Genome-wide association study of copy number variants suggests ltbp1 and fgd4 are important for alcohol drinking

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Pei, Yu Fang ^a   Zhang, Lei ^a   Yang, Tie Lin ^b   Han, Yingying ^a   Hai, Rong ^a,c   Ran, Shu ^a   Tian, Qing ^d   Shen, Hui ^d   Li, Jian ^d   Zhu, Xue Zhen ^a   Luo, Xingguang ^e   Deng, Hong Wen ^a,d,f  

^a UNIVERSITY OF SHANGHAI FOR SCIENCE AND TECHNOLOGY   (China)

^b XI'AN JIAOTONG UNIVERSITY   (China)

^c INNER MONGOLIA MEDICAL COLLEGE   (China)

^d TULANE UNIVERSITY   (United States)

^e YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f HUNAN NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID A RECEPTOR; PROTEIN CDC42; TRANSFORMING GROWTH FACTOR BETA1; ACTIN BINDING PROTEIN; FGD4 PROTEIN, HUMAN; LATENT TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN; LTBP1 PROTEIN, HUMAN;

ADULT; ALCOHOL CONSUMPTION; ALCOHOL METABOLISM; ARTICLE; CAUCASIAN; CHINESE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA FLANKING REGION; DOWN REGULATION; FEMALE; FGD4 GENE; GENE; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE LOCATION; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENOTYPE; HUMAN; LATENT TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN 1 GENE; MALE; PROMOTER REGION; ASIAN; DRINKING BEHAVIOR; GENETICS; GENOTYPING TECHNIQUE; MIDDLE AGED; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; ALCOHOL DRINKING; ASIAN CONTINENTAL ANCESTRY GROUP; DNA COPY NUMBER VARIATIONS; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPING TECHNIQUES; HUMANS; LATENT TGF-BETA BINDING PROTEINS; MALE; MICROFILAMENT PROTEINS; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84856262671     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030860     Document Type: Article

References (49)

