Pooled association genome scanning for alcohol dependence using 104,268 SNPs: Validation and use to identify alcoholism vulnerability loci in unrelated individuals from the collaborative study on the genetics of alcoholism

American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics

Volumn 141, Issue 8, 2006, Pages 844-853

  Johnson, Catherine ^a   Drgon, Tomas ^a   Liu, Qing Rong ^a   Walther, Donna ^a   Edenberg, Howard ^b   Rice, John ^c   Foroud, Tatiana ^b   Uhl, George R ^a,d  

^a NATIONAL INSTITUTE ON DRUG ABUSE   (United States)

^b INDIANA UNIVERSITY   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d Molecular Neurobiology   (United States)

Author keywords

Addiction; Complex genetics; Microarray; Substance dependence

Indexed keywords

GENOMIC DNA;

ALCOHOL ABUSE; ALCOHOLISM; ARTICLE; CELL ADHESION; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DEVELOPMENTAL GENETICS; DNA MICROARRAY; GENE CLUSTER; GENE FREQUENCY; GENE MAPPING; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC LINKAGE; GENETIC REGULATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; MULTIFACTORIAL INHERITANCE; NONHUMAN; PEDIGREE ANALYSIS; POLYMORPHIC LOCUS; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY;

ALCOHOLISM; CHROMOSOMES, HUMAN; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC SCREENING; GENOME, HUMAN; GENOMICS; HUMANS; MICROARRAY ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33845465213     PISSN: 15524841     EISSN: 1552485X     Source Type: Journal    
DOI: 10.1002/ajmg.b.30346     Document Type: Article

References (44)

