A genome-wide survey of copy number variations in Han Chinese residing in Taiwan

Genomics

Volumn 94, Issue 4, 2009, Pages 241-246

  Lin, Chien Hsing ^a,b   Lin, Ying Chao ^c   Wu, Jer Yuarn ^a   Pan, Wen Harn ^a   Chen, Yuan Tsong ^a   Fann, Cathy S J ^a  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^b NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

^c ACADEMIA SINICA   (Taiwan)

Author keywords

BeadChip; CNIT; CNV; GeneChip; Han Chinese; PennCNV

Indexed keywords

ARTICLE; CHINESE; CONTROLLED STUDY; DNA SEQUENCE; GENE DUPLICATION; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCATION; GENE NUMBER; GENE STRUCTURE; GENETIC DISORDER; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN GENOME; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TAIWAN;

ALLELES; ASIAN CONTINENTAL ANCESTRY GROUP; COMPARATIVE GENOMIC HYBRIDIZATION; DATA COLLECTION; DATABASES, GENETIC; DNA; ETHNIC GROUPS; GENE DOSAGE; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TAIWAN;

EID: 70349166718     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.06.004     Document Type: Article

References (25)

1. Freeman J.L., Perry G.H., Feuk L., Redon R., McCarroll S.A., Altshuler D.M., Aburatani H., Jones K.W., Tyler-Smith C., Hurles M.E., Carter N.P., Scherer S.W., and Lee C. Copy number variation: new insights in genome diversity. Genome Res. 16 (2006) 949-961
2. Iafrate A.J., Feuk L., Rivera M.N., Listewnik M.L., Donahoe P.K., Qi Y., Scherer S.W., and Lee C. Detection of large-scale variation in the human genome. Nat. Genet. 36 (2004) 949-951
3. Jakobsson M., Scholz S.W., Scheet P., Gibbs J.R., VanLiere J.M., Fung H.C., Szpiech Z.A., Degnan J.H., Wang K., Guerreiro R., Bras J.M., Schymick J.C., Hernandez D.G., Traynor B.J., Simon-Sanchez J., Matarin M., Britton A., van de Leemput J., Rafferty I., Bucan M., Cann H.M., Hardy J.A., Rosenberg N.A., and Singleton A.B. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451 (2008) 998-1003
4. Redon R., Ishikawa S., Fitch K.R., Feuk L., Perry G.H., Andrews T.D., Fiegler H., Shapero M.H., Carson A.R., Chen W., Cho E.K., Dallaire S., Freeman J.L., Gonzalez J.R., Gratacos M., Huang J., Kalaitzopoulos D., Komura D., MacDonald J.R., Marshall C.R., Mei R., Montgomery L., Nishimura K., Okamura K., Shen F., Somerville M.J., Tchinda J., Valsesia A., Woodwark C., Yang F., Zhang J., Zerjal T., Zhang J., Armengol L., Conrad D.F., Estivill X., Tyler-Smith C., Carter N.P., Aburatani H., Lee C., Jones K.W., Scherer S.W., and Hurles M.E. Global variation in copy number in the human genome. Nature 444 (2006) 444-454
5. 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 T.C., Trask B., Patterson N., Zetterberg A., and Wigler M. Large-scale copy number polymorphism in the human genome. Science 305 (2004) 525-528
6. Wong K.K., deLeeuw R.J., Dosanjh N.S., Kimm L.R., Cheng Z., Horsman D.E., MacAulay C., Ng R.T., Brown C.J., Eichler E.E., and Lam W.L. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80 (2007) 91-104
7. Perry G.H., Ben-Dor A., Tsalenko A., Sampas N., Rodriguez-Revenga L., Tran C.W., Scheffer A., Steinfeld I., Tsang P., Yamada N.A., Park H.S., Kim J.I., Seo J.S., Yakhini Z., Laderman S., Bruhn L., and Lee C. The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet. 82 (2008) 685-695
8. Sebat J., Lakshmi B., Malhotra D., Troge J., Lese-Martin C., Walsh T., Yamrom B., Yamrom B., Yoon S., Krasnitz A., Kendall J., Leotta A., Pai D., Zhang R., Lee Y.H., Hicks J., Spence S.J., Lee A.T., Puura K., Lehtimaki T., Ledbetter D., Gregersen P.K., Bregman J., Sutcliffe J.S., Jobanputra V., Chung W., Warburton D., King M.C., Skuse D., Geschwind D.H., Gilliam T.C., Ye K., and Wigler M. Strong association of de novo copy number mutations with autism. Science (2007)
