Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W: Global variation in copy number in the human genome. Nature. 2006, 444 (7118): 444-454. 10.1038/nature05329.
Article
PubMed Central
CAS
PubMed
Google Scholar
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet. 2004, 36 (9): 949-951. 10.1038/ng1416.
Article
CAS
PubMed
Google Scholar
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK: Mapping copy number variation by population-scale genome sequencing. Nature. 2011, 470 (7332): 59-65. 10.1038/nature09708.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS: Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics. 2011, 12: 559-10.1186/1471-2164-12-559.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhan B, Fadista J, Thomsen B, Hedegaard J, Panitz F, Bendixen C: Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics. 2011, 12: 557-10.1186/1471-2164-12-557.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ramayo-Caldas Y, Castello A, Pena RN, Alves E, Mercade A, Souza CA, Fernandez AI, Perez-Enciso M, Folch JM: Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC Genomics. 2010, 11: 593-10.1186/1471-2164-11-593.
Article
PubMed Central
PubMed
Google Scholar
Clop A, Vidal O, Amills M: Copy number variation in the genomes of domestic animals. Anim Genet. 2011, 43:
Google Scholar
Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF: Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 2012, 22 (4): 778-790. 10.1101/gr.133967.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen WK, Swartz JD, Rush LJ, Alvarez CE: Mapping DNA structural variation in dogs. Genome Res. 2009, 19 (3): 500-509.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL: A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001, 409 (6822): 928-933. 10.1038/35057149.
Article
CAS
PubMed
Google Scholar
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M: Large-scale copy number polymorphism in the human genome. Science. 2004, 305 (5683): 525-528. 10.1126/science.1098918.
Article
CAS
PubMed
Google Scholar
Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006, 7 (2): 85-97.
Article
CAS
PubMed
Google Scholar
Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping. Nat Rev Genet. 2011, 12 (5): 363-376. 10.1038/nrg2958.
Article
PubMed Central
CAS
PubMed
Google Scholar
Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP: Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet. 2010, 42 (5): 400-405. 10.1038/ng.555.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC: Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 2010, 11 (5): R52-10.1186/gb-2010-11-5-r52.
Article
PubMed Central
PubMed
Google Scholar
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE: Diversity of human copy number variation and multicopy genes. Science. 2010, 330 (6004): 641-646. 10.1126/science.1197005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM: A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 2007, 3 (1): e3-10.1371/journal.pgen.0030003.
Article
PubMed Central
PubMed
Google Scholar
She X, Cheng Z, Zollner S, Church DM, Eichler EE: Mouse segmental duplication and copy number variation. Nat Genet. 2008, 40 (7): 909-914. 10.1038/ng.172.
Article
PubMed Central
CAS
PubMed
Google Scholar
Watkins-Chow DE, Pavan WJ: Genomic copy number and expression variation within the C57BL/6J inbred mouse strain. Genome Res. 2008, 18 (1): 60-66.
Article
PubMed Central
CAS
PubMed
Google Scholar
Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M: Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 2008, 320 (5883): 1629-1631. 10.1126/science.1158078.
Article
CAS
PubMed
Google Scholar
Wang J, Jiang J, Fu W, Jiang L, Ding X, Liu JF, Zhang Q: A genome-wide detection of copy number variations using SNP genotyping arrays in swine. BMC Genomics. 2012, 13: 273-10.1186/1471-2164-13-273.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C: A snapshot of CNVs in the pig genome. PLoS One. 2008, 3 (12): e3916-10.1371/journal.pone.0003916.
Article
PubMed Central
PubMed
Google Scholar
Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, Chun JY, Kim JY, Pasaje CF, Lee JS, Shin HD: Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics. 2010, 11: 232-10.1186/1471-2164-11-232.
Article
PubMed Central
PubMed
Google Scholar
Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME: Analysis of copy number variations among diverse cattle breeds. Genome Res. 2010, 20 (5): 693-703. 10.1101/gr.105403.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fadista J, Thomsen B, Holm LE, Bendixen C: Copy number variation in the bovine genome. BMC Genomics. 2010, 11: 284-10.1186/1471-2164-11-284.
Article
PubMed Central
PubMed
Google Scholar
Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim ES, Matukumalli LK, Ventura M, Song J, VanRaden PM: Genomic characteristics of cattle copy number variations. BMC Genomics. 2011, 12: 127-10.1186/1471-2164-12-127.
Article
PubMed Central
PubMed
Google Scholar
Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G: The diploid genome sequence of an individual human. PLoS Biol. 2007, 5 (10): e254-10.1371/journal.pbio.0050254.
Article
PubMed Central
PubMed
Google Scholar
Margareto J, Leis O, Larrarte E, Pomposo IC, Garibi JM, Lafuente JV: DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM. Cancer Invest. 2009, 27 (5): 541-548. 10.1080/07357900802563044.
