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Wang Z, Lin X, Luo X, Xiao J, Zhang Y, Xu J, Wang S, Zhao F, Wang H, Zheng H, Zhang W, Lin C, Tan Z, Cao L, Wang Z, Tan Y, Chen W, Cao Y, Guo X, Pittenger C, Luo X. Pleiotropic Association of CACNA1C Variants With Neuropsychiatric Disorders. Schizophr Bull 2023; 49:1174-1184. [PMID: 37306960 PMCID: PMC10483336 DOI: 10.1093/schbul/sbad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
BACKGROUND Neuropsychiatric disorders are highly heritable and have overlapping genetic underpinnings. Single nucleotide polymorphisms (SNPs) in the gene CACNA1C have been associated with several neuropsychiatric disorders, across multiple genome-wide association studies. METHOD A total of 70,711 subjects from 37 independent cohorts with 13 different neuropsychiatric disorders were meta-analyzed to identify overlap of disorder-associated SNPs within CACNA1C. The differential expression of CACNA1C mRNA in five independent postmortem brain cohorts was examined. Finally, the associations of disease-sharing risk alleles with total intracranial volume (ICV), gray matter volumes (GMVs) of subcortical structures, cortical surface area (SA), and average cortical thickness (TH) were tested. RESULTS Eighteen SNPs within CACNA1C were nominally associated with more than one neuropsychiatric disorder (P < .05); the associations shared among schizophrenia, bipolar disorder, and alcohol use disorder survived false discovery rate correction (five SNPs with P < 7.3 × 10-4 and q < 0.05). CACNA1C mRNA was differentially expressed in brains from individuals with schizophrenia, bipolar disorder, and Parkinson's disease, relative to controls (three SNPs with P < .01). Risk alleles shared by schizophrenia, bipolar disorder, substance dependence, and Parkinson's disease were significantly associated with ICV, GMVs, SA, or TH (one SNP with P ≤ 7.1 × 10-3 and q < 0.05). CONCLUSION Integrating multiple levels of analyses, we identified CACNA1C variants associated with multiple psychiatric disorders, and schizophrenia and bipolar disorder were most strongly implicated. CACNA1C variants may contribute to shared risk and pathophysiology in these conditions.
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Affiliation(s)
- Zuxing Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
- Sichuan Provincial Center for Mental Health, The Center of Psychosomatic Medicine of Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian 350014, China
| | - Xinqun Luo
- Department of Neurosurgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350001, China
| | - Jun Xiao
- Sichuan Provincial Center for Mental Health, The Center of Psychosomatic Medicine of Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Yong Zhang
- Tianjin Mental Health Center, Tianjin 300180, China
| | - Jianying Xu
- Zhuhai Center for Maternal and Child Health Care, Zhuhai, Guangdong 519000, China
| | - Shibin Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
| | - Fen Zhao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
| | - Huifen Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
| | - Hangxiao Zheng
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
| | - Wei Zhang
- Department of Pharmacology, Institute of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, 050017, P. R. China
| | - Chen Lin
- Beijing Huilongguan Hospital, Peking University Huilongguan School of Clinical Medicine, Beijing 100096, China
| | - Zewen Tan
- Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510370, China
| | - Liping Cao
- Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510370, China
| | - Zhiren Wang
- Beijing Huilongguan Hospital, Peking University Huilongguan School of Clinical Medicine, Beijing 100096, China
| | - Yunlong Tan
- Beijing Huilongguan Hospital, Peking University Huilongguan School of Clinical Medicine, Beijing 100096, China
| | - Wenzhong Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
| | - Yuping Cao
- Department of Psychiatry, Second Xiangya Hospital, Central South University; China National Clinical Research Center on Mental Disorders, China National Technology Institute on Mental Disorders, Changsha, Hunan 410011, China
| | - Xiaoyun Guo
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of medicine, Shanghai 200030, China
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, US
| | - Christopher Pittenger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, US
| | - Xingguang Luo
- Beijing Huilongguan Hospital, Peking University Huilongguan School of Clinical Medicine, Beijing 100096, China
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Association of ADH7 Gene Polymorphism with Schizophrenia in the Han Population of Northern China: a Case-Control Study. J Mol Neurosci 2020; 70:1851-1857. [PMID: 32388801 DOI: 10.1007/s12031-020-01578-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/01/2020] [Indexed: 10/24/2022]
Abstract
Schizophrenia is a serious neurodevelopmental disorder. Genetics is an important factor leading to schizophrenia, but its exact role is still unclear. Many studies have focused on neurotransmitters and regulators that participate in the processes mediated by these neurotransmitters. Alcohol dehydrogenase may not only catalyze the oxidation of retinol and ethanol but also be involved in a variety of neurotransmitter metabolic pathways. Therefore, our study investigated whether ADH7 gene variations in the Chinese Han population were associated with schizophrenia. Genomic DNA was extracted from a cohort of 275 schizophrenic patients (136 men and 139 women) and 313 healthy controls (160 men and 153 women) from the Northern Han Chinese population. The Hardy-Weinberg equilibrium test and linkage disequilibrium analysis were performed. Differences in genotypes, alleles, and haplotypes between the schizophrenic and control groups were determined using the chi-square test and correlation analysis. The distribution of the CC + TT genotype of rs284787 was statistically different between the case and control groups (p = 0.026, OR = 1.448); however, the difference disappeared after Bonferroni correction. Linkage analysis indicated that rs739147, rs284787, rs3805329, rs894369, rs3805331, and rs284786 were closely linked in one block. The haplotype analysis found no association between the composed haplotypes and the occurrence of schizophrenia. Our study showed that the ADH7 gene was not associated with the risk of schizophrenia. Additional studies with larger cohorts of different ethnicities are needed to validate our findings.
