Considerable Haplotype Diversity within the 23kb Encompassing the ADH7 Gene Yi Han, Hiroki Oota, Michael V. Osier, Andrew J. Pakstis, William C. Speed, Adekunle Odunsi, Friday Okonofua, Sylvester L. B. Kajuna, Nganyirwa J. Karoma, Selemani Kungulilo, Elena Grigorenko, Olga V. Zhukova, Batsheva Bonne-Tamir, Ru-B Lu, Josef Parnas, Leslie O. Schulz, Judith R. Kidd, and Kenneth K. Kidd Background: Of the seven known human alcohol dehydrogenase (ADH) genes, the nonliver expressed ADH7 gene codes for the enzyme with the highest maximal activity for ethanol. Previous study from our laboratory has suggested that ADH7 has an epistatic role for protection against alcoholism based on a single ADH7 SNP. Methods: We have now studied seven SNPs, additional populations for the SNP previously examined, and six more new SNPs, across 23 kb of ADH7 in 38 population samples originating from different geographical regions of the world. Results: The overall linkage disequilibrium is moderate to strong across this region even though con- siderable 7-SNP haplotype diversity is observed. This uncommonly high haplotype diversity is explained by high LD within each “half,” the three upstream SNPs and the four downstream SNPs, but near random- ization between the “halves.” This division significantly simplified the haplotype pattern: only four major haplotypes account for almost all chromosomes in all populations in each “half.” Conclusions: The low linkage disequilibrium between these two “halves” suggests multiple recombina- tion(s) have occurred in this region, specifically, within intron 7. The absence of strong LD between the functional variation in ADH1B that is strongly associated with alcoholism and any of the variation in ADH7 supports the genetic independence of ADH7 in association studies. Thus, the previously observed epistatic effect of ADH7 cannot be explained by its linkage disequilibrium with a causative factor in ADH1B. Key Words: Alcohol Dehydrogenase, ADH7, Linkage Disequilibrium, Haplotype, Evolution. T HERE ARE SEVEN known human alcohol dehydro- genase (ADH) genes that are divided into five classes (Class I: ADH1A, ADH1B, ADH1C; Class II: ADH4; Class III: ADH5; Class IV: ADH7; Class V: ADH6) on the basis of their distinct structural, kinetic and functional charac- teristics. These ADH enzymes catalyze the reversible oxi- dation of a wide variety of alcohols including ethanol and retinol to aldehydes and retinal (Chambon, 1995; Edenberg et al., 2000; Satre et al., 1994). The seven human ADH genes are located in a cluster of approximately 370 kb on the long arm of chromosome 4. All seven ADH enzymes have very similar sequences (the coding regions of all ADH genes (ADHs) are 60 –70% identical) and structure (they all have nine exons and eight introns with one exception – the loss of the last exon in ADH6), but they have different expression patterns, kinetic properties, and preferred sub- strates (Edenberg et al., 2000). The exons of ADH7 code for a polypeptide of 374 amino acids (Satre et al., 1994). Unlike Class I and Class II genes, which are primarily expressed in liver, ADH7 is not found in liver in humans, but has the highest expression level in the epithelial tissues of the upper gastrointestinal tract, down to the stomach, and in the eyes (Engeland et al., 1993; Moreno and Pare ´s, 1991; Pare ´s et al., 1992; Yin et al., 1990; Yin et al., 1993). The ADH7 protein: -ADH subunit was first discovered in stomach (Moreno and Pare ´s, 1991). ADH7 has the highest maximal activity for ethanol among the ADHs, which suggests that ADH7 is probably the first of the ADHs to start metabolizing ingested alcohol while From the Department of Genetics (YH, HO, AJP, WCS, JRK, KKK), Department of Psychology (EG), Yale University, School of Medicine, New Haven, CT; College of Sciences (MVO), Biological Sciences, Rochester Institute of Technology, Roches- ter, NY; Laboratory of Neurogenetics (DG), National Institute of Alcohol Abuse and Alcoholism, Rockville, MD; Department of Gynecological Oncology (AO), Roswell Park Cancer Institute, Buffalo, NY; Department of Obstetrics and Gynecology (FO), Faculty of Medicine, University of Benin, Benin City, Nigeria; The Hubert Kairuki Memorial University (SLBK, NJK), Muhimbili University College of Health Sciences (SK), Dar es Salaam, Tanzania; N.I. Vavilov Institute of General Genetics (OVZ), Moscow, Russia; Department of Human Genetics (BB-T), Sackler School of Med- icine, Tel Aviv University, Tel Aviv, Israel; Department of Psychiatry (R-BL), Tri- Service General hospital, National Defense Medical Center, Taipei, Taiwan The Danish National Research Foundation (JP), Center for Subjectivity Research, Uni- versity of Copenhagen, Denmark; College of Health Sciences (LOS), University of Texas at El Paso, El Paso, Texas. Received for publication March 23, 2005; accepted October 3, 2005. This work was funded, in part, by National Institute of Health grant AA09379 and GM57672 (KKK), NSF BCS-9912-28 (JRK), and in part by National Health Research Institute, Taiwan, ROC, Grant NHRI-EX91- 8939SP and National Science Council, Taiwan, ROC, Grant NSC 90-2314- B-016-081 (RBL). Reprint requests: Dr. Kenneth. K. Kidd, 333 Cedar Street, Yale University, School of Medicine, SHM I-353, New Haven, CT 06520-8005; Fax: 203-785- 6568; E-mail: Copyright © 2005 by the Research Society on Alcoholism. DOI: 10.1097/01.alc.0000191769.92667.04 0145-6008/05/2912-2091$03.00/0 ALCOHOLISM:CLINICAL AND EXPERIMENTAL RESEARCH Vol. 29, No. 12 December 2005 Alcohol Clin Exp Res, Vol 29, No 12, 2005: pp 2091–2100 2091