SgD-CNV, a database for common and rare copy number variants in three Asian populations

Human Mutation

Volumn 32, Issue 12, 2011, Pages 1341-1349

  Xu, Haiyan ^a   Poh, Wan Ting ^a   Sim, Xueling ^a   Ong, Rick Twee Hee ^a   Suo, Chen ^a   Tay, Wan Ting ^b   Khor, Chiea Chuen ^c   Seielstad, Mark ^d   Liu, Jianjun ^c   Aung, Tin ^a,b   Tai, E Shyong ^a   Wong, Tien Yin ^a,b,e   Chia, Kee Seng ^a   Teo, Yik Ying ^a,c  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b SINGAPORE EYE RESEARCH INSTITUTE   (Singapore)

^c GENOME INSTITUTE OF SINGAPORE   (Singapore)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Copy number variant; Population genetics; Rare variant

Indexed keywords

ADULT; AGED; ARTICLE; CAUCASIAN; CHINESE; CONTROLLED STUDY; COPY NUMBER VARIATION; DATA BASE; FEMALE; GENOME; HEALTH SURVEY; HUMAN; INDIAN; LANDSCAPE; MAJOR CLINICAL STUDY; MALAYSIA; MALE; POPULATION DIFFERENTIATION; PRIORITY JOURNAL; RANDOMIZED CONTROLLED TRIAL; SINGAPORE; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIVERSITY;

ADULT; AGED; AGED, 80 AND OVER; ASIAN CONTINENTAL ANCESTRY GROUP; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MALE; MIDDLE AGED; SINGAPORE; YOUNG ADULT;

EID: 81255197018     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21601     Document Type: Article

References (40)