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Dai Y, Hu R, Pei G, Zhang H, Zhao Z, Jia P. Diverse types of genomic evidence converge on alcohol use disorder risk genes. J Med Genet 2020; 57:733-743. [PMID: 32170004 DOI: 10.1136/jmedgenet-2019-106490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/08/2020] [Accepted: 02/10/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Alcohol use disorder (AUD) is one of the most common forms of substance use disorders with a strong contribution of genetic (50%-60%) and environmental factors. Genome-wide association studies (GWAS) have identified a number of AUD-associated variants, including those in alcohol metabolism genes. These genetic variants may modulate gene expression, making individuals more susceptible to AUD. A long-term alcohol consumption can also change the transcriptome patterns of subjects via epigenetic modulations. METHODS To explore the interactive effect of genetic and epigenetic factors on AUD, we conducted a secondary analysis by integrating GWAS, CNV, brain transcriptome and DNA methylation data to unravel novel AUD-associated genes/variants. We applied the mega-analysis of OR (MegaOR) method to prioritise AUD candidate genes (AUDgenes). RESULTS We identified a consensus set of 206 AUDgenes based on the multi-omics data. We demonstrated that these AUDgenes tend to interact with each other more frequent than chance expectation. Functional annotation analysis indicated that these AUDgenes were involved in substance dependence, synaptic transmission, glial cell proliferation and enriched in neuronal and liver cells. We obtained a multidimensional evidence that AUD is a polygenic disorder influenced by both genetic and epigenetic factors as well as the interaction of them. CONCLUSION We characterised multidimensional evidence of genetic, epigenetic and transcriptomic data in AUD. We found that 206 AUD associated genes were highly expressed in liver, brain cerebellum, frontal cortex, hippocampus and pituitary. Our studies provides important insights into the molecular mechanism of AUD and potential target genes for AUD treatment.
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Affiliation(s)
- Yulin Dai
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ruifeng Hu
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Guangsheng Pei
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, Massachusetts, USA.,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Zhongming Zhao
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peilin Jia
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
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4
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Genome-wide association study of alcohol dependence in male Han Chinese and cross-ethnic polygenic risk score comparison. Transl Psychiatry 2019; 9:249. [PMID: 31591379 PMCID: PMC6779867 DOI: 10.1038/s41398-019-0586-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 09/01/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Alcohol-related behaviors are moderately heritable and have ethnic-specific characteristics. At present, genetic studies for alcohol dependence (AD) in Chinese populations are underrepresented. We are the first to conduct a genome-wide association study (GWAS) for AD using 533 male alcoholics and 2848 controls of Han Chinese ethnicity and replicate our findings in 146 male alcoholics and 200 male controls. We then assessed genetic effects on AD characteristics (drinking volume/age onset/Michigan Alcoholism Screening Test (MAST)/Barratt Impulsiveness Scale (BIS-11)), and compared the polygenic risk of AD in Han Chinese with other populations (Thai, European American and African American). We found and validated two significant loci, one located in 4q23, with lead SNP rs2075633*ADH1B (Pdiscovery = 6.64 × 10-16) and functional SNP rs1229984*ADH1B (Pdiscovery = 3.93 × 10-13); and the other located in 12q24.12-12q24.13, with lead SNP rs11066001*BRAP (Pdiscovery = 1.63 × 10-9) and functional SNP rs671*ALDH2 (Pdiscovery = 3.44 × 10-9). ADH1B rs1229984 was associated with MAST, BIS_total score and average drinking volume. Polygenic risk scores from the Thai AD and European American AD GWAS were significantly associated with AD in Han Chinese, which were entirely due to the top two loci, however there was no significant prediction from African Americans. This is the first case-control AD GWAS in Han Chinese. Our findings demonstrate that these variants, which were highly linked with ALDH2 rs671 and ADH1B rs1229984, were significant modulators for AD in our Han Chinese cohort. A larger replication cohort is still needed to validate our findings.
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5
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Clark SL, McClay JL, Adkins DE, Kumar G, Aberg KA, Nerella S, Xie L, Collins AL, Crowley JJ, Quackenbush CR, Hilliard CE, Shabalin AA, Vrieze SI, Peterson RE, Copeland WE, Silberg JL, McGue M, Maes H, Iacono WG, Sullivan PF, Costello EJ, van den Oord EJ. Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence. Alcohol Clin Exp Res 2017; 41:711-718. [PMID: 28196272 DOI: 10.1111/acer.13352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Previous genomewide association studies (GWASs) have identified a number of putative risk loci for alcohol dependence (AD). However, only a few loci have replicated and these replicated variants only explain a small proportion of AD risk. Using an innovative approach, the goal of this study was to generate hypotheses about potentially causal variants for AD that can be explored further through functional studies. METHODS We employed targeted capture of 71 candidate loci and flanking regions followed by next-generation deep sequencing (mean coverage 78X) in 806 European Americans. Regions included in our targeted capture library were genes identified through published GWAS of alcohol, all human alcohol and aldehyde dehydrogenases, reward system genes including dopaminergic and opioid receptors, prioritized candidate genes based on previous associations, and genes involved in the absorption, distribution, metabolism, and excretion of drugs. We performed single-locus tests to determine if any single variant was associated with AD symptom count. Sets of variants that overlapped with biologically meaningful annotations were tested for association in aggregate. RESULTS No single, common variant was significantly associated with AD in our study. We did, however, find evidence for association with several variant sets. Two variant sets were significant at the q-value <0.10 level: a genic enhancer for ADHFE1 (p = 1.47 × 10-5 ; q = 0.019), an alcohol dehydrogenase, and ADORA1 (p = 5.29 × 10-5 ; q = 0.035), an adenosine receptor that belongs to a G-protein-coupled receptor gene family. CONCLUSIONS To our knowledge, this is the first sequencing study of AD to examine variants in entire genes, including flanking and regulatory regions. We found that in addition to protein coding variant sets, regulatory variant sets may play a role in AD. From these findings, we have generated initial functional hypotheses about how these sets may influence AD.