Article
CAS
PubMed
Google Scholar
Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007, 315 (5813): 848-853. 10.1126/science.1136678.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang F, Gu W, Hurles ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009, 10: 451-481. 10.1146/annurev.genom.9.081307.164217.
Article
PubMed Central
CAS
PubMed
Google Scholar
Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E: Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature. 2006, 439 (7078): 851-855. 10.1038/nature04489.
Article
CAS
PubMed
Google Scholar
Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V: A copy number variation morbidity map of developmental delay. Nat Genet. 2011, 43 (9): 838-846. 10.1038/ng.909.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, Hebert M, Jones KN, Shu Y, Kitzmiller K: Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet. 2007, 80 (6): 1037-1054. 10.1086/518257.
Article
PubMed Central
CAS
PubMed
Google Scholar
Diskin SJ, Hou C, Glessner JT, Attiyeh EF, Laudenslager M, Bosse K, Cole K, Mosse YP, Wood A, Lynch JE: Copy number variation at 1q21.1 associated with neuroblastoma. Nature. 2009, 459 (7249): 987-991. 10.1038/nature08035.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stankiewicz P, Lupski JR: Structural variation in the human genome and its role in disease. Annu Rev Med. 2010, 61: 437-455. 10.1146/annurev-med-100708-204735.
Article
CAS
PubMed
Google Scholar
Girirajan S, Campbell CD, Eichler EE: Human copy number variation and complex genetic disease. Annu Rev Genet. 2011, 45: 203-226. 10.1146/annurev-genet-102209-163544.
Article
CAS
PubMed
Google Scholar
Wright D, Boije H, Meadows JR, Bed'hom B, Gourichon D, Vieaud A, Tixier-Boichard M, Rubin CJ, Imsland F, Hallbook F: Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet. 2009, 5 (6): e1000512-10.1371/journal.pgen.1000512.
Article
PubMed Central
PubMed
Google Scholar
Giuffra E, Tornsten A, Marklund S, Bongcam-Rudloff E, Chardon P, Kijas JM, Anderson SI, Archibald AL, Andersson L: A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mamm Genome. 2002, 13 (10): 569-577. 10.1007/s00335-002-2184-5.
Article
CAS
PubMed
Google Scholar
Fontanesi L, Beretti F, Riggio V, Gomez Gonzalez E, Dall'Olio S, Davoli R, Russo V, Portolano B: Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors. Cytogenet Genome Res. 2009, 126 (4): 333-347. 10.1159/000268089.
Article
CAS
PubMed
Google Scholar
Salmon Hillbertz NH, Isaksson M, Karlsson EK, Hellmen E, Pielberg GR, Savolainen P, Wade CM, von Euler H, Gustafson U, Hedhammar A: Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nat Genet. 2007, 39 (11): 1318-1320. 10.1038/ng.2007.4.
Article
CAS
PubMed
Google Scholar
Goldstein O, Mezey JG, Boyko AR, Gao C, Wang W, Bustamante CD, Anguish LJ, Jordan JA, Pearce-Kelling SE, Aguirre GD: An ADAM9 mutation in canine cone-rod dystrophy 3 establishes homology with human cone-rod dystrophy 9. Mol Vis. 2010, 16: 1549-1569.
PubMed Central
CAS
PubMed
Google Scholar
Gill JL, Capper D, Vanbellinghen JF, Chung SK, Higgins RJ, Rees MI, Shelton GD, Harvey RJ: Startle disease in Irish wolfhounds associated with a microdeletion in the glycine transporter GlyT2 gene. Neurobiol Dis. 2011, 43 (1): 184-189. 10.1016/j.nbd.2011.03.010.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meyers SN, McDaneld TG, Swist SL, Marron BM, Steffen DJ, O'Toole D, O'Connell JR, Beever JE, Sonstegard TS, Smith TP: A deletion mutation in bovine SLC4A2 is associated with osteopetrosis in Red Angus cattle. BMC Genomics. 2010, 11: 337-10.1186/1471-2164-11-337.
Article
PubMed Central
PubMed
Google Scholar
Flisikowski K, Venhoranta H, Nowacka-Woszuk J, McKay SD, Flyckt A, Taponen J, Schnabel R, Schwarzenbacher H, Szczerbal I, Lohi H: A novel mutation in the maternally imprinted PEG3 domain results in a loss of MIMT1 expression and causes abortions and stillbirths in cattle (Bos taurus). PLoS One. 2010, 5 (11): e15116-10.1371/journal.pone.0015116.
Article
PubMed Central
CAS
PubMed
Google Scholar
Seroussi E, Glick G, Shirak A, Yakobson E, Weller JI, Ezra E, Zeron Y: Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genomics. 2010, 11: 673-10.1186/1471-2164-11-673.
