomain (PHD) finger protein 3 gene - eyes shut homolog gene (PTP4A1-PHF3-EYS)] for alcohol dependence in a genome-wide association study (1). This 765kb region (Chr6: 64,066,604-64,831,120) included PTP4A1, PHF3, and their flanking regions, and part of EYS (close to 3’ of PHF3). It was enriched with common risk variants [minor allele frequency (MAF) > 0.05] for alcohol dependence across African-Americans (see Supplementary Figure S1B), European-Americans (Figure S1D) and European-Australians (Figure S1F). Within 90Mb range surrounding this region in the discovery sample, all variants with p<10-4 were concentrated in this region. Most of these risk variants had significant cis-acting regulatory effects on mRNA expression. The distributions of –log(p) values for association and functional signals in this region were highly consistent across six independent populations. Additionally, we tested 1,896 rare SNPs (MAF < 0.05) within this 765kb region in another association study (2) and found 22 (9.5×10-4≤p≤0.05), 17 (0.015≤p≤0.05) and 9 (0.006≤p≤0.05) individual rare SNPs that were nominally associated with alcohol dependence in above three populations, respectively. Furthermore, a rare variant constellation across the entire 765kb region was significantly associated with alcohol dependence in European-Australians (p=4.2×10-3). We speculated that this region might harbor a causal variant(s) for alcohol dependence. These findings were novel. The possibility that these genes are associated with other neuropsychiatric diseases, especially those comorbid with alcohol dependence, cannot be excluded until it has been tested. In the present study, we imputed this PTP4A1-PHF3-EYS region across 21 independent cohorts with 11 different neuropsychiatric disorders (Table 1). We examined the associations between common PTP4A1-PHF3-EYS variants [minor allele frequency (MAF) > 0.05 in both cases and controls] and these disorders, in order to test whether this PTP4A1-PHF3-EYS region is specific for alcohol dependence. The data of these disorders were all of those with neuropsychiatric and neurological disorders available for us from the dbGaP database (http://www.ncbi.nlm.nih.gov/gap/). Table 1 Associations between common PTP4A1-PHF3-EYS variants and different neuropsychiatric disorders A total of 49,268 subjects in these 21 cohorts were analyzed (Table 1), including one African-American discovery cohort [681 cases with alcohol dependence (DSM-IV) and 508 controls], one European-American replication cohort [1,409 alcohol dependent cases and 1,518 controls], and one European-Australian replication cohort [a total of 6,438 family subjects with 1,645 alcohol dependent probands]. 38,714 subjects in other 18 non-alcoholism cohorts served as contrast. Detailed demographic information for these samples has been published (1-9). We imputed the missing SNPs across the entire PTP4A1-PHF3-EYS region using the same reference panels (1,000 Genome Project and HapMap 3). We used the same strategies as previously to maximize the success rate and accuracy of imputation, to stringently clean the phenotype and genotype data, and then to test the variant-disease associations (7). Finally, a total of 477-1,095 SNPs with MAF>0.05 in both cases and controls were extracted for association analysis. The MAFs and minimal p values of the most significant risk SNPs are shown in Table 1. The experiment-wide significance level (α) was set at 1.6×10-5 via correction for the number of the cohorts (i.e., n=21) and the number of effective markers (i.e., n=144) that were calculated from the entire marker set by the adjusted Bonferroni-type program SNPSpD (10). We found that among a total of 1,095 common SNPs in the African-American cohort, 289 SNPs were nominally associated with alcohol dependence (p<0.05). Fifty-six associations of them were significant after correction (1.9×10-6≤p≤1.6×10-5) (Table 1). Most top-ranked SNPs (p<10-5) were located in the 5’ regulatory region of PTP4A1 (Figure S1A). Among a total of 477-1,042 common SNPs in other cohorts, 1-272 SNPs were nominally associated with diseases (p<0.05); however, none of them were significant after experiment-wide correction (Table 1; Figure S1). Furthermore, 200 SNPs were nominally associated with alcohol dependence both in African-Americans (1.9×10-6≤p<0.05) and European-Americans (3.9×10-4≤p<0.05); 15 SNPs were nominally associated with alcohol dependence across African-Americans (2.3×10-4≤p<0.05), European-Americans (0.006≤p<0.05) and European-Australians (0.009≤p<0.05). Most of the replicable SNPs were located in EYS (data not shown). By expanding the marker set, we confirmed with our previous findings that common PTP4A1-PHF3-EYS variants were significantly associated with alcohol dependence, which were replicable across African-Americans, European-Americans and European-Australians. Furthermore, by testing 10 other non-alcoholism neuropsychiatric disorders, we found that common PTP4A1-PHF3-EYS variants were specific to alcohol dependence; that is, they were not significantly associated with any other disorder examined. This study supports our previous conclusion that this region might harbor a causal variant(s) for alcohol dependence. PTP4A1 protein may interact with an activating transcription factor 7 (ATF7), which is a cAMP responsive element (CRE) binding protein and may interact with FOSB. CRE and FOSB have been implicated in addiction, including alcohol dependence. Functional connections of other genes within this region with alcohol dependence warrant further investigation.