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Affiliation(s)
- Shaunna L Clark
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph L McClay
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Daniel E Adkins
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Gaurav Kumar
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Srilaxmi Nerella
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Linying Xie
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Ann L Collins
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Corey R Quackenbush
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christopher E Hilliard
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Scott I Vrieze
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado.,Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Roseann E Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - William E Copeland
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Judy L Silberg
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Hermine Maes
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elizabeth J Costello
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Edwin J van den Oord
- Center for Biomarker Research and Precision Medicine , School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
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Zuo L, Saba L, Lin X, Tan Y, Wang K, Krystal JH, Tabakoff B, Luo X. Significant association between rare IPO11-HTR1A variants and attention deficit hyperactivity disorder in Caucasians. Am J Med Genet B Neuropsychiatr Genet 2015; 168:544-56. [PMID: 26079129 PMCID: PMC4851708 DOI: 10.1002/ajmg.b.32329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/22/2015] [Indexed: 12/28/2022]
Abstract
We comprehensively examined the rare variants in the IPO11-HTR1A region to explore their roles in neuropsychiatric disorders. Five hundred seventy-three to 1,181 rare SNPs in subjects of European descent and 1,234-2,529 SNPs in subjects of African descent (0 < minor allele frequency (MAF) < 0.05) were analyzed in a total of 49,268 subjects in 21 independent cohorts with 11 different neuropsychiatric disorders. Associations between rare variant constellations and diseases and associations between individual rare variants and diseases were tested. RNA expression changes of this region were also explored. We identified a rare variant constellation across the entire IPO11-HTR1A region that was associated with attention deficit hyperactivity disorder (ADHD) in Caucasians (T5: P = 7.9 × 10(-31) ; Fp: P = 1.3 × 10(-32) ), but not with any other disorder examined; association signals mainly came from IPO11 (T5: P = 3.6 × 10(-10) ; Fp: P = 3.2 × 1 0(-10) ) and the intergenic region between IPO11 and HTR1A (T5: P = 4.1 × 10(-30) ; Fp: P = 5.4 × 10(-32) ). One association between ADHD and an intergenic rare variant, i.e., rs10042956, exhibited region- and cohort-wide significance (P = 5.2 × 10(-6) ) and survived correction for false discovery rate (q = 0.006). Cis-eQTL analysis showed that, 29 among the 41 SNPs within or around IPO11 had replicable significant regulatory effects on IPO11 exon expression (1.5 × 10(-17) ≤P < 0.002) in human brain or peripheral blood mononuclear cell tissues. We concluded that IPO11-HTR1A was a significant risk gene region for ADHD in Caucasians.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Laura Saba
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Xiandong Lin
- Provincial Key Laboratory of Translational Cancer Medicine, Fujian Provincial Cancer Hospital, Fuzhou, Fujian, China
| | - Yunlong Tan
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Alcohol Research Center, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Boris Tabakoff
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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Bühler KM, Giné E, Echeverry-Alzate V, Calleja-Conde J, de Fonseca FR, López-Moreno JA. Common single nucleotide variants underlying drug addiction: more than a decade of research. Addict Biol 2015; 20:845-71. [PMID: 25603899 DOI: 10.1111/adb.12204] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-related phenotypes are common complex and highly heritable traits. In the last few years, candidate gene (CGAS) and genome-wide association studies (GWAS) have identified a huge number of single nucleotide polymorphisms (SNPs) associated with drug use, abuse or dependence, mainly related to alcohol or nicotine. Nevertheless, few of these associations have been replicated in independent studies. The aim of this study was to provide a review of the SNPs that have been most significantly associated with alcohol-, nicotine-, cannabis- and cocaine-related phenotypes in humans between the years of 2000 and 2012. To this end, we selected CGAS, GWAS, family-based association and case-only studies published in peer-reviewed international scientific journals (using the PubMed/MEDLINE and Addiction GWAS Resource databases) in which a significant association was reported. A total of 371 studies fit the search criteria. We then filtered SNPs with at least one replication study and performed meta-analysis of the significance of the associations. SNPs in the alcohol metabolizing genes, in the cholinergic gene cluster CHRNA5-CHRNA3-CHRNB4, and in the DRD2 and ANNK1 genes, are, to date, the most replicated and significant gene variants associated with alcohol- and nicotine-related phenotypes. In the case of cannabis and cocaine, a far fewer number of studies and replications have been reported, indicating either a need for further investigation or that the genetics of cannabis/cocaine addiction are more elusive. This review brings a global state-of-the-art vision of the behavioral genetics of addiction and collaborates on formulation of new hypothesis to guide future work.
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Affiliation(s)
- Kora-Mareen Bühler
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | - Elena Giné
- Department of Cellular Biology; School of Medicine; Complutense University of Madrid; Málaga Spain
| | - Victor Echeverry-Alzate
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
| | - Javier Calleja-Conde
- Department of Psychobiology; School of Psychology; Complutense University of Madrid; Málaga Spain
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8
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Grotewiel M, Bettinger JC. Drosophila and Caenorhabditis elegans as Discovery Platforms for Genes Involved in Human Alcohol Use Disorder. Alcohol Clin Exp Res 2015; 39:1292-311. [PMID: 26173477 PMCID: PMC4656040 DOI: 10.1111/acer.12785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/18/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND Despite the profound clinical significance and strong heritability of alcohol use disorder (AUD), we do not yet have a comprehensive understanding of the naturally occurring genetic variance within the human genome that drives its development. This lack of understanding is likely to be due in part to the large phenotypic and genetic heterogeneities that underlie human AUD. As a complement to genetic studies in humans, many laboratories are using the invertebrate model organisms (iMOs) Drosophila melanogaster (fruit fly) and Caenorhabditis elegans (nematode worm) to identify genetic mechanisms that influence the effects of alcohol (ethanol) on behavior. While these extremely powerful models have identified many genes that influence the behavioral responses to alcohol, in most cases it has remained unclear whether results from behavioral-genetic studies in iMOs are directly applicable to understanding the genetic basis of human AUD. METHODS In this review, we critically evaluate the utility of the fly and worm models for identifying genes that influence AUD in humans. RESULTS Based on results published through early 2015, studies in flies and worms have identified 91 and 50 genes, respectively, that influence 1 or more aspects of behavioral responses to alcohol. Collectively, these fly and worm genes correspond to 293 orthologous genes in humans. Intriguingly, 51 of these 293 human genes have been implicated in AUD by at least 1 study in human populations. CONCLUSIONS Our analyses strongly suggest that the Drosophila and C. elegans models have considerable utility for identifying orthologs of genes that influence human AUD.
