Abstract
Several genome-wide association studies (GWASs) reported tens of risk genes for alcohol dependence, but most of them have not been replicated or confirmed by functional studies. The present study used a GWAS to search for novel, functional and replicable risk gene regions for alcohol dependence. Associations of all top-ranked SNPs identified in a discovery sample of 681 African-American (AA) cases with alcohol dependence and 508 AA controls were retested in a primary replication sample of 1,409 European-American (EA) cases and 1,518 EA controls. The replicable associations were then subjected to secondary replication in a sample of 6,438 Australian family subjects. A functional expression quantitative trait locus (eQTL) analysis of these replicable risk SNPs was followed-up in order to explore their cis-acting regulatory effects on gene expression. We found that within a 90 Mb region around PHF3-PTP4A1 locus in AAs, a linkage disequilibrium (LD) block in PHF3-PTP4A1 formed the only peak associated with alcohol dependence at p<10−4. Within this block, 30 SNPs associated with alcohol dependence in AAs (1.6×10−5≤p≤0.050) were replicated in EAs (1.3×10−3≤p≤0.038), and 18 of them were also replicated in Australians (1.8×10−3≤p≤0.048). Most of these risk SNPs had strong cis-acting regulatory effects on PHF3-PTP4A1 mRNA expression across three HapMap samples. The distributions of −log(p) values for association and functional signals throughout this LD block were highly consistent across AAs, EAs, Australians and three HapMap samples. We conclude that the PHF3-PTP4A1 region appears to harbor a causal locus for alcohol dependence, and proteins encoded by PHF3 and/or PTP4A1 might play a functional role in the disorder.
Highlights
Alcohol dependence is a common, highly familial disorder that is a leading cause of morbidity and premature death
Testing all available SNPs (n = 131) in the PHF3-PTP4A1 region in AAs, we found 38 SNPs that were nominally associated (1.661025#p#0.050) with alcohol dependence, among which, 28 survived region-wide correction for multiple testing (a = 0.01)
Testing these 38 SNPs in EAs, we found 30 in one linkage disequilibrium (LD) block (D9.0.9; Figure 1) that were well replicated in EAs (1.361023#p#0.038), and 23 of them that survived region-wide correction (a = 0.01) (Table 1)
Summary
Alcohol dependence is a common, highly familial disorder that is a leading cause of morbidity and premature death. It results in serious medical, legal, social and psychiatric problems and influences many facets of American society. It affects 4 to 5% of the United States population at any given time, with a lifetime prevalence of 12.5% [1,2]. Twin and adoption studies have demonstrated that genetic factors constitute a significant cause for alcohol dependence. A large number of risk loci have been reported for alcohol dependence (AD) by candidate gene approach.
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