Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Liu, Jiasen ^a,b   Zhang, Li ^a   Xu, Lingyang ^a   Ren, Hangxing ^c   Lu, Jian ^a   Zhang, Xiaoning ^a   Zhang, Shifang ^a   Zhou, Xinlei ^a   Wei, Caihong ^a   Zhao, Fuping ^a   Du, Lixin ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences   (China)

^c Chongqing Academy of Animal Science   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CONTROLLED STUDY; COPY NUMBER VARIATION; EVOLUTIONARY ADAPTATION; FEMALE; GENE FREQUENCY; GENE FUNCTION; GENE LOSS; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC GAIN; GENETIC IDENTIFICATION; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; MALE; MICROARRAY ANALYSIS; NONHUMAN; PHENOTYPIC VARIATION; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CHROMOSOME MAPPING; DNA COPY NUMBER VARIATIONS; FEMALE; GENOME; GENOTYPE; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SHEEP;

OVIS; OVIS ARIES;

EID: 84875845927     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-229     Document Type: Article

References (63)

1. Manolio TA, Collins FS. The HapMap and genome-wide association studies in diagnosis and therapy. Annu Rev Med 2009, 60:443-456.
2. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006, 7(2):85-97.
3. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P. Origins and functional impact of copy number variation in the human genome. Nature 2010, 464(7289):704-712.
4. 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.
5. 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.
6. Stankiewicz P, Lupski JR. Structural Variation in the Human Genome and its Role in Disease. Annu Rev Med 2010, 437-455. Palo Alto: Annual Reviews, Volume 61.
7. 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.
8. 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.
9. 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. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Caceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci USA 2006, 103(21):8006-8011.
11. Lee AS, Gutierrez-Arcelus M, Perry GH, Vallender EJ, Johnson WE, Miller GM, Korbel JO, Lee C. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum Mol Genet 2008, 17(8):1127-1136.
12. 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.
13. Maydan JS, Lorch A, Edgley ML, Flibotte S, Moerman DG. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics 2010, 11:62.
14. 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.
15. Fadista J, Thomsen B, Holm LE, Bendixen C. Copy number variation in the bovine genome. BMC Genomics 2010, 11:284.
16. 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.
17. Kijas JW, Barendse W, Barris W, Harrison B, McCulloch R, McWilliam S, Whan V. Analysis of copy number variants in the cattle genome. Gene 2011, 482(1-2):73-77.
18. Zhan BJ, 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.
19. 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.
20. 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.
21. Alvarez CE, Akey JM. Copy number variation in the domestic dog. Mamm Genome 2012, 23(1-2):144-163.
22. Wang X, Nahashon S, Feaster T, Bohannon-Stewart A, Adefope N. An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 2010, 11(1):351.
23. Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C. A snapshot of CNVs in the pig genome. PLoS One 2008, 3(12):e3916.
24. 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.
25. Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'Olio S, Colombo M, Casadio R, Russo V, Portolano B. An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics 2010, 11:639.
26. Fontanesi L, Beretti F, Martelli PL, Colombo M, Dall'olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V. A first comparative map of copy number variations in the sheep genome. Genomics 2011, 97(3):158-165.
27. Fontanesi L, Martelli PL, Scotti E, Russo V, Rogel-Gaillard C, Casadio R, Vernesi C. Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization. Genomics 2012, 100(4):245-251.
28. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006, 16(9):1136-1148.
29. Rincon G, Weber K, Van Eenennaam A, Golden B, Medrano J. Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 2011, 94(12):6116-6121.
30. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008, 40(10):1166-1174.
31. 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:D613-619.
32. Wain LV, Armour JA, Tobin MD. Genomic copy number variation, human health, and disease. Lancet 2009, 374(9686):340-350.
33. Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid BM, Nordenskjold M. Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). J Med Genet 2005, 42(9):699-705.
34. He YJ, Hoskins JM, McLeod HL. Copy number variants in pharmacogenetic genes. Trends Mol Med 2011, 17(5):244-251.
35. Lou H, Li S, Yang Y, Kang L, Zhang X, Jin W, Wu B, Jin L, Xu S. A map of copy number variations in Chinese populations. PLoS One 2011, 6(11):e27341.
36. McCarroll SA. Copy number variation and human genome maps. Nat Genet 2010, 42(5):365-366.
37. 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.
38. Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, Maddox JF, McEwan JC, Hutton Oddy V, Raadsma HW, Wade C. The sheep genome reference sequence: a work in progress. Anim Genet 2010, 41(5):449-453.
39. 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.
40. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007, 35(6):2013-2025.
41. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 2008, 40(10):1253-1260.
42. Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S. Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics 2008, 24(3):309-318.
43. Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 2008, 36(19):e126.
44. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921.
45. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA. The sequence of the human genome. Science 2001, 291(5507):1304-1351.
46. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432(7018):695-716.
47. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324(5926):522-528.
48. Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M. A high utility integrated map of the pig genome. Genome Biol 2007, 8(7):R139.
49. Moon S, Kim YJ, Hong CB, Kim DJ, Lee JY, Kim BJ. Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort. Eur J Hum Genet 2011, 19(11):1167-1172.
50. Nei M, Niimura Y, Nozawa M. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 2008, 9(12):951-963.
51. McCarroll SA, Bradner JE, Turpeinen H, Volin L, Martin PJ, Chilewski SD, Antin JH, Lee SJ, Ruutu T, Storer B. Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease. Nat Genet 2009, 41(12):1341-1344.
52. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 2006, 38(1):75-81.
53. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME. Copy number variation: new insights in genome diversity. Genome Res 2006, 16(8):949-961.
54. Kantaputra PN, Klopocki E, Hennig BP, Praphanphoj V, Le Caignec C, Isidor B, Kwee ML, Shears DJ, Mundlos S. Mesomelic dysplasia Kantaputra type is associated with duplications of the HOXD locus on chromosome 2q. Eur J Hum Genet 2010, 18(12):1310-1314.
55. Kurth I, Klopocki E, Stricker S, van Oosterwijk J, Vanek S, Altmann J, Santos HG, van Harssel JJ, de Ravel T, Wilkie AO. Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia. Nat Genet 2009, 41(8):862-863.
56. Dathe K, Kjaer KW, Brehm A, Meinecke P, Nurnberg P, Neto JC, Brunoni D, Tommerup N, Ott CE, Klopocki E. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet 2009, 84(4):483-492.
57. Wieczorek D, Pawlik B, Li Y, Akarsu NA, Caliebe A, May KJ, Schweiger B, Vargas FR, Balci S, Gillessen-Kaesbach G. A specific mutation in the distant sonic hedgehog (SHH) cis-regulator (ZRS) causes Werner mesomelic syndrome (WMS) while complete ZRS duplications underlie Haas type polysyndactyly and preaxial polydactyly (PPD) with or without triphalangeal thumb. Hum Mutat 2010, 31(1):81-89.
58. Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C. Copy number variation and evolution in humans and chimpanzees. Genome Res 2008, 18(11):1698-1710.
59. Dellinger AE, Saw SM, Goh LK, Seielstad M, Young TL, Li YJ. Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res 2010, 38(9):e105.
60. 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.
61. 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.
62. D'haene B, Vandesompele J, Hellemans J. Accurate and objective copy number profiling using real-time quantitative PCR. Methods 2010, 50(4):262-270.
63. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 2001, 25(4):402-408.