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Affiliation(s)
- Mike Grotewiel
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
- Virginia Commonwealth University Alcohol Research Center, Richmond, Virginia
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology , Virginia Commonwealth University, Richmond, Virginia
- Virginia Commonwealth University Alcohol Research Center, Richmond, Virginia
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9
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Zuo L, Tan Y, Zhang X, Wang X, Krystal J, Tabakoff B, Zhong C, Luo X. A New Genomewide Association Meta-Analysis of Alcohol Dependence. Alcohol Clin Exp Res 2015; 39:1388-95. [PMID: 26173551 PMCID: PMC5587504 DOI: 10.1111/acer.12786] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 05/18/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Conventional meta-analysis based on genetic markers may be less powerful for heterogeneous samples. In this study, we introduced a new meta-analysis for 4 genomewide association studies on alcohol dependence that integrated the information of putative causal variants. METHODS A total of 12,481 subjects in 4 independent cohorts were analyzed, including 1 European American cohort (1,409 cases with alcohol dependence and 1,518 controls), 1 European Australian cohort (a total of 6,438 family subjects with 1,645 probands), 1 African American cohort from SAGE + COGA (681 cases and 508 controls), and 1 African American cohort from Yale (1,429 cases and 498 controls). The genomewide association analysis was conducted for each cohort, and then, a new meta-analysis was performed to derive the combined p-values. cis-Acting expression of quantitative locus (cis-eQTL) analysis of each risk variant in human tissues and RNA expression analysis of each risk gene in rat brain served as functional validation. RESULTS In meta-analysis of European American and European Australian cohorts, we found 10 top-ranked single nucleotide polymorphisms (SNPs) (p < 10(-6) ) that were associated with alcohol dependence. They included 6 at SERINC2 (3.1 × 10(-8) ≤ p ≤ 9.6 × 10(-8) ), 1 at STK40 (p = 1.3 × 10(-7) ), 2 at KIAA0040 (3.3 × 10(-7) ≤ p ≤ 5.2 × 10(-7) ), and 1 at IPO11 (p = 6.9 × 10(-7) ). In meta-analysis of 2 African American cohorts, we found 2 top-ranked SNPs including 1 at SLC6A11 (p = 2.7 × 10(-7) ) and 1 at CBLN2 (p = 7.4 × 10(-7) ). In meta-analysis of all 4 cohorts, we found 2 top-ranked SNPs in PTP4A1-PHF3 locus (6.0 × 10(-7) ≤ p ≤ 7.2 × 10(-7) ). In an African American cohort only, we found 1 top-ranked SNP at PLD1 (p = 8.3 × 10(-7) ; OR = 1.56). Many risk SNPs had positive cis-eQTL signals, and all these risk genes except KIAA0040 were found to express in both rat and mouse brains. CONCLUSIONS We found multiple genes that were significantly or suggestively associated with alcohol dependence. They are among the most appropriate for follow-up as contributors to risk for alcohol dependence.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Yunlong Tan
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Xiangyang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Xiaoping Wang
- Department of Neurology, First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - John Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Boris Tabakoff
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Chunlong Zhong
- Department of Neurosurgery, Dongfang Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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10
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Oniszczenko W, Rybakowski JK, Dragan WŁ, Grzywacz A, Samochowiec J. The ADH gene cluster SNP rs1789891 and temperamental dimensions in patients with alcohol dependence and affective disorders. Scand J Psychol 2015; 56:420-7. [PMID: 26013422 DOI: 10.1111/sjop.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 04/02/2015] [Indexed: 11/29/2022]
Abstract
This study had three objectives: (1) to assess the relationship between the single nucleotide polymorphism (SNP) rs1789891 in the alcohol dehydrogenase gene cluster and alcohol dependence and affective disorders; (2) to assess the differences in the Regulative Theory of Temperament (RTT) traits between an alcohol dependent group, an affective disorders group, and a healthy group; and (3) to assess the relationship between rs1789891 and temperament traits in a healthy group, taking into account the interaction of genotype and sex. The SNP rs1789891 was genotyped in a group of 194 alcohol dependent men, aged 21 to 71 years; 137 patients with affective disorders, including 51 males and 86 females, aged 19 to 85 years; and a group of 207 healthy individuals, including 89 males and 118 females, aged 18 to 71 years. Temperament traits (briskness, perseveration, sensory sensitivity, emotional reactivity, endurance, and activity) were assessed in all groups using the Formal Characteristics of Behaviour-Temperament Inventory. The comparative analysis of genotypic frequencies showed no significant differences between patients with alcoholism or affective disorders and those in the control group. Alcohol dependent men and the affective disorder group were characterised by higher levels of emotional reactivity (p-value 1.4e-5 and 9.84e-7, respectively) and lower levels of briskness, sensory sensitivity, endurance, and activity (p-value from 3.76e-8 to 0.012) when compared to the healthy group. The rs1789891 polymorphism was associated with briskness (p = 0.02), sensory sensitivity (p = 0.036), and activity (p = 0.049). None of the results were statistically significant after Bonferroni correction.
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Affiliation(s)
| | - Janusz K Rybakowski
- Department of Adult Psychiatry, Poznań University of Medical Sciences, Poznań, Poland
| | | | - Anna Grzywacz
- Department of Psychiatry, Pomeranian Medical University, Szczecin, Poland
| | - Jerzy Samochowiec
- Department of Psychiatry, Pomeranian Medical University, Szczecin, Poland
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Norden-Krichmar TM, Gizer IR, Wilhelmsen KC, Schork NJ, Ehlers CL. Protective variant associated with alcohol dependence in a Mexican American cohort. BMC MEDICAL GENETICS 2014; 15:136. [PMID: 25527893 PMCID: PMC4337107 DOI: 10.1186/s12881-014-0136-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/08/2014] [Indexed: 01/11/2023]
Abstract
Background Mexican Americans, particularly those born in the United States, are at greater risk for alcohol associated morbidity and mortality. The present study sought to investigate whether specific genetic variants may be associated with alcohol use disorder phenotypes in a select population of Mexican American young adults. Methods The study evaluated a cohort of 427 (age 18 – 30 years) Mexican American men (n = 171) and women (n = 256). Information on alcohol dependence was obtained through interview using the Semi-Structured Assessment for the Genetics of Alcoholism (SSAGA). For all subjects, DNA was extracted from blood samples, followed by genotyping using an Affymetrix Axiom Exome1A chip. Results A protective variant (rs991316) located downstream from the ADH7 (alcohol dehydrogenase 7) gene showed suggestive significance in association with alcohol dependence symptom counts derived from DSM-III-R and DSM-IV criteria, as well as to clustered alcohol dependence symptoms. Additional linkage analysis suggested that nearby variants in linkage disequilibrium with rs991316 were not responsible for the observed association with the alcohol dependence phenotypes in this study. Conclusions ADH7 has been shown to have a protective role against alcohol dependence in previous studies involving other ethnicities, but has not been reported for Mexican Americans. These results suggest that variants near ADH7 may play a role in protection from alcohol dependence in this Mexican American cohort.
