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, et al: Global variation in copy number in the human genome. Nature. 2006, 444 (7118): 444-454. 10.1038/nature05329.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE: Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 2012, 22 (4): 778-790. 10.1101/gr.133967.111.
Article
CAS
PubMed Central
PubMed
Google Scholar
McCarroll SA, Altshuler DM: Copy-number variation and association studies of human disease. Nat Genet. 2007, 39 (7 Suppl): S37-S42.
Article
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
CAS
PubMed Central
PubMed
Google Scholar
Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Bonnen PE, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, et al: Integrating common and rare genetic variation in diverse human populations. Nature. 2010, 467 (7311): 52-58. 10.1038/nature09298.
Article
CAS
PubMed
Google Scholar
Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellaker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, Mott R, Adams DJ, Flint J: Sequence-based characterization of structural variation in the mouse genome. Nature. 2011, 477 (7364): 326-329. 10.1038/nature10432.
Article
CAS
PubMed Central
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
CAS
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, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LC, Smith TP, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW: Analysis of copy number variations among diverse cattle breeds. Genome Res. 2010, 20 (5): 693-703. 10.1101/gr.105403.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wang Y, Gu X, Feng C, Song C, Hu X, Li N: A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. Anim Genet. 2012, 43 (3): 282-289. 10.1111/j.1365-2052.2011.02308.x.
Article
CAS
PubMed
Google Scholar
Hastings PJ, Ira G, Lupski JR: A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 2009, 5 (1): e1000327-10.1371/journal.pgen.1000327.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE: Segmental duplications and copy-number variation in the human genome. Am J Hum Genet. 2005, 77 (1): 78-88. 10.1086/431652.
Article
CAS
PubMed Central
PubMed
Google Scholar
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE: Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 2009, 41 (10): 1061-1067. 10.1038/ng.437.
Article
CAS
PubMed Central
PubMed
Google Scholar
Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C: Copy number variation: new insights in genome diversity. Genome Res. 2006, 16 (8): 949-961. 10.1101/gr.3677206.
Article
CAS
PubMed
Google Scholar
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: Finding the missing heritability of complex diseases. Nature. 2009, 461 (7265): 747-753. 10.1038/nature08494.
Article
CAS
PubMed Central
PubMed
Google Scholar
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: Origins and functional impact of copy number variation in the human genome. Nature. 2010, 464 (7289): 704-712. 10.1038/nature08516.
Article
CAS
PubMed Central
PubMed
Google Scholar
Liu GE, Bickhart DM: Copy number variation in the cattle genome. Funct Integr Genomics. 2012, 12 (4): 609-624. 10.1007/s10142-012-0289-9.
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, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007, 315 (5813): 848-853. 10.1126/science.1136678.
Article
CAS
PubMed Central
PubMed
Google Scholar
Henrichsen CN, Chaignat E, Reymond A: Copy number variants, diseases and gene expression. Hum Mol Genet. 2009, 18 (R1): R1-R8. 10.1093/hmg/ddp011.
Article
CAS
PubMed
Google Scholar
LaFramboise T: Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res. 2009, 37 (13): 4181-4193. 10.1093/nar/gkp552.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, Macdonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L: Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011, 29 (6): 512-520. 10.1038/nbt.1852.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al: Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008, 456 (7218): 53-59. 10.1038/nature07517.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yoon S, Xuan Z, Makarov V, Ye K, Sebat J: Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009, 19 (9): 1586-1592. 10.1101/gr.092981.109.
Article
CAS
PubMed Central
PubMed
Google Scholar
Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, Vives L, Tsang P, Bruhn L, Eichler EE: Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet. 2011, 88 (3): 317-332. 10.1016/j.ajhg.2011.02.004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A: Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics. 2012, 28 (21): 2711-2718. 10.1093/bioinformatics/bts535.