1. Bansal A. 2001. Trends in reporting of SNP associations. Lancet 358:2016.
2. Barcellos LF, Klitz W, Field LL, Tobias R, Bowcock AM, Wilson R, Nelson MP, Nagatomi J, Thomson G. 1997. Association mapping of disease loci, by use of a pooled DNA genomic screen. Am J Hum Genet 61:734-747.
3. Bergen AW, Yang XR, Bai Y, Beerman MB, Goldstein AM, Goldin LR. 2003. Genomic regions linked to alcohol consumption in the Framingham Heart Study. BMC Genet 4(Suppl 1):S101.
4. Bierut LJ, Saccone NL, Rice JP, Goate A, Foroud T, Edenberg H, Almasy L, Conneally PM, Crowe R, Hesselbrock V, et al. 2002. Defining alcohol-related phenotypes in humans. The Collaborative Study on the genetics of Alcoholism. Alcohol Res Health 26:208-213.
5. Butcher LM, Meaburn E, Liu L, Fernandes C, Hill L, Al-Chalabi A, Plomin R, Schalkwyk L, Craig IW. 2004. Genotyping pooled DNA on microarrays: A systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behav Genet 34:549-555.
6. Cadoret RJ, Troughton E, O'Gorman TW, Heywood E. 1986. An adoption study of genetic and environmental factors in drug abuse. Arch Gen Psychiatry 43:1131-1136.
7. Cadoret RJ, Yates WR, Troughton E, Wood-worth G, Stewart MA. 1995. Adoption study demonstrating two genetic pathways to drug abuse. Arch Gen Psychiatry 52:42-52.
8. Cervino AC, Hill AV. 2000. Comparison of tests for association and linkage in incomplete families. Am J Hum Genet 67:120-132.
9. Drgon T, Lui OR, Johnson C, Walther D, Hishimoto A, Ujike H, Komiyama T, Harano M, Sekine Y, Inada T, Ozaki N, Iyo M, Iwata N, Yamada M, Sora I and Uhl GR. 2006. Addiction molecular genetics in Japanese methamphetamine-dependent individuals: Pooled association genome scanning identifies addiction vulnerability loci and genes, (submitted).
10. Dupont WD, Plummer WD Jr. 1990. Power and sample size calculations. A review and computer program. Control Clin Trials 11:116-128.
11. Germer S, Holland MJ, Higuchi R. 2000. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res 10:258-266.
12. Goldberg J, Henderson WG, Eisen SA, True W, Ramakrishnan V, Lyons MJ, Tsuang MT. 1993. A strategy for assembling samples of adult twin pairs in the United States. Stat Med 12:1693-1702.
13. Grove WM, Eckert ED, Heston L, Bouchard TJ Jr, Segal N, Lykken DT. 1990. Heritability of substance abuse and antisocial behavior: A study of monozygotic twins reared apart. Biol Psychiatry 27:1293-1304.
14. Gynther LM, Carey G, Gottesman II, Vogler GP. 1995. A twin study of non-alcohol substance abuse. Psychiatry Res 56:213-220.
15. Hacia JG, Fan JB, Ryder O, Jin L, Edgemon K, Ghandour G, Mayer RA, Sun B, Hsie L, Robbins CM, et al. 1999. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat Genet 22:164-167.
16. Ishiguro H, Liu QR, Gong JP, Hall FS, Ujike H, Morales M, Sakurai T, Grumet M, Uhl GR. 2006. NrCAM in addiction vulnerability: Positional cloning, drug-regulation, haplotype-specific expression, and altered drug reward in knockout mice. Neuropsychopharmacology 31:572-584.
17. Kaprio J, Hammar N, Koskenvuo M, Floderus-Myrhed B, Langinvainio H, Sarna S. 1982. Cigarette smoking and alcohol use in Finland and Sweden: A cross-national twin study. Int J Epidemiol 11:378-386.
18. Karkowski LM, Prescott CA, Kendler KS. 2000. Multivariate assessment of factors influencing illicit substance use in twins from female-female pairs. Am J Med Genet 96:665-670.
19. Kendler KS, Prescott CA. 1998. Cocaine use, abuse and dependence in a population-based sample of female twins. Br J Psychiatry 173:345-350.
20. Kendler KS, Karkowski LM, Corey LA, Prescott CA, Neale MC. 1999. Genetic and environmental risk factors in the aetiology of illicit drug initiation and subsequent misuse in women. Br J Psychiatry 175:351-356.
21. Liu QR, Drgon T, Johnson C, Walther D, Hess J and Uhl GR. 2006. Addiction molecular genetics: 639,401 SNP whole genome association reveals many "cell adhesion" gene variants, (submitted).
22. Liu QR, Drgon T, Walther D, Johnson C, Poleskaya O, Hess J, Uhl GR. 2005. Pooled association genome scanning: Validation and use to identify addiction vulnerability loci in two samples. Proc Natl Acad Sci USA 102:11864-11869.
23. 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.
24. Ma JZ, Zhang D, Dupont RT, Dockter M, Elston RC, Li MD. 2003. Mapping susceptibility loci for alcohol consumption using number of grams of alcohol consumed per day as a phenotype measure. BMC Genet 4(Suppl 1):S104.
25. Maes HH, Woodard CE, Murrelle L, Meyer JM, Silberg JL, Hewitt JK, Rutter M, Simonoff E, Pickles A, Carbonneau R, et al. 1999. Tobacco, alcohol and drug use in eight- to sixteen-year-old twins: The Virginia Twin Study of Adolescent Behavioral Development. J Stud Alcohol 60:293-305.
26. Merikangas KR, Stolar M, Stevens DE, Goulet J, Preisig MA, Fenton B, Zhang H, O'Malley SS, Rounsaville BJ. 1998. Familial transmission of substance use disorders. Arch Gen Psychiatry 55:973-979.
27. Reich T, Edenberg HJ, Goate A, Williams JT, Rice JP, Van Eerdewegh P, Foroud T, Hesselbrock V, Schuckit MA, Bucholz K, et al. 1998. Genomewide search for genes affecting the risk for alcohol dependence. Am J Med Genet 81:207-215.
28. Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science 273:1516-1517.
29. Schork NJ, Nath SK, Fallin D, Chakravarti A. 2000. Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects. Am J Hum Genet 67:1208-1218.
30. Sham PC, Cherny SS, Purcell S, Hewitt JK. 2000. Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data. Am J Hum Genet 66:1616-1630.
31. Storey JD. 2002. A direct approach to false discovery rates. J R Stat Soc B 64:479-498.
32. Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440-9445.
33. Tsuang MT, Lyons MJ, Eisen SA, Goldberg J, True W, Lin N, Meyer JM, Toomey R, Faraone SV, Eaves L. 1996. Genetic influences on DSM-III-R drug abuse and dependence: A study of 3,372 twin pairs. Am J Med Genet 67:473-477.
34. Tsuang MT, Lyons MJ, Meyer JM, Doyle T, Eisen SA, Goldberg J, True W, Lin N, Toomey R, Eaves L. 1998. Co-occurrence of abuse of different drugs in men: The role of drug-specific and shared vulnerabilities. Arch Gen Psychiatry 55:967-972.
35. Tsuang MT, Lyons MJ, Harley RM, Xian H, Eisen S, Goldberg J, True WR, Faraone SV. 1999. Genetic and environmental influences on transitions in drug use. Behav Genet 29:473-479.
36. Uhl GR. 1999. Molecular genetics of substance abuse vulnerability: A current approach. Neuropsychopharmacology 20:3-9.
37. Uhl GR. 2004. Molecular genetic underpinnings of human substance abuse vulnerability: Likely contributions to understanding addiction as a mnemonic process. Neuropharmacology 47(Suppl 1):140-147.
38. Uhl GR, Elmer GI, Labuda MC, Pickens RW. 1995. Genetic influences in drug abuse. In: Gloom FE, Kupfer DJ, editors. Psychopharmacology: The fourth generation of progress. New York: Raven Press, pp 1793-2783.
39. Uhl GR, Gold LH, Risch N. 1997. Genetic analyses of complex behavioral disorders. Proc Natl Acad Sci USA 94:2785-2786.
40. Uhl GR, Liu QR, Walther D, Hess J, Naiman D. 2001. Polysubstance abuse-vulnerability genes: Genome scans for association, using 1,004 subjects and 1,494 single-nucleotide polymorphisms. Am J Hum Genet 69:1290-1300.
41. Uhl GR, Liu QR, Naiman D. 2002, Substance abuse vulnerability loci: Converging genome scanning data. Trends Genet 18:420-425.
42. Wood JD, Yuan J, Margolis RL, Colomer V, Duan K, Kushi J, Kaminsky Z, Kleiderlein JJ, Sharp AH, Ross CA. 1998. Atrophin-1, the DRPLA gene product, interacts with two families of WW domain-containing proteins. Mol Cell Neurosci 11:149-160.
43. Woodward CE, Maes HH, Silberg JL, Meyer JM, Eaves LJ. 1996. Tobacco, alcohol and drug use in 8-16 year old twins. NIDA Res Monograph 162:309.
44. Xu YL, Reinscheid RK, Huitron-Resendiz S, Clark SD, Wang Z, Lin SH, Brucher FA, Zeng J, Ly NK, Henriksen SJ, et al. 2004. Neuropeptide S: A neuropeptide promoting arousal and anxiblytic-like effects. Neuron 43:487-497.