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Peng Q, Gizer IR, Libiger O, Bizon C, Wilhelmsen KC, Schork NJ, Ehlers CL. Association and ancestry analysis of sequence variants in ADH and ALDH using alcohol-related phenotypes in a Native American community sample. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:673-83. [PMID: 25270064 PMCID: PMC4364382 DOI: 10.1002/ajmg.b.32272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/03/2014] [Indexed: 12/30/2022]
Abstract
Higher rates of alcohol use and other drug-dependence have been observed in some Native American (NA) populations relative to other ethnic groups in the US. Previous studies have shown that alcohol dehydrogenase (ADH) genes and aldehyde dehydrogenase (ALDH) genes may affect the risk of development of alcohol dependence, and that polymorphisms within these genes may differentially affect risk for the disorder depending on the ethnic group evaluated. We evaluated variations in the ADH and ALDH genes in a large study investigating risk factors for substance use in a NA population. We assessed ancestry admixture and tested for associations between alcohol-related phenotypes in the genomic regions around the ADH1-7 and ALDH2 and ALDH1A1 genes. Seventy-two ADH variants showed significant evidence of association with a severity level of alcohol drinking-related dependence symptoms phenotype. These significant variants spanned across the entire 7 ADH gene cluster regions. Two significant associations, one in ADH and one in ALDH2, were observed with alcohol dependence diagnosis. Seventeen variants showed significant association with the largest number of alcohol drinks ingested during any 24-hour period. Variants in or near ADH7 were significantly negatively associated with alcohol-related phenotypes, suggesting a potential protective effect of this gene. In addition, our results suggested that a higher degree of NA ancestry is associated with higher frequencies of potential risk variants and lower frequencies of potential protective variants for alcohol dependence phenotypes.
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Affiliation(s)
- Qian Peng
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA 92037, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037,Corresponding author: 4120 Torrey Pines Road, La Jolla, CA 92037 Tel (858) 200-1888; Corresponding author: 10550 North Torrey Pines Road, La Jolla, CA 92037, Mail SP30-1501 Tel (858) 784-7058; Fax (858) 784-7409
| | - Ian R. Gizer
- Department of Psychological Sciences, University of Missouri-Columbia, Columbia, MO 65211
| | - Ondrej Libiger
- Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517
| | - Kirk C. Wilhelmsen
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, Department of Genetics and Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nicholas J. Schork
- Department of Human Biology, J. Craig Venter Institute, La Jolla, CA 92037
| | - Cindy L. Ehlers
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037,Corresponding author: 4120 Torrey Pines Road, La Jolla, CA 92037 Tel (858) 200-1888; Corresponding author: 10550 North Torrey Pines Road, La Jolla, CA 92037, Mail SP30-1501 Tel (858) 784-7058; Fax (858) 784-7409
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Wium-Andersen MK, Orsted DD, Tolstrup JS, Nordestgaard BG. Increased alcohol consumption as a cause of alcoholism, without similar evidence for depression: a Mendelian randomization study. Int J Epidemiol 2014; 44:526-39. [DOI: 10.1093/ije/dyu220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2014] [Indexed: 02/03/2023] Open
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Zuo L, Lu L, Tan Y, Pan X, Cai Y, Wang X, Hong J, Zhong C, Wang F, Zhang XY, Vanderlinden LA, Tabakoff B, Luo X. Genome-wide association discoveries of alcohol dependence. Am J Addict 2014; 23:526-39. [PMID: 25278008 PMCID: PMC4187224 DOI: 10.1111/j.1521-0391.2014.12147.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 04/17/2014] [Accepted: 05/12/2014] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE To report the genome-wide significant and/or replicable risk variants for alcohol dependence and explore their potential biological functions. METHODS We searched in PubMed for all genome-wide association studies (GWASs) of alcohol dependence. The following three types of the results were extracted: genome-wide significant associations in an individual sample, the combined samples, or the meta-analysis (p < 5 × 10(-8) ); top-ranked associations in an individual sample (p < 10(-5) ) that were nominally replicated in other samples (p < .05); and nominally replicable associations across at least three independent GWAS samples (p < .05). These results were meta-analyzed. cis-eQTLs in human, RNA expression in rat and mouse brains and bioinformatics properties of all of these risk variants were analyzed. RESULTS The variants located within the alcohol dehydrogenase (ADH) cluster were significantly associated with alcohol dependence at the genome-wide level (p < 5 × 10(-8) ) in at least one sample. Some associations with the ADH cluster were replicable across six independent GWAS samples. The variants located within or near SERINC2, KIAA0040, MREG-PECR or PKNOX2 were significantly associated with alcohol dependence at the genome-wide level (p < 5 × 10(-8) ) in meta-analysis or combined samples, and these associations were replicable across at least one sample. The associations with the variants within NRD1, GPD1L-CMTM8 or MAP3K9-PCNX were suggestive (5 × 10(-8) < p < 10(-5) ) in some samples, and nominally replicable in other samples. The associations with the variants at HTR7 and OPA3 were nominally replicable across at least three independent GWAS samples (10(-5) < p < .05). Some risk variants at the ADH cluster, SERINC2, KIAA0040, NRD1, and HTR7 had potential biological functions. CONCLUSION The most robust risk locus was the ADH cluster. SERINC2, KIAA0040, NRD1, and HTR7 were also likely to play important roles in alcohol dependence. PKNOX2, MREG, PECR, GPD1L, CMTM8, MAP3K9, PCNX, and OPA3 might play less important roles in risk for alcohol dependence based on the function analysis. This conclusion will significantly contribute to the post-GWAS follow-up studies on alcohol dependence.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Yunlong Tan
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Xinghua Pan
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yiqiang Cai
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Xiaoping Wang
- Department of Neurology, First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jiang Hong
- Department of Internal Medicine, First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Chunlong Zhong
- Department of Neurosurgery, Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Fei Wang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Xiang-yang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | | | - Boris Tabakoff