Article
PubMed Central
CAS
PubMed
Google Scholar
Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 2006, 16 (12): 1575-1584. 10.1101/gr.5629106.
Article
PubMed Central
CAS
PubMed
Google Scholar
de Smith AJ, Tsalenko A, Sampas N, Scheffer A, Yamada NA, Tsang P, Ben-Dor A, Yakhini Z, Ellis RJ, Bruhn L: Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. Hum Mol Genet. 2007, 16 (23): 2783-2794. 10.1093/hmg/ddm208.
Article
CAS
PubMed
Google Scholar
Baumbusch LO, Aaroe J, Johansen FE, Hicks J, Sun H, Bruhn L, Gunderson K, Naume B, Kristensen VN, Liestol K: Comparison of the Agilent. ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics. 2008, 9: 379-
CAS
PubMed
Google Scholar
Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, Futreal PA, Wooster R, Jones KW, Shapero MH: Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics. 2004, 1 (4): 287-299. 10.1186/1479-7364-1-4-287.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yau C, Holmes CC: CNV discovery using SNP genotyping arrays. Cytogenet Genome Res. 2008, 123 (1–4): 307-312.
Article
CAS
PubMed
Google Scholar
Ionita-Laza I, Rogers AJ, Lange C, Raby BA, Lee C: Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. Genomics. 2009, 93 (1): 22-26. 10.1016/j.ygeno.2008.08.012.
Article
PubMed Central
CAS
PubMed
Google Scholar
Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavare S, Caldas C: The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics. 2009, 10: 588-10.1186/1471-2164-10-588.
Article
PubMed Central
PubMed
Google Scholar
Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Hoglund M, Borg A, Ringner M: Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics. 2008, 9: 409-10.1186/1471-2105-9-409.
Article
PubMed Central
PubMed
Google Scholar
Winchester L, Yau C, Ragoussis J: Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic. 2009, 8 (5): 353-366. 10.1093/bfgp/elp017.
Article
CAS
PubMed
Google Scholar
Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, Denise S, Wiggans GR: Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics. 2012, 13 (1): 376-10.1186/1471-2164-13-376.
Article
PubMed Central
CAS
PubMed
Google Scholar
Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP: Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature. 2009, 459 (7246): 569-573. 10.1038/nature07953.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marenne G, Rodriguez-Santiago B, Closas MG, Perez-Jurado L, Rothman N, Rico D, Pita G, Pisano DG, Kogevinas M, Silverman DT: Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Hum Mutat. 2011, 32 (2): 240-248. 10.1002/humu.21398.
Article
PubMed Central
PubMed
Google Scholar
Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasbarre LC, Van Tassell CP, Sonstegard TS: Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Funct Integr Genomics. 2012, 12 (1): 81-92. 10.1007/s10142-011-0252-1.
Article
CAS
PubMed
Google Scholar
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ: The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010, 38 (Database issue): 613-619.
Article
Google Scholar
Jiang L, Jiang J, Wang J, Ding X, Liu J, Zhang Q: Genome-wide identification of copy number variations in Chinese Holstein. PLoS One. 2012, 7 (11): e48732-10.1371/journal.pone.0048732.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM: The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res. 2009, 19 (3): 491-499.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M: PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007, 17 (11): 1665-1674. 10.1101/gr.6861907.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS: A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009, 10 (4): R42-10.1186/gb-2009-10-4-r42.
Article
PubMed Central
PubMed
Google Scholar
Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R: Genotype, haplotype and copy-number variation in worldwide human populations. Nature. 2008, 451 (7181): 998-1003. 10.1038/nature06742.
Article
CAS
PubMed
Google Scholar
Glessner JT, Reilly MP, Kim CE, Takahashi N, Albano A, Hou C, Bradfield JP, Zhang H, Sleiman PM, Flory JH: Strong synaptic transmission impact by copy number variations in schizophrenia. Proc Natl Acad Sci U S A. 2010, 107 (23): 10584-10589. 10.1073/pnas.1000274107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38 (Database issue): 355-360.
Article
Google Scholar
da Huang W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009, 4 (1): 44-57.
Article
PubMed
Google Scholar
Bodin L, Beaune PH, Loriot MA: Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real-time quantitative PCR. J Biomed Biotechnol. 2005, 2005 (3): 248-253. 10.1155/JBB.2005.248.
Article
PubMed Central
PubMed
Google Scholar
D'Haene B, Vandesompele J, Hellemans J: Accurate and objective copy number profiling using real-time quantitative PCR. Methods. 2010, 50 (4): 262-270. 10.1016/j.ymeth.2009.12.007.
Article
PubMed
Google Scholar