Copy Number Variations in 6q14.1 and 5q13.2 are Associated with Alcohol Dependence

Alcoholism: Clinical and Experimental Research

Volumn 36, Issue 9, 2012, Pages 1512-1518

  Lin, Peng ^a   Hartz, Sarah M ^a   Wang, Jen Chyong ^a   Agrawal, Arpana ^a   Zhang, Tian Xiao ^a   McKenna, Nicholas ^a   Bucholz, Kathleen ^a   Brooks, Andrew I ^b   Tischfield, Jay A ^b   Edenberg, Howard J ^c   Hesselbrock, Victor M ^d   Kramer, John R ^e   Kuperman, Samuel ^e   Schuckit, Marc A ^f   Goate, Alison M ^a   Bierut, Laura J ^a   Rice, John P ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

^d UNIVERSITY OF CONNECTICUT SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF IOWA   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alcohol dependence; CNV accuracy; Copy number variations

Indexed keywords

ALCOHOL; CANNABIS; COCAINE; OPIATE;

ADULT; ALCOHOLISM; ARTICLE; CANNABIS ADDICTION; CHROMOSOME 5Q; CHROMOSOME 6Q; COCAINE DEPENDENCE; COMPUTER PROGRAM; COPY NUMBER VARIATION; EUROPEAN AMERICAN; FEMALE; GENE DELETION; GENE DUPLICATION; GENETIC ASSOCIATION; HUMAN; INTERVIEW; LANGUAGE DISABILITY; MAJOR CLINICAL STUDY; MALE; MENTAL DEFICIENCY; NEUROLOGIC DISEASE; OPIATE ADDICTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE POLYMERASE CHAIN REACTION;

ADULT; AGE OF ONSET; ALCOHOL DRINKING; ALCOHOLISM; DIAGNOSTIC AND STATISTICAL MANUAL OF MENTAL DISORDERS; DNA COPY NUMBER VARIATIONS; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS;

EID: 84866000638     PISSN: 01456008     EISSN: 15300277     Source Type: Journal    
DOI: 10.1111/j.1530-0277.2012.01758.x     Document Type: Article

References (37)