Article
CAS
PubMed
Google Scholar
Abyzov A, Urban AE, Snyder M, Gerstein M: CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011, 21 (6): 974-984. 10.1101/gr.114876.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Szatkiewicz JP, Wang W, Sullivan PF, Sun W: Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation. Nucleic Acids Res. 2013, 41 (3): 1519-1532. 10.1093/nar/gks1363.
Article
CAS
PubMed Central
PubMed
Google Scholar
Norris BJ, Whan VA: A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Res. 2008, 18 (8): 1282-1293. 10.1101/gr.072090.107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rosengren Pielberg G, Golovko A, Sundstrom E, Curik I, Lennartsson J, Seltenhammer MH, Druml T, Binns M, Fitzsimmons C, Lindgren G, Sandberg K, Baumung R, Vetterlein M, Stromberg S, Grabherr M, Wade C, Lindblad-Toh K, Ponten F, Heldin CH, Solkner J, Andersson L: A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nat Genet. 2008, 40 (8): 1004-1009. 10.1038/ng.185.
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, Andersson L: 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
Dorshorst B, Molin AM, Rubin CJ, Johansson AM, Stromstedt L, Pham MH, Chen CF, Hallbook F, Ashwell C, Andersson L: A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. 2011, 7 (12): e1002412-10.1371/journal.pgen.1002412.
Article
CAS
PubMed Central
PubMed
Google Scholar
Elferink MG, Vallee AA, Jungerius AP, Crooijmans RP, Groenen MA: Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics. 2008, 9: 391-10.1186/1471-2164-9-391.
Article
PubMed Central
PubMed
Google Scholar
Jia X, Chen S, Zhou H, Li D, Liu W, Yang N: Copy number variations identified in the chicken using a 60 K SNP BeadChip. Anim Genet. 2013, 44 (3): 276-284. 10.1111/age.12009.
Article
CAS
PubMed
Google Scholar
Tian M, Wang Y, Gu X, Feng C, Fang S, Hu X, Li N: Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization. BMC Genomics. 2013, 14 (1): 262-10.1186/1471-2164-14-262.
Article
CAS
PubMed Central
PubMed
Google Scholar
Crooijmans RP, Fife MS, Fitzgerald TW, Strickland S, Cheng HH, Kaiser P, Redon R, Groenen MA: Large scale variation in DNA copy number in chicken breeds. BMC Genomics. 2013, 14: 398-10.1186/1471-2164-14-398.
Article
PubMed Central
PubMed
Google Scholar
Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RP, Groenen MA, Deryusheva S, Gaginskaya E, Carre W, Waddington D, Talbot R, Volker M, Masabanda JS, Burt DW: Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics. 2008, 9: 168-10.1186/1471-2164-9-168.
Article
PubMed Central
PubMed
Google Scholar
Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH: Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol Evol. 2013, 5 (7): 1376-1392. 10.1093/gbe/evt097.
Article
PubMed Central
PubMed
Google Scholar
Qu L, Li X, Xu G, Chen K, Yang H, Zhang L, Wu G, Hou Z, Yang N: Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. Sci China C Life Sci. 2006, 49 (4): 332-341. 10.1007/s11427-006-2001-6.
Article
CAS
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
CAS
PubMed Central
PubMed
Google Scholar
Luo J, Yu Y, Mitra A, Chang S, Zhang H, Liu G, Yang N, Song J: Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek’s disease. G3 (Bethesda). 2013, 3 (2): 217-223. 2013.
Article
Google Scholar
Wang X, Nahashon S, Feaster TK, Bohannon-Stewart A, Adefope N: An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics. 2010, 11: 351-10.1186/1471-2164-11-351.
Article
PubMed Central
PubMed
Google Scholar
Abernathy J, Li X, Jia X, Chou W, Lamont SJ, Crooijmans R, Zhou H: Copy number variation in fayoumi and leghorn chickens analyzed using array comparative genomic hybridization. Anim Genet. 2014, 45 (3): 400-411. 10.1111/age.12141.