9. Walsh T., McClellan J.M., McCarthy S.E., Addington A.M., Pierce S.B., Cooper G.M., Nord A.S., Kusenda M., Malhotra D., Bhandari A., Stray S.M., Rippey C.F., Roccanova P., Makarov V., Lakshmi B., Findling R.L., 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 E.E., Meltzer P.S., Nelson S.F., Singleton A.B., Lee M.K., Rapoport J.L., King M.C., and Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320 (2008) 539-543
10. Perry G.H., Dominy N.J., Claw K.G., Lee A.S., Fiegler H., Redon R., Werner J., Villanea F.A., Mountain J.L., Misra R., Carter N.P., Lee C., and Stone A.C. Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39 (2007) 1256-1260
11. Huang J., Wei W., Zhang J., Liu G., Bignell G.R., Stratton M.R., Futreal P.A., Wooster R., Jones K.W., and Shapero M.H. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genomics 1 (2004) 287-299
12. Slater H.R., Bailey D.K., Ren H., Cao M., Bell K., Nasioulas S., Henke R., Choo K.H., and Kennedy G.C. High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs. Am. J. Hum. Genet. 77 (2005) 709-726
13. Wang K., Li M., Hadley D., Liu R., Glessner J., Grant S.F., Hakonarson H., and Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17 (2007) 1665-1674
14. Campbell P.J., Stephens P.J., Pleasance E.D., O'Meara S., Li H., Santarius T., Stebbings L.A., Leroy C., Edkins S., Hardy C., Teague J.W., Menzies A., Goodhead I., Turner D.J., Clee C.M., Quail M.A., Cox A., Brown C., Durbin R., Hurles M.E., Edwards P.A., Bignell G.R., Stratton M.R., and Futreal P.A. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40 (2008) 722-729
15. Lin C.H., Li L.H., Ho S.F., Chuang T.P., Wu J.Y., Chen Y.T., and Fann C.S. A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan. BMC Genet. 9 (2008) 92
16. Lin C.H., Huang M.C., Li L.H., Wu J.Y., Chen Y.T., and Fann C.S. Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling. Hum. Mutat. 29 (2008) 1055-1062
17. Michalk A., Stricker S., Becker J., Rupps R., Pantzar T., Miertus J., Botta G., Naretto V.G., Janetzki C., Yaqoob N., Ott C.E., Seelow D., Wieczorek D., Fiebig B., Wirth B., Hoopmann M., Walther M., Korber F., Blankenburg M., Mundlos S., Heller R., and Hoffmann K. Acetylcholine receptor pathway mutations explain various fetal akinesia deformation sequence disorders. Am. J. Hum. Genet. 82 (2008) 464-476
18. Futreal P.A., Coin L., Marshall M., Down T., Hubbard T., Wooster R., Rahman N., and Stratton M.R. A census of human cancer genes. Nat. Rev., Cancer 4 (2004) 177-183
19. Piecha G., Chudek J., and Wiecek A. Multiple endocrine neoplasia type 1. Eur. J. Intern. Med. 19 (2008) 99-103
20. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
21. Stranger B.E., Forrest M.S., Dunning M., Ingle C.E., Beazley C., Thorne N., Redon R., Bird C.P., de Grassi A., Lee C., Tyler-Smith C., Carter N., Scherer S.W., Tavare S., Deloukas P., Hurles M.E., and Dermitzakis E.T. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315 (2007) 848-853
22. Pan W.H., Fann C.S., Wu J.Y., Hung Y.T., Ho M.S., Tai T.H., Chen Y.J., Liao C.J., Yang M.L., Cheng A.T., and Chen Y.T. Han Chinese cell and genome bank in Taiwan: purpose, design and ethical considerations. Hum. Hered. 61 (2006) 27-30
23. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Bender D., Maller J., Sklar P., de Bakker P.I., Daly M.J., and Sham P.C. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81 (2007) 559-575
24. Li L.H., Ho S.F., Chen C.H., Wei C.Y., Wong W.C., Li L.Y., Hung S.I., Chung W.H., Pan W.H., Lee M.T., Tsai F.J., Chang C.F., Wu J.Y., and Chen Y.T. Long contiguous stretches of homozygosity in the human genome. Hum. Mutat. 27 (2006) 1115-1121
25. Retief J.D. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 132 (2000) 243-258