1. Also-Rallo E, Alias L, Martinez-Hernandez R, Caselles L, Barcelo MJ, Baiget M, Bernal S, Tizzano EF (2011) Treatment of spinal muscular atrophy cells with drugs that upregulate SMN expression reveals inter- and intra-patient variability. Eur J Hum Genet 19:1059-1065.
2. Bierut LJ, Agrawal A, Bucholz KK, Doheny KF, Laurie C, Pugh E, Fisher S, Fox L, Howells W, Bertelsen S, Hinrichs AL, Almasy L, Breslau N, Culverhouse RC, Dick DM, Edenberg HJ, Foroud T, Grucza RA, Hatsukami D, Hesselbrock V, Johnson EO, Kramer J, Krueger RF, Kuperman S, Lynskey M, Mann K, Neuman RJ, Nothen MM, Nurnberger JI Jr, Porjesz B, Ridinger M, Saccone NL, Saccone SF, Schuckit MA, Tischfield JA, Wang JC, Rietschel M, Goate AM, Rice JP (2010) A genome-wide association study of alcohol dependence. Proc Natl Acad Sci U S A 107:5082-5087.
3. Bierut LJ, Dinwiddie SH, Begleiter H, Crowe RR, Hesselbrock V, Nurnberger JI Jr, Porjesz B, Schuckit MA, Reich T (1998) Familial transmission of substance dependence: alcohol, marijuana, cocaine, and habitual smoking: a report from the Collaborative Study on the Genetics of Alcoholism. Arch Gen Psychiatry 55:982-988.
4. Braillon A, Dubois G (2005) Alcohol and public health. Lancet 365:1387.
5. Caan W, De Belleroche J (2002) Drink, Drugs and Dependence: From Science to Clinical Practice. Routledge, London, New York, NY.
6. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J (2007) QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 35:2013-2025.
7. Cornelis MC, Agrawal A, Cole JW, Hansel NN, Barnes KC, Beaty TH, Bennett SN, Bierut LJ, Boerwinkle E, Doheny KF, Feenstra B, Feingold E, Fornage M, Haiman CA, Harris EL, Hayes MG, Heit JA, Hu FB, Kang JH, Laurie CC, Ling H, Manolio TA, Marazita ML, Mathias RA, Mirel DB, Paschall J, Pasquale LR, Pugh EW, Rice JP, Udren J, van Dam RM, Wang X, Wiggs JL, Williams K, Yu K (2010) The Gene, Environment Association Studies consortium (GENEVA): maximizing the knowledge obtained from GWAS by collaboration across studies of multiple conditions. Genet Epidemiol 34:364-372.
8. Dachs E, Hereu M, Piedrafita L, Casanovas A, Caldero J, Esquerda JE (2011) Defective neuromuscular junction organization and postnatal myogenesis in mice with severe spinal muscular atrophy. J Neuropathol Exp Neurol 70:444-461.
9. Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K (2008) Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 36:e126.
10. Edenberg HJ, Foroud T (2006) The genetics of alcoholism: identifying specific genes through family studies. Addict Biol 11:386-396.
11. Edenberg HJ, Koller DL, Xuei X, Wetherill L, McClintick JN, Almasy L, Bierut LJ, Bucholz KK, Goate A, Aliev F, Dick D, Hesselbrock V, Hinrichs A, Kramer J, Kuperman S, Nurnberger JI Jr, Rice JP, Schuckit MA, Taylor R, Todd Webb B, Tischfield JA, Porjesz B, Foroud T (2010) Genome-wide association study of alcohol dependence implicates a region on chromosome 11. Alcohol Clin Exp Res 34:840-852.
12. Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, Imielinski M, Frackelton EC, Reichert J, Crawford EL, Munson J, Sleiman PM, Chiavacci R, Annaiah K, Thomas K, Hou C, Glaberson W, Flory J, Otieno F, Garris M, Soorya L, Klei L, Piven J, Meyer KJ, Anagnostou E, Sakurai T, Game RM, Rudd DS, Zurawiecki D, McDougle CJ, Davis LK, Miller J, Posey DJ, Michaels S, Kolevzon A, Silverman JM, Bernier R, Levy SE, Schultz RT, Dawson G, Owley T, McMahon WM, Wassink TH, Sweeney JA, Nurnberger JI, Coon H, Sutcliffe JS, Minshew NJ, Grant SF, Bucan M, Cook EH, Buxbaum JD, Devlin B, Schellenberg GD, Hakonarson H (2009) Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459:569-573.
13. Hasin DS, Stinson FS, Ogburn E, Grant BF (2007) Prevalence, correlates, disability, and comorbidity of DSM-IV alcohol abuse and dependence in the United States: results from the National Epidemiologic Survey on Alcohol and Related Conditions. Arch Gen Psychiatry 64:830-842.
14. Heath AC, Bucholz KK, Madden PA, Dinwiddie SH, Slutske WS, Bierut LJ, Statham DJ, Dunne MP, Whitfield JB, Martin NG (1997) Genetic and environmental contributions to alcohol dependence risk in a national twin sample: consistency of findings in women and men. Psychol Med 27:1381-1396.
15. Heath AC, Whitfield JB, Martin NG, Pergadia ML, Goate AM, Lind PA, McEvoy BP, Schrage AJ, Grant JD, Chou YL, Zhu R, Henders AK, Medland SE, Gordon SD, Nelson EC, Agrawal A, Nyholt DR, Bucholz KK, Madden PA, Montgomery GW (2011) A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications. Biol Psychiatry 70:513-518.
16. Hill SY, Shen S, Zezza N, Hoffman EK, Perlin M, Allan W (2004) A genome wide search for alcoholism susceptibility genes. Am J Med Genet B Neuropsychiatr Genet 128B:102-113.
17. Kanny D, Liu Y, Brewer RD (2011) Binge drinking-United States, 2009. MMWR Surveill Summ 60(Suppl):101-104.
18. Kendler KS, Neale MC, Heath AC, Kessler RC, Eaves LJ (1994) A twin-family study of alcoholism in women. Am J Psychiatry 151:707-715.
