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Luo X, Kranzler HR, Zuo L, Wang S, Schork NJ, Gelernter J. Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Am J Hum Genet 2006; 78:973-87. [PMID: 16685648 PMCID: PMC1474098 DOI: 10.1086/504113] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 03/10/2006] [Indexed: 11/03/2022] Open
Abstract
The set of alcohol-metabolizing enzymes has considerable genetic and functional complexity. The relationships between some alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) genes and alcohol dependence (AD) have long been studied in many populations, but not comprehensively. In the present study, we genotyped 16 markers within the ADH gene cluster (including the ADH1A, ADH1B, ADH1C, ADH5, ADH6, and ADH7 genes), 4 markers within the ALDH2 gene, and 38 unlinked ancestry-informative markers in a case-control sample of 801 individuals. Associations between markers and disease were analyzed by a Hardy-Weinberg equilibrium (HWE) test, a conventional case-control comparison, a structured association analysis, and a novel diplotype trend regression (DTR) analysis. Finally, the disease alleles were fine mapped by a Hardy-Weinberg disequilibrium (HWD) measure (J). All markers were found to be in HWE in controls, but some markers showed HWD in cases. Genotypes of many markers were associated with AD. DTR analysis showed that ADH5 genotypes and diplotypes of ADH1A, ADH1B, ADH7, and ALDH2 were associated with AD in European Americans and/or African Americans. The risk-influencing alleles were fine mapped from among the markers studied and were found to coincide with some well-known functional variants. We demonstrated that DTR was more powerful than many other conventional association methods. We also found that several ADH genes and the ALDH2 gene were susceptibility loci for AD, and the associations were best explained by several independent risk genes.
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Affiliation(s)
- Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT; VA Connecticut Healthcare System, West Haven; Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York; and Department of Psychiatry, University of California School of Medicine–San Diego, La Jolla
| | - Henry R. Kranzler
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT; VA Connecticut Healthcare System, West Haven; Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York; and Department of Psychiatry, University of California School of Medicine–San Diego, La Jolla
| | - Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT; VA Connecticut Healthcare System, West Haven; Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York; and Department of Psychiatry, University of California School of Medicine–San Diego, La Jolla
| | - Shuang Wang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT; VA Connecticut Healthcare System, West Haven; Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York; and Department of Psychiatry, University of California School of Medicine–San Diego, La Jolla
| | - Nicholas J. Schork
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT; VA Connecticut Healthcare System, West Haven; Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York; and Department of Psychiatry, University of California School of Medicine–San Diego, La Jolla
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT; VA Connecticut Healthcare System, West Haven; Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York; and Department of Psychiatry, University of California School of Medicine–San Diego, La Jolla
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Osier MV, Pakstis AJ, Soodyall H, Comas D, Goldman D, Odunsi A, Okonofua F, Parnas J, Schulz LO, Bertranpetit J, Bonne-Tamir B, Lu RB, Kidd JR, Kidd KK. A global perspective on genetic variation at the ADH genes reveals unusual patterns of linkage disequilibrium and diversity. Am J Hum Genet 2002; 71:84-99. [PMID: 12050823 PMCID: PMC384995 DOI: 10.1086/341290] [Citation(s) in RCA: 214] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2002] [Accepted: 04/15/2002] [Indexed: 11/03/2022] Open
Abstract
Variants of different Class I alcohol dehydrogenase (ADH) genes have been shown to be associated with an effect that is protective against alcoholism. Previous work from our laboratory has shown that the two sites showing the association are in linkage disequilibrium and has identified the ADH1B Arg47His site as causative, with the ADH1C Ile349Val site showing association only because of the disequilibrium. Here, we describe an initial study of the nature of linkage disequilibrium and genetic variation, in population samples from different regions of the world, in a larger segment of the ADH cluster (including the three Class I ADH genes and ADH7). Linkage disequilibrium across approximately 40 kb of the Class I ADH cluster is moderate to strong in all population samples that we studied. We observed nominally significant pairwise linkage disequilibrium, in some populations, between the ADH7 site and some Class I ADH sites, at moderate values and at a molecular distance as great as 100 kb. Our data indicate (1) that most ADH-alcoholism association studies have failed to consider many sites in the ADH cluster that may harbor etiologically significant alleles and (2) that the relevance of the various ADH sites will be population dependent. Some individual sites in the Class I ADH cluster show Fst values that are among the highest seen among several dozen unlinked sites that were studied in the same subset of populations. The high Fst values can be attributed to the discrepant frequencies of specific alleles in eastern Asia relative to those in other regions of the world. These alleles are part of a single haplotype that exists at high (>65%) frequency only in the eastern-Asian samples. It seems unlikely that this haplotype, which is rare or unobserved in other populations, reached such high frequency because of random genetic drift alone.
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Affiliation(s)
- Michael V. Osier
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Andrew J. Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Himla Soodyall
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - David Comas
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - David Goldman
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Adekunle Odunsi
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Friday Okonofua
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Josef Parnas
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Leslie O. Schulz
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jaume Bertranpetit
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Batsheva Bonne-Tamir
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ru-Band Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Judith R. Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kenneth K. Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT; Human Genomic Diversity and Disease Research Unit/South African Institute for Medical Research and University of the Witwatersrand, Johannesburg; Facultat de Ciències de la Salut i de la Vida, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona; Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Benin, Benin City, Nigeria; Copenhagen University Department of Psychiatry, Hvidovre Hospital, Hvidovre, Denmark; University of Wisconsin–Milwaukee, Milwaukee; Department of Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv; and Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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