1. Prescott CA, Sullivan PF, Kuo PH, Webb BT, Vittum J, et al. (2006) Genomewide linkage study in the Irish affected sib pair study of alcohol dependence: evidence for a susceptibility region for symptoms of alcohol dependence on chromosome 4. Mol Psychiatry 11: 603-611.
2. Kendler KS, Heath AC, Neale MC, Kessler RC, Eaves LJ, (1992) A population-based twin study of alcoholism in women. Jama 268: 1877-1882.
3. Kendler KS, Prescott CA, Neale MC, Pedersen NL, (1997) Temperance board registration for alcohol abuse in a national sample of Swedish male twins, born 1902 to 1949. Arch Gen Psychiatry 54: 178-184.
4. Prescott CA, Kendler KS, (1999) Genetic and environmental contributions to alcohol abuse and dependence in a population-based sample of male twins. Am J Psychiatry 156: 34-40.
5. Heath AC, Whitfield JB, Martin NG, Pergadia ML, Goate AM, et al. A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications. Biol Psychiatry 70: 513-518.
6. Schumann G, Coin LJ, Lourdusamy A, Charoen P, Berger KH, et al. (0000) Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption. Proc Natl Acad Sci U S A 108: 7119-7124.
7. Grant JD, Agrawal A, Bucholz KK, Madden PA, Pergadia ML, et al. (2009) Alcohol consumption indices of genetic risk for alcohol dependence. Biol Psychiatry 66: 795-800.
8. Whitfield JB, Zhu G, Madden PA, Neale MC, Heath AC, et al. (2004) The genetics of alcohol intake and of alcohol dependence. Alcohol Clin Exp Res 28: 1153-1160.
9. D'Alfonso S, (1999) Nonparametric linkage analysis of alcohol dependence with chromosome 1 and 7 markers. Genet Epidemiol 17 (Suppl 1): S127-131.
10. Dick DM, Nurnberger J Jr, Edenberg HJ, Goate A, Crowe R, et al. (2002) Suggestive linkage on chromosome 1 for a quantitative alcohol-related phenotype. Alcohol Clin Exp Res 26: 1453-1460.
11. Foroud T, Bucholz KK, Edenberg HJ, Goate A, Neuman RJ, et al. (1998) Linkage of an alcoholism-related severity phenotype to chromosome 16. Alcohol Clin Exp Res 22: 2035-2042.
12. Zhu X, Cooper R, Kan D, Cao G, Wu X, (2005) A genome-wide linkage and association study using COGA data. BMC Genet 6 (Suppl 1): S128.
13. Edenberg HJ, Dick DM, Xuei X, Tian H, Almasy L, et al. (2004) Variations in GABRA2, encoding the alpha 2 subunit of the GABA(A) receptor, are associated with alcohol dependence and with brain oscillations. Am J Hum Genet 74: 705-714.
14. Gelernter J, Yu Y, Weiss R, Brady K, Panhuysen C, et al. (2006) Haplotype spanning TTC12 and ANKK1, flanked by the DRD2 and NCAM1 loci, is strongly associated to nicotine dependence in two distinct American populations. Hum Mol Genet 15: 3498-3507.
15. Luo X, Kranzler HR, Zuo L, Wang S, Schork NJ, et al. (2006) Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Am J Hum Genet 78: 973-987.
16. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, et al. (2007) Strong association of de novo copy number mutations with autism. Science 316: 445-449.
17. Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, et al. (2008) Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet 40: 880-885.
18. Feuk L, Carson AR, Scherer SW, (2006) Structural variation in the human genome. Nat Rev Genet 7: 85-97.
19. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
20. Buckland PR, (2003) Polymorphically duplicated genes: their relevance to phenotypic variation in humans. Ann Med 35: 308-315.
21. McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, et al. (2006) Common deletion polymorphisms in the human genome. Nat Genet 38: 86-92.
22. Nguyen DQ, Webber C, Ponting CP, (2006) Bias of selection on human copy-number variants. PLoS Genet 2: e20.
23. Repping S, van Daalen SK, Brown LG, Korver CM, Lange J, et al. (2006) High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nat Genet 38: 463-467.
24. Feuk L, Marshall CR, Wintle RF, Scherer SW, (2006) Structural variants: changing the landscape of chromosomes and design of disease studies. Hum Mol Genet 15 Spec No 1: R57-66.
25. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, et al. (2006) Copy number variation: new insights in genome diversity. Genome Res 16: 949-961.
26. Lupski JR, Stankiewicz P, (2005) Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1: e49.
27. Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, et al. (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320: 539-543.
28. Consortium IS, (2008) Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature 455: 237-241.
29. Ibanez P, Bonnet AM, Debarges B, Lohmann E, Tison F, et al. (2004) Causal relation between alpha-synuclein gene duplication and familial Parkinson's disease. Lancet 364: 1169-1171.
30. Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, et al. (2009) Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459: 569-573.
31. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, et al. (2005) The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307: 1434-1440.
32. Berney A, Preisig M, Matthey ML, Ferrero F, Fenton BT, (2002) Diagnostic interview for genetic studies (DIGS): inter-rater and test-retest reliability of alcohol and drug diagnoses. Drug Alcohol Depend 65: 149-158.
33. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, et al. (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 40: 1253-1260.
34. Team. RDC (2010) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria ISBN 3-900051-07-0, URL http://www.R-project.org/.
35. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
36. Fisher KA, Miles R, (2008) Modeling the acoustic radiation force in microfluidic chambers. J Acoust Soc Am 123: 1862-1865.
37. Zuo L, Gelernter J, Zhang CK, Zhao H, Lu L, et al. Genome-Wide Association Study of Alcohol Dependence Implicates KIAA0040 on Chromosome 1q. Neuropsychopharmacology.
38. Gualandris A, Annes JP, Arese M, Noguera I, Jurukovski V, et al. (2000) The latent transforming growth factor-beta-binding protein-1 promotes in vitro differentiation of embryonic stem cells into endothelium. Mol Biol Cell 11: 4295-4308.
39. Saltzman BS, Yamamoto JF, Decker R, Yokochi L, Theriault AG, et al. (2008) Association of genetic variation in the transforming growth factor beta-1 gene with serum levels and risk of colorectal neoplasia. Cancer Res 68: 1236-1244.
40. Ciuclan L, Ehnert S, Ilkavets I, Weng HL, Gaitantzi H, et al. TGF-beta enhances alcohol dependent hepatocyte damage via down-regulation of alcohol dehydrogenase I. J Hepatol 52: 407-416.
41. Kneussel M, Betz H, (2000) Clustering of inhibitory neurotransmitter receptors at developing postsynaptic sites: the membrane activation model. Trends Neurosci 23: 429-435.
42. Ridley AJ, (2006) Rho GTPases and actin dynamics in membrane protrusions and vesicle trafficking. Trends Cell Biol 16: 522-529.
43. Grobin AC, Matthews DB, Devaud LL, Morrow AL, (1998) The role of GABA(A) receptors in the acute and chronic effects of ethanol. Psychopharmacology (Berl) 139: 2-19.
44. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
45. Merla G, Howald C, Henrichsen CN, Lyle R, Wyss C, et al. (2006) Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. Am J Hum Genet 79: 332-341.
46. Liu SL, Lei SF, Yang F, Li X, Liu R, et al. Copy Number Variation in CNP267 Region May Be Associated with Hip Bone Size. PLoS One 6: e22035.
47. Cahan P, Li Y, Izumi M, Graubert TA, (2009) The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nat Genet 41: 430-437.
48. Henrichsen CN, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, et al. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat Genet 41: 424-429.
49. Economou M, Trikalinos TA, Loizou KT, Tsianos EV, Ioannidis JP, (2004) Differential effects of NOD2 variants on Crohn's disease risk and phenotype in diverse populations: a metaanalysis. Am J Gastroenterol 99: 2393-2404.