19. Knopik VS, Heath AC, Madden PA, Bucholz KK, Slutske WS, Nelson EC, Statham D, Whitfield JB, Martin NG (2004) Genetic effects on alcohol dependence risk: re-evaluating the importance of psychiatric and other heritable risk factors. Psychol Med 34:1519-1530.
20. Krajewski KM, Lewis RA, Fuerst DR, Turansky C, Hinderer SR, Garbern J, Kamholz J, Shy ME (2000) Neurological dysfunction and axonal degeneration in Charcot-Marie-Tooth disease type 1A. Brain 123 (Pt 7):1516-1527.
21. Lachman HM, Pedrosa E, Petruolo OA, Cockerham M, Papolos A, Novak T, Papolos DF, Stopkova P (2007) Increase in GSK3beta gene copy number variation in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 144B:259-265.
22. Lespinasse J, Gimelli S, Bena F, Antonarakis SE, Ansermet F, Paoloni-Giacobino A (2009) Characterization of an interstitial deletion 6q13-q14.1 in a female with mild mental retardation, language delay and minor dysmorphisms. Eur J Med Genet 52:49-52.
23. Lin P, Hartz SM, Wang J-C, Krueger RF, Foroud TM, Edenberg HJ, Nurnberger JI Jr, Brooks AI, Tischfield JA, Almasy L, Webb BT, Hesselbrock VM, Porjesz B, Goate AM, Bierut LJ, Rice JP, Collaborators C, Collaborators C, GENEVA (2011) Copy number variation accuracy in genome wide studies. Hum Hered 71:141-147.
24. Long JC, Knowler WC, Hanson RL, Robin RW, Urbanek M, Moore E, Bennett PH, Goldman D (1998) Evidence for genetic linkage to alcohol dependence on chromosomes 4 and 11 from an autosome-wide scan in an American Indian population. Am J Med Genet 81:216-221.
25. Martens MA, Wilson SJ, Reutens DC (2008) Research review: Williams syndrome: a critical review of the cognitive, behavioral, and neuroanatomical phenotype. J Child Psychol Psychiatry 49:576-608.
26. Muller PY, Janovjak H, Miserez AR, Dobbie Z (2002) Processing of gene expression data generated by quantitative real-time RT-PCR. Biotechniques, 32:1372-1374, 1376, 1378-1379.
27. O'Driscoll MC, Daly SB, Urquhart JE, Black GC, Pilz DT, Brockmann K, McEntagart M, Abdel-Salam G, Zaki M, Wolf NI, Ladda RL, Sell S, D'Arrigo S, Squier W, Dobyns WB, Livingston JH, Crow YJ (2010) Recessive mutations in the gene encoding the tight junction protein occludin cause band-like calcification with simplified gyration and polymicrogyria. Am J Hum Genet 87:354-364.
28. Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39:1256-1260.
29. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI Jr, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466:368-372.
30. Puppala S, Coletta DK, Schneider J, Hu SL, Farook VS, Dyer TD, Arya R, Blangero J, Duggirala R, Defronzo RA, Jenkinson CP (2011) Genome-wide linkage screen for systolic blood pressure in the Veterans Administration Genetic Epidemiology Study (VAGES) of Mexican-Americans and confirmation of a major susceptibility locus on chromosome 6q14.1. Hum Hered 71:1-10.
31. Reich T, Edenberg HJ, Goate A, Williams JT, Rice JP, Van Eerdewegh P, Foroud T, Hesselbrock V, Schuckit MA, Bucholz K, Porjesz B, Li TK, Conneally PM, Nurnberger JI Jr, Tischfield JA, Crowe RR, Cloninger CR, Wu W, Shears S, Carr K, Crose C, Willig C, Begleiter H (1998) Genome-wide search for genes affecting the risk for alcohol dependence. Am J Med Genet 81:207-215.
32. Stefansson H, Rujescu D, Cichon S, Pietilainen OP, Ingason A, Steinberg S, Fossdal R, Sigurdsson E, Sigmundsson T, Buizer-Voskamp JE, Hansen T, Jakobsen KD, Muglia P, Francks C, Matthews PM, Gylfason A, Halldorsson BV, Gudbjartsson D, Thorgeirsson TE, Sigurdsson A, Jonasdottir A, Jonasdottir A, Bjornsson A, Mattiasdottir S, Blondal T, Haraldsson M, Magnusdottir BB, Giegling I, Moller HJ, Hartmann A, Shianna KV, Ge D, Need AC, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Paunio T, Toulopoulou T, Bramon E, Di Forti M, Murray R, Ruggeri M, Vassos E, Tosato S, Walshe M, Li T, Vasilescu C, Muhleisen TW, Wang AG, Ullum H, Djurovic S, Melle I, Olesen J, Kiemeney LA, Franke B, Sabatti C, Freimer NB, Gulcher JR, Thorsteinsdottir U, Kong A, Andreassen OA, Ophoff RA, Georgi A, Rietschel M, Werge T, Petursson H, Goldstein DB, Nothen MM, Peltonen L, Collier DA, St Clair D, Stefansson K (2008) Large recurrent microdeletions associated with schizophrenia. Nature 455:232-236.
33. Testino G (2008) Alcoholic diseases in hepato-gastroenterology: a point of view. Hepatogastroenterology 55:371-377.
34. Treutlein J, Cichon S, Ridinger M, Wodarz N, Soyka M, Zill P, Maier W, Moessner R, Gaebel W, Dahmen N, Fehr C, Scherbaum N, Steffens M, Ludwig KU, Frank J, Wichmann HE, Schreiber S, Dragano N, Sommer WH, Leonardi-Essmann F, Lourdusamy A, Gebicke-Haerter P, Wienker TF, Sullivan PF, Nothen MM, Kiefer F, Spanagel R, Mann K, Rietschel M (2009) Genome-wide association study of alcohol dependence. Arch Gen Psychiatry 66:773-784.
35. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17:1665-1674.
36. Wong KK, deLeeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, Horsman DE, MacAulay C, Ng RT, Brown CJ, Eichler EE, Lam WL (2007) A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 80:91-104.
37. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115:205-214.