Genomic copy number variations in three southeast Asian populations

Human Mutation

Volumn 31, Issue 7, 2010, Pages 851-857

  Ku, Chee Seng ^a   Pawitan, Yudi ^b   Sim, Xueling ^a   Ong, Rick T H ^a,c   Seielstad, Mark ^c,d   Lee, Edmund J D ^a   Teo, Yik Ying ^a,e,f   Chia, Kee Seng ^a,b   Salim, Agus ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b KAROLINSKA INSTITUTE   (Sweden)

^c GENOME INSTITUTE OF SINGAPORE   (Singapore)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Asian populations; CNV; Copy number variation; Data resources; PennCNV; SNP array

Indexed keywords

CYTOCHROME P450 2A6; CYP2A6 PROTEIN, HUMAN; UNSPECIFIC MONOOXYGENASE;

ADULT; ARTICLE; ASIAN; CHINESE; CONTROLLED STUDY; COPY NUMBER VARIATION; DISEASE PREDISPOSITION; ETHNIC GROUP; FEMALE; GENE DELETION; GENE IDENTIFICATION; GENE LOCUS; GENE NUMBER; GENETIC RISK; GENETIC VARIABILITY; HUMAN; INDIAN; MAJOR CLINICAL STUDY; MALE; POPULATION DIFFERENTIATION; POPULATION RESEARCH; PRIORITY JOURNAL; SINGAPORE; ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOME MAP; ETHNOLOGY; GENE DOSAGE; GENE DUPLICATION; GENETIC PREDISPOSITION; GENETICS; INDIA; LUNG TUMOR; MALAYSIA; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS;

ARYL HYDROCARBON HYDROXYLASES; ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOME MAPPING; CYTOCHROME P-450 CYP2A6; GENE DELETION; GENE DOSAGE; GENE DUPLICATION; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; INDIA; LUNG NEOPLASMS; MALAYSIA; PRINCIPAL COMPONENT ANALYSIS; SINGAPORE;

EID: 77954094635     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21287     Document Type: Article

References (26)

1. Bellwood P, Fox JJ, Tryon D, editors. The Austronesians: historical and comparative perspectives. Canberra, Australia: Australian National University. 1995.
2. Chen J, Zheng H, Bei JX, Sun L, Jia WH, Li T, Zhang F, Seielstad M, Zeng YX, Zhang X, Liu J. 2009. Genetic structure of the Han Chinese population revealed by genome-wide SNP variation. Am J Hum Genet 85:775-785.
3. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, The Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. 2009. Origins and functional impact of copy number variation in the human genome. Nature 2009 Oct 7 [Epub ahead of print].
4. de Stahl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. 2008. Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. Hum Mutat 29:398-408.
5. Estivill X, Armengol L. 2007. Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PLoS Genet 3:1787-1799. (Pubitemid 350072046)
6. Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SC, de Smith A, Blakemore AI, Froguel P, Owen CJ, Pearce SH, Teixeira L, Guillevin L, Graham DS, Pusey CD, Cook HT, Vyse TJ, Aitman TJ. 2007. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet 39:721-723.
7. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'Connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307:1434-1440.
8. Hollox EJ, Huffmeier U, Zeeuwen PL, Palla R, Lascorz J, Rodijk-Olthuis D, van de Kerkhof PC, Traupe H, de Jongh G, den Heijer M, Reis A, Armour JA, Schalkwijk J. 2008. Psoriasis is associated with increased beta-defensin genomic copy number. Nat Genet 40:23-25.
9. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36:949-951. (Pubitemid 39167488)
10. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998-1003.
11. Li J, Yang T, Wang L, Yan H, Zhang Y, Guo Y, Pan F, Zhang Z, Peng Y, Zhou Q, He L, Zhu X, Deng H, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Recker RR, Cheng J, Deng HW. 2009. Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations. PLoS ONE 4:e7958.
12. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. 2008. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40:1166-1174.
13. Miyamoto M, Umetsu Y, Dosaka-Akita H, Sawamura Y, Yokota J, Kunitoh H, Nemoto N, Sato K, Ariyoshi N, Kamataki T. 1999. CYP2A6 gene deletion reduces susceptibility to lung cancer. Biochem Biophys Res Commun 261:658-660. (Pubitemid 29408114)
14. Oguri M, Kato K, Yokoi K, Yoshida T, Watanabe S, Metoki N, Yoshida H, Satoh K, Aoyagi Y, Nozawa Y, Yamada Y. 2010. Assessment of a polymorphism of SDK1 with hypertension in Japanese individuals. Am J Hypertens 23:70-77.
15. Ouahchi K, Lindeman N, Lee C. 2006. Copy number variants and pharmacogenomics. Pharmacogenomics 7:25-29.
16. Park J, Chen L, Ratnashinge L, Sellers TA, Tanner JP, Lee JH, Dossett N, Lang N, Kadlubar FF, Ambrosone CB, Zachariah B, Heysek RV, Patterson S, Pow-Sang J. 2006. Deletion polymorphism of UDP-glucuronosyltransferase 2B17 and risk of prostate cancer in African American and Caucasian men. Cancer Epidemiol Biomarkers Prev 15:1473-1478.
17. Pinto D, Marshall C, Feuk L, Scherer SW. 2007. Copy-number variation in control population cohorts. Hum Mol Genet 16:R168-R173.
18. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. 2006. Global variation in copy number in the human genome. Nature 444:444-454. (Pubitemid 44809057)
19. Reich D, Thangaraj K, Patterson N, Price AL, Singh L. 2009. Reconstructing Indian population history. Nature 461:489-494.
20. Saw SH. 2007. The population of Singapore, 2nd edition. Singapore: Institute of South East Asian Studies.
21. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Mãnér S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science 305:525-528.
22. Singapore Cancer Registry. 2008. Trends in cancer incidence in Singapore 2002-2006. Interim Report. Singapore: Singapore Cancer Registry.
23. Teo YY, Sim X, Ong RT, Tan AK, Chen J, Tantoso E, Small KS, Ku CS, Lee EJ, Seielstad M, Chia KS. 2009. Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations. Genome Res 19:2154-2162.
24. Wain LV, Armour JA, Tobin MD. 2009. Genomic copy number variation, human health, and disease. Lancet 374:340-350.
25. 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. (Pubitemid 350074862)
26. Yim SH, Kim TM, Hu HJ, Kim JH, Kim BJ, Lee JY, Han BG, Shin SH, Jung SH, Chung YJ. Copy number variations in East-Asian population and their evolutionary and functional implications. Hum Mol Genet. 2010 Jan 15 [Epub ahead of print].