1. Bochukova EG, Huang N, Keogh J, Henning E, Purmann C, Blaszczyk K, Saeed S, Hamilton-Shield J, Clayton-Smith J, O'Rahilly S, Hurles ME, Farooqi IS. 2010. Large, rare chromosomal deletions associated with severe early-onset obesity. Nature 463:666-670.
2. Bucan M, Abrahams BS, Wang K, Glessner JT, Herman EI, Sonnenblick LI, Alvarez Retuerto AI, Imielinski M, Hadley D, Bradfield JP, Kim C, Gidaya NB, Lindquist I, Hutman T, Sigman M, Kustanovich V, Lajonchere CM, Singleton A, Kim J, Wassink TH, McMahon WM, Owley T, Sweeney JA, Coon H, Nurnberger JI, Li M, Cantor RM, Minshew NJ, Sutcliffe JS, Cook EH, Dawson G, Buxbaum JD, Grant SF, Schellenberg GD, Geschwind DH, Hakonarson H. 2009. Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. PLoS Genet 5:e1000536.
3. 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.
4. Conrad DF, Hurles ME. 2007. The population genetics of structural variation. Nat Genet 39(7 Suppl):S30-S36.
5. 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, 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 464:704-712.
6. Consortium WTCC. 2010. Genome-wide association study of CNVs in 16, 000 cases of eight common diseases and 3, 000 shared controls. Nature 464:713-720.
7. Cusco I, Medrano A, Gener B, Vilardell M, Gallastegui F, Villa O, Gonzalez E, Rodriguez-Santiago B, Vilella E, Del Campo M, Perez-Jurado LA. 2009. Autism-specific copy number variants further implicate the phosphatidylinositol signaling pathway and the glutamatergic synapse in the etiology of the disorder. Hum Mol Genet 18:1795-1804.
8. Dellinger AE, Saw SM, Goh LK, Seielstad M, Young TL, Li YJ. 2010. Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res 38:e105.
9. Diskin SJ, Hou C, Glessner JT, Attiyeh EF, Laudenslager M, Bosse K, Cole K, Mosse YP, Wood A, Lynch JE, Pecor K, Diamond M, Winter C, Wang K, Kim C, Geiger EA, McGrady PW, Blakemore AI, London WB, Shaikh TH, Bradfield J, Grant SF, Li H, Devoto M, Rappaport ER, Hakonarson H, Maris JM. 2009. Copy number variation at 1q21.1 associated with neuroblastoma. Nature 459:987-991.
10. Foong AW, Saw SM, Loo JL, Shen S, Loon SC, Rosman M, Aung T, Tan DT, Tai ES, Wong TY. 2007. Rationale and methodology for a population-based study of eye diseases in Malay people: The Singapore Malay Eye Study (SiMES). Ophthalmic Epidemiol 14:25-35.
11. 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.
12. 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.
13. Jacob K, Albrecht S, Sollier C, Faury D, Sader E, Montpetit A, Serre D, Hauser P, Garami M, Bognar L, Hanzely Z, Montes JL, Atkinson J, Farmer JP, Bouffet E, Hawkins C, Tabori U, Jabado N. 2009. Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours. Br J Cancer 101:722-733.
14. Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Church GM, Lee C, Kingsmore SF, Seo JS. 2009. A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011-1015.
15. Ku CS, Pawitan Y, Sim X, Ong RT, Seielstad M, Lee EJ, Teo YY, Chia KS, Salim A. 2010. Genomic copy number variations in three Southeast Asian populations. Hum Mutat 31:851-857.
16. Lavanya R, Jeganathan VS, Zheng Y, Raju P, Cheung N, Tai ES, Wang JJ, Lamoureux E, Mitchell P, Young TL, Cajucom-Uy H, Foster PJ, Aung T, Saw SM, Wong TY. 2009. Methodology of the Singapore Indian Chinese Cohort (SICC) eye study: quantifying ethnic variations in the epidemiology of eye diseases in Asians. Ophthalmic Epidemiol 16:325-336.
17. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC. 2007. The diploid genome sequence of an individual human. PLoS Biol 5:e254.
18. 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.
19. Lin C-H, Lin Y-C, Wu J-Y, Pan W-H, Chen Y-T, Fann CSJ. 2009. A genome-wide survey of copy number variations in Han Chinese residing in Taiwan. Genomics 94:241-246.
20. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
21. Need AC, Ge D, Weale ME, Maia J, Feng S, Heinzen EL, Shianna KV, Yoon W, Kasperaviciute D, Gennarelli M, Strittmatter WJ, Bonvicini C, Rossi G, Jayathilake K, Cola PA, McEvoy JP, Keefe RS, Fisher EM, St Jean PL, Giegling I, Hartmann AM, Moller HJ, Ruppert A, Fraser G, Crombie C, Middleton LT, St Clair D, Roses AD, Muglia P, Francks C, Rujescu D, Meltzer HY, Goldstein DB. 2009. A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genet 5:e1000373.
22. Nejentsev S, Walker N, Riches D, Egholm M, Todd JA. 2009. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324:387-389.
23. Nelson WJ, Nusse R. 2004. Convergence of Wnt, beta-catenin, and cadherin pathways. Science 303:1483-1487.
24. Nguyen DQ, Webber C, Ponting CP. 2006. Bias of selection on human copy-number variants. PLoS Genet 2:e20.
25. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee C, Seo JS. 2010. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 42:400-405.
26. 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, Gonzalez JR, Gratacos 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, 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.
27. Rodriguez-Santiago B, Brunet A, Sobrino B, Serra-Juhe C, Flores R, Armengol L, Vilella E, Gabau E, Guitart M, Guillamat R, Martorell L, Valero J, Gutierrez-Zotes A, Labad A, Carracedo A, Estivill X, Perez-Jurado LA. 2009. Association of common copy number variants at the glutathione S-transferase genes and rare novel genomic changes with schizophrenia. Mol Psychiatry 15:1023-1033.
28. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M. 2007. Strong association of de novo copy number mutations with autism. Science 316:445-449.
29. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner 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.
30. Sebat J, Levy DL, McCarthy SE. 2009. Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders. Trends Genet 25:528-535.
31. Sim X, Ong RT-H, Suo C, Tay W-T, Liu J, Ng DP-K, Boehnke M, Chia K-S, Wong T-Y, Seielstad M, Teo YY, Tai ES. 2011. Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from south-east Asia. PLoS Genet 7:e1001363.
32. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848-853.
33. 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.
34. Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. 2008. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320:539-543.
35. Walters RG, Jacquemont S, Valsesia A, de Smith AJ, Martinet D, Andersson J, Falchi M, Chen F, Andrieux J, Lobbens S, Delobel B, Stutzmann F, El-Sayed Moustafa JS, Chevre JC, Lecoeur C, Vatin V, Bouquillon S, Buxton JL, Boute O, Holder-Espinasse M, Cuisset JM, Lemaitre MP, Ambresin AE, Brioschi A, Gaillard M, Giusti V, Fellmann F, Ferrarini A, Hadjikhani N, Campion D, Guilmatre A, Goldenberg A, Calmels N, Mandel JL, Le Caignec C, David A, Isidor B, Cordier MP, Dupuis-Girod S, Labalme A, Sanlaville D, Beri-Dexheimer M, Jonveaux P, Leheup B, Ounap K, Bochukova EG, Henning E, Keogh J, Ellis RJ, Macdermot KD, van Haelst MM, Vincent-Delorme C, Plessis G, Touraine R, Philippe A, Malan V, Mathieu-Dramard M, Chiesa J, Blaumeiser B, Kooy RF, Caiazzo R, Pigeyre M, Balkau B, Sladek R, Bergmann S, Mooser V, Waterworth D, Reymond A, Vollenweider P, Waeber G, Kurg A, Palta P, Esko T, Metspalu A, Nelis M, Elliott P, Hartikainen AL, McCarthy MI, Peltonen L, Carlsson L, Jacobson P, Sjostrom L, Huang N, Hurles ME, O'Rahilly S, Farooqi IS, Mannik K, Jarvelin MR, Pattou F, Meyre D, Walley AJ, Coin LJ, Blakemore AI, Froguel P, Beckmann JS. 2010. A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature 463:671-675.
36. 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.
37. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Yang H. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
38. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872-876.
39. Yim SH, Kim TM, Hu HJ, Kim JH, Kim BJ, Lee JY, Han BG, Shin SH, Jung SH, Chung YJ. 2010. Copy number variations in East-Asian population and their evolutionary and functional implications. Hum Mol Genet 19:1001-1008.
40. Zheng Y, Lavanya R, Wu R, Wong W, Wang J, Mitchell P, Cheung N, Cajucom-Uy H, Lamoureux E, Aung T, Saw SM, Wong TY. 2011. Prevalence and causes of visual impairment and blindness in an urban Indian population: The Singapore Indian Eye Study. Ophthalmology. in press.