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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Zuo L, Wang K, Wang G, Pan X, Zhang X, Zhang H, Luo X. Common PTP4A1-PHF3-EYS variants are specific for alcohol dependence. Am J Addict 2014; 23:411-4. [PMID: 24961364 PMCID: PMC4111256 DOI: 10.1111/j.1521-0391.2013.12115.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/20/2013] [Accepted: 08/19/2013] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND OBJECTIVES We previously reported a risk genomic region (ie, PTP4A1-PHF3-EYS) for alcohol dependence in a genome-wide association study (GWAS). We also reported a rare variant constellation across this region that was significantly associated with alcohol dependence. In the present study, we significantly increased the marker density within this region and examined the specificity of the associations of common variants for alcohol dependence. METHODS One African-American discovery sample (681 cases with alcohol dependence and 508 controls), one European-American replication sample (1,409 alcohol dependent cases and 1,518 controls), and one European-Australian replication sample (a total of 6,438 family subjects with 1,645 alcohol dependent probands) underwent association analysis. A total of 38,714 subjects from 18 other cohorts with 10 different neuropsychiatric disorders served as contrast groups. RESULTS We found 289 SNPs that were nominally associated with alcohol dependence in the discovery sample (p < .05). Fifty-six associations of them were significant after correction (1.9 × 10(-6) ≤ p ≤ 1.6 × 10(-5)). No markers were significantly associated with other neuropsychiatric disorders after experiment-wide correction. CONCLUSIONS AND SCIENTIFIC SIGNIFICANCE We confirmed with our previous findings that PTP4A1-PHF3-EYS variants were significantly associated with alcohol dependence, which were replicable across multiple independent populations and were specific for alcohol dependence. These findings suggested that this region might harbor a causal variant(s) for alcohol dependence.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT,
USA
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East
Tennessee State University, Johnson City, TN, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Departments of Genetics, Yale University
School of Medicine, Orange, CT, USA
| | - Xinghua Pan
- Departments of Genetics, Yale University School of Medicine, New Haven, CT,
USA
| | - Xiangyang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College
of Medicine, Houston, Texas, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New
Haven, CT, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT,
USA
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Neuman MG, Cohen L, Zakhari S, Nanau RM, Mueller S, Schneider M, Parry C, Isip R, Seitz HK. Alcoholic liver disease: a synopsis of the Charles Lieber's Memorial Symposia 2009-2012. Alcohol Alcohol 2014; 49:373-80. [PMID: 24816574 DOI: 10.1093/alcalc/agu021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This paper is based upon the 'Charles Lieber Satellite Symposia' organized by Manuela G. Neuman at each of the 2009-2012 Research Society on Alcoholism (RSA) Annual Meetings. The presentations represent a broad spectrum dealing with alcoholic liver disease (ALD). In addition, a literature search (2008-2013) in the discussed area was performed in order to obtain updated data. The presentations are focused on genetic polymorphisms of ethanol metabolizing enzymes and the role of cytochrome P4502E1 (CYP2E1) in ALD. In addition, alcohol-mediated hepatocarcinogenesis, immune response to alcohol and fibrogenesis in alcoholic hepatitis as well as its co-morbidities with chronic viral hepatitis infections in the presence or absence of human deficiency virus are discussed. Finally, emphasis was led on alcohol and drug interactions as well as liver transplantation for end-stage ALD.
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Affiliation(s)
- Manuela G Neuman
- In Vitro Drug Safety and Biotechnology, University of Toronto, Toronto, ON, Canada Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lawrence Cohen
- Division of Gastroenterology, Sunnybrook Health Sciences Centre, Department of Medicine, Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Samir Zakhari
- Division of Metabolism and Health Effects, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Radu M Nanau
- In Vitro Drug Safety and Biotechnology, University of Toronto, Toronto, ON, Canada Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Sebastian Mueller
- Centre of Alcohol Research, University of Heidelberg and Department of Medicine (Gastroenterology and Hepatology), Salem Medical Centre, Heidelberg, Germany
| | - Michelle Schneider
- Alcohol and Drug Abuse Research Unit, Medical Research Council, Stellenbosch University, Cape Town, South Africa
| | - Charles Parry
- Alcohol and Drug Abuse Research Unit, Medical Research Council, Stellenbosch University, Cape Town, South Africa Department of Psychiatry, Stellenbosch University, Cape Town, South Africa
| | - Romina Isip
- In Vitro Drug Safety and Biotechnology, University of Toronto, Toronto, ON, Canada Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Helmut K Seitz
- Centre of Alcohol Research, University of Heidelberg and Department of Medicine (Gastroenterology and Hepatology), Salem Medical Centre, Heidelberg, Germany
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Wang K, Luo X, Zuo L. Genetic factors for alcohol dependence and schizophrenia: common and rare variants. AUSTIN JOURNAL OF DRUG ABUSE AND ADDICTION 2014; 1:3. [PMID: 27512730 PMCID: PMC4976769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, USA
- Biological psychiatry research center, Beijing Huilongguan Hospital, China
| | - Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, USA
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Maturu P, Vaddi DR, Pannuru P, Nallanchakravarthula V. Modification of Erythrocyte Membrane Proteins, Enzymes and Transport Mechanisms in Chronic Alcoholics: An In vivo and In vitro Study. Alcohol Alcohol 2013; 48:679-86. [DOI: 10.1093/alcalc/agt071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Zuo L, Wang KS, Zhang XY, Li CSR, Zhang F, Wang X, Chen W, Gao G, Zhang H, Krystal JH, Luo X. Rare SERINC2 variants are specific for alcohol dependence in individuals of European descent. Pharmacogenet Genomics 2013; 23:395-402. [PMID: 23778322 PMCID: PMC4287355 DOI: 10.1097/fpc.0b013e328362f9f2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVES We have previously reported a top-ranked risk gene [i.e., serine incorporator 2 gene (SERINC2)] for alcohol dependence in individuals of European descent by analyzing the common variants in a genome-wide association study. In the present study, we comprehensively examined the rare variants [minor allele frequency (MAF)<0.05] in the NKAIN1-SERINC2 region to confirm our previous finding. MATERIALS AND METHODS A discovery sample (1409 European-American patients with alcohol dependence and 1518 European-American controls) and a replication sample (6438 European-Australian family participants with 1645 alcohol-dependent probands) were subjected to an association analysis. A total of 39,903 individuals from 19 other cohorts with 11 different neuropsychiatric and neurological disorders served as contrast groups. The entire NKAIN1-SERINC2 region was imputed in all cohorts using the same reference panels of genotypes that included rare variants from the whole-genome sequencing data. We stringently cleaned the phenotype and genotype data, and obtained a total of about 220 single-nucleotide polymorphisms in individuals of European descent and about 450 single-nucleotide polymorphisms in the individuals of African descent with 0 RESULTS Using a weighted regression analysis implemented in the program SCORE-Seq, we found a rare variant constellation across the entire NKAIN1-SERINC2 region that was associated with alcohol dependence in European-Americans (Fp: overall, P=1.8×10(-4); VT: overall, P=1.4×10(-4); Collapsing, P=6.5×10(-5)) and European-Australians (Fp: overall, P=0.028; Collapsing, P=0.025), but not in African-Americans, and not associated with any other disorder examined. Association signals in this region came mainly from SERINC2, a gene that codes for an activity-regulated protein expressed in the brain that incorporates serine into lipids. In addition, 26 individual rare variants were nominally associated with alcohol dependence in European-Americans (P<0.05). The associations of five of these rare variants that lay within SERINC2 showed region-wide significance (P<α=0.0006) and 25 associations survived correction for a false discovery rate (q<0.05). The associations of two rare variants at SERINC2 were replicated in European-Australians (P<0.05). CONCLUSION We concluded that SERINC2 was a replicable and significant risk gene specific for alcohol dependence in individuals of European descent.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Ke-Sheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Xiang-Yang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Chiang-Shan R. Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Fengyu Zhang
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Xiaoping Wang
- Department of Neurology, First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Wenan Chen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Guimin Gao
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Epidemiology and Public Health, New Haven, CT, USA
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Psychiatry Services, Yale-New Haven Hospital, New Haven, CT
- VA Alcohol Research Center, VA Connecticut Healthcare System, West Haven, CT
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
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Zuo L, Wang K, Zhang XY, Pan X, Wang G, Tan Y, Zhong C, Krystal JH, State M, Zhang H, Luo X. Association between common alcohol dehydrogenase gene (ADH) variants and schizophrenia and autism. Hum Genet 2013; 132:735-43. [PMID: 23468174 PMCID: PMC3683370 DOI: 10.1007/s00439-013-1277-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 02/16/2013] [Indexed: 01/25/2023]
Abstract
Humans express at least seven alcohol dehydrogenase (ADH) isoforms that are encoded by ADH gene cluster (ADH7-ADH1C-ADH1B-ADH1A-ADH6-ADH4-ADH5) at chromosome 4. ADHs are key catabolic enzymes for retinol and ethanol. The functional ADH variants (mostly rare) have been implicated in alcoholism risk. In addition to catalyzing the oxidation of retinol and ethanol, ADHs may be involved in the metabolic pathways of several neurotransmitters that are implicated in the neurobiology of neuropsychiatric disorders. In the present study, we comprehensively examined the associations between common ADH variants [minor allele frequency (MAF) >0.05] and 11 neuropsychiatric and neurological disorders. A total of 50,063 subjects in 25 independent cohorts were analyzed. The entire ADH gene cluster was imputed across these 25 cohorts using the same reference panels. Association analyses were conducted, adjusting for multiple comparisons. We found 28 and 15 single nucleotide polymorphisms (SNPs), respectively, that were significantly associated with schizophrenia in African-Americans and autism in European-Americans after correction by false discovery rate (FDR) (q < 0.05); and 19 and 6 SNPs, respectively, that were significantly associated with these two disorders after region-wide correction by SNPSpD (8.9 × 10(-5) ≤ p ≤ 0.0003 and 2.4 × 10(-5) ≤ p ≤ 0.0003, respectively). No variants were significantly associated with the other nine neuropsychiatric disorders, including alcohol dependence. We concluded that common ADH variants conferred risk for both schizophrenia in African-Americans and autism in European-Americans.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven CT 06516, USA
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Xiang-Yang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Xinghua Pan
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale University School of Medicine, Orange, CT, USA
| | - Yunlong Tan
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Chunlong Zhong
- Department of Neurology, Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven CT 06516, USA
| | - Matthew State
- Department of Psychiatry, Yale University School of Medicine, New Haven CT 06516, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Epidemiology and Public Health, New Haven, CT, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven CT 06516, USA
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Zuo L, Saba L, Wang K, Zhang X, Krystal JH, Tabakoff B, Luo X. Exome-wide association study of replicable nonsynonymous variants conferring risk for alcohol dependence. J Stud Alcohol Drugs 2013; 74:622-5. [PMID: 23739027 PMCID: PMC3711352 DOI: 10.15288/jsad.2013.74.622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/06/2013] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE In the present study, we scanned the whole exome in three independent samples to search for replicable risk nonsynonymous (ns) variants (ns single-nucleotide polymorphisms [nsSNPs]) for alcohol dependence. METHOD A total of 10,554 subjects in three independent samples were analyzed for association with alcohol dependence, including one European American sample (1,409 cases with alcohol dependence and 1,518 controls), one African American sample (681 cases and 508 controls), and one European Australian sample (a total of 6,438 family subjects with 1,645 alcohol-dependent probands). RNA expression of the risk genes in human, mouse, and rat brains was also explored. RESULTS We identified a total of 70 nsSNPs at 65 genes with nominally replicable associations; 22 nsSNPs at 21 genes among them survived corrections for multiple testing in meta-analysis (α = .0007). By incorporating the information from bioinformatics and RNA expression analyses, we identified at least two of the most promising risk genes for alcohol dependence: APOER2 and UBAP2. CONCLUSIONS The gene coding for apolipoprotein E receptor 2 (APOER2) and the gene coding for ubiquitin-associated protein-2 (UBAP2) are among the most appropriate for follow-up in human and nonhuman species as contributors to risk for alcohol dependence.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Laura Saba
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, Colorado
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, Tennessee
| | - Xiangyang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Boris Tabakoff
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, Colorado
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
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Zuo L, Wang K, Zhang XY, Krystal JH, Li CSR, Zhang F, Zhang H, Luo X. NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent. Drug Alcohol Depend 2013; 129:254-64. [PMID: 23455491 PMCID: PMC3628730 DOI: 10.1016/j.drugalcdep.2013.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 02/04/2013] [Accepted: 02/05/2013] [Indexed: 12/22/2022]
Abstract
OBJECTIVE We aimed to identify novel, functional, replicable and genome-wide significant risk regions specific for alcohol dependence using genome-wide association studies (GWASs). METHODS A discovery sample (1409 European-American cases with alcohol dependence and 1518 European-American controls) and a replication sample (6438 European-Australian family subjects with 1645 alcohol dependent probands) underwent association analysis. Nineteen other cohorts with 11 different neuropsychiatric disorders served as contrast groups. Additional eight samples underwent expression quantitative locus (eQTL) analysis. RESULTS A genome-wide significant risk gene region (NKAIN1-SERINC2) was identified in a meta-analysis of the discovery and replication samples. This region was enriched with 74 risk SNPs (unimputed); half of them had significant cis-acting regulatory effects. The distributions of -log(p) values for the SNP-disease associations or SNP-expression associations in this region were consistent throughout eight independent samples. Furthermore, imputing across the NKAIN1-SERINC2 region, we found that among all 795 SNPs in the discovery sample, 471 SNPs were nominally associated with alcohol dependence (1.7×10(-7)≤p≤0.047); 53 survived region- and cohort-wide correction for multiple testing; 92 SNPs were replicated in the replication sample (0.002≤p≤0.050). This region was neither significantly associated with alcohol dependence in African-Americans, nor with other non-alcoholism diseases. Finally, transcript expression of genes in NKAIN1-SERINC2 was significantly (p<3.4×10(-7)) associated with expression of numerous genes in the neurotransmitter systems or metabolic pathways previously associated with alcohol dependence. CONCLUSION NKAIN1-SERINC2 may harbor a causal variant(s) for alcohol dependence. It may contribute to the disease risk by way of neurotransmitter systems or metabolic pathways.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of
Medicine, New Haven, CT, USA
- VA Alcohol Research Center, VA Connecticut Healthcare
System, West Haven, CT
| | - Kesheng Wang
- Department of Biostatistics and Epidemiology, College of
Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Xiang-Yang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences,
Baylor College of Medicine, Houston, Texas, USA
| | - John H. Krystal
- Department of Psychiatry, Yale University School of
Medicine, New Haven, CT, USA
- VA Alcohol Research Center, VA Connecticut Healthcare
System, West Haven, CT
- Psychiatry Services, Yale-New Haven Hospital, New Haven,
CT
| | - Chiang-Shan R. Li
- Department of Psychiatry, Yale University School of
Medicine, New Haven, CT, USA
| | - Fengyu Zhang
- Lieber Institute for Brain Development, Johns Hopkins
University Medical Campus, Baltimore, MD, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of
Public Health, New Haven, CT, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of
Medicine, New Haven, CT, USA
- VA Alcohol Research Center, VA Connecticut Healthcare
System, West Haven, CT
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Zuo L, Zhang XY, Wang F, Li CSR, Lu L, Ye L, Zhang H, Krystal JH, Deng HW, Luo X. Genome-wide significant association signals in IPO11-HTR1A region specific for alcohol and nicotine codependence. Alcohol Clin Exp Res 2013; 37:730-9. [PMID: 23216389 PMCID: PMC3610804 DOI: 10.1111/acer.12032] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 08/31/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Alcohol and nicotine codependence can be considered as a more severe subtype of alcohol dependence. A portion of its risk may be attributable to genetic factors. METHODS We searched for significant risk genomic regions specific for this disorder using a genome-wide association study. A total of 8,847 subjects underwent gene-disease association analysis, including (i) a discovery cohort of 818 European American cases with alcohol and nicotine codependence and 1,396 European American controls, (ii) a replication cohort of 5,704 Australian family subjects with 907 affected offspring, and (iii) a replication cohort of 449 African American cases and 480 African American controls. Additionally, a total of 38,714 subjects of European or African descent in 18 independent cohorts with 10 other nonalcoholism neuropsychiatric disorders were analyzed as contrast. Furthermore, 90 unrelated HapMap CEU individuals, 93 European brain tissue samples, and 80 European peripheral blood mononuclear cell samples underwent cis-acting expression quantitative locus (cis-eQTL) analysis. RESULTS We identified a significant risk region for alcohol and nicotine codependence between IPO11 and HTR1A on chromosome 5q that was reported to be suggestively associated with alcohol dependence previously. In the European American discovery cohort, 381 single nucleotide polymorphisms (SNPs) in this region were nominally associated with alcohol and nicotine codependence (p < 0.05); 57 associations of them survived region- and cohort-wide correction (α = 3.6 × 10(-6) ); and the top SNP (rs7445832) was significantly associated with alcohol and nicotine codependence at the genome-wide significance level (p = 6.2 × 10(-9) ). Furthermore, associations for 34 and 11 SNPs were replicated in the Australian and African American replication cohorts, respectively. Among these replicable associations, 4 reached genome-wide significance level in the meta-analysis of European Americans and European Australians: rs7445832 (p = 9.6 × 10(-10) ), rs13361996 (p = 8.2 × 10(-9) ), rs62380518 (p = 2.3 × 10(-8) ), and rs7714850 (p = 3.4 × 10(-8) ). Cis-eQTL analysis showed that many risk SNPs in this region had nominally significant cis-acting regulatory effects on HTR1A or IPO11 mRNA expression. Finally, no markers were significantly associated with any other neuropsychiatric disorder examined. CONCLUSIONS We speculate that this IPO11-HTR1A region might harbor a causal variant for alcohol and nicotine codependence.
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Affiliation(s)
- Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Xiang-Yang Zhang
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Fei Wang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Chiang-Shan R. Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Lingeng Lu
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
| | - Liefu Ye
- Department of Urology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Heping Zhang
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
| | - John H. Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Hong-Wen Deng
- Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
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Zuo L, Zhang X, Deng HW, Luo X. Association of rare PTP4A1-PHF3-EYS variants with alcohol dependence. J Hum Genet 2013; 58:178-9. [PMID: 23324950 DOI: 10.1038/jhg.2012.153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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