Article
CAS
PubMed
Google Scholar
Munoz-Amatriain M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N: Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 2013, 14 (6): R58-10.1186/gb-2013-14-6-r58.
Article
PubMed Central
PubMed
Google Scholar
Skinner BM, Al Mutery A, Smith D, Volker M, Hojjat N, Raja S, Trim S, Houde P, Boecklen WJ, Griffin DK: Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization. Chromosome Res. 2014, 22 (1): 59-70. 10.1007/s10577-014-9405-0.
Article
CAS
PubMed
Google Scholar
Clop A, Vidal O, Amills M: Copy number variation in the genomes of domestic animals. Anim Genet. 2012, 43 (5): 503-517. 10.1111/j.1365-2052.2012.02317.x.
Article
CAS
PubMed
Google Scholar
Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H, Ding X, Liu J, Zhang Q: Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics. 2013, 14: 131-10.1186/1471-2164-14-131.
Article
CAS
PubMed Central
PubMed
Google Scholar
Burt DW: Chicken genome: current status and future opportunities. Genome Res. 2005, 15 (12): 1692-1698. 10.1101/gr.4141805.
Article
CAS
PubMed
Google Scholar
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. 10.1038/ng1697.
Article
CAS
PubMed
Google Scholar
International Chicken Genome Sequencing Consortium: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004, 432 (7018): 695-716. 10.1038/nature03154.
Article
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
CAS
PubMed Central
PubMed
Google Scholar
Lee C, Iafrate AJ, Brothman AR: Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet. 2007, 39 (7 Suppl): S48-S54.
Article
CAS
PubMed
Google Scholar
Greenwold MJ, Sawyer RH: Genomic organization and molecular phylogenies of the beta (beta) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution. BMC Evol Biol. 2010, 10: 148-10.1186/1471-2148-10-148.
Article
PubMed Central
PubMed
Google Scholar
Wang-Rodriguez J, Dreilinger AD, Alsharabi GM, Rearden A: The signaling adapter protein PINCH is up-regulated in the stroma of common cancers, notably at invasive edges. Cancer. 2002, 95 (6): 1387-1395. 10.1002/cncr.10878.
Article
CAS
PubMed
Google Scholar
Chen K, Tu Y, Zhang Y, Blair HC, Zhang L, Wu C: PINCH-1 regulates the ERK-Bim pathway and contributes to apoptosis resistance in cancer cells. J Biol Chem. 2008, 283 (5): 2508-2517. 10.1074/jbc.M707307200.
Article
CAS
PubMed
Google Scholar
Metcalf D, Greenhalgh CJ, Viney E, Willson TA, Starr R, Nicola NA, Hilton DJ, Alexander WS: Gigantism in mice lacking suppressor of cytokine signalling-2. Nature. 2000, 405 (6790): 1069-1073. 10.1038/35016611.
Article
CAS
PubMed
Google Scholar
Lorentzon M, Greenhalgh CJ, Mohan S, Alexander WS, Ohlsson C: Reduced bone mineral density in SOCS-2-deficient mice. Pediatr Res. 2005, 57 (2): 223-226. 10.1203/01.PDR.0000148735.21084.D3.
Article
CAS
PubMed
Google Scholar
Brand T: The Popeye domain-containing gene family. Cell Biochem Biophys. 2005, 43 (1): 95-103. 10.1385/CBB:43:1:095.
Article
CAS
PubMed
Google Scholar
Andree B, Hillemann T, Kessler-Icekson G, Schmitt-John T, Jockusch H, Arnold HH, Brand T: Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart. Dev Biol. 2000, 223 (2): 371-382. 10.1006/dbio.2000.9751.
Article
CAS
PubMed
Google Scholar
Hincke MT, Nys Y, Gautron J, Mann K, Rodriguez-Navarro AB, McKee MD: The eggshell: structure, composition and mineralization. Front Biosci (Landmark Ed). 2012, 17: 1266-1280. 10.2741/3985.
Article
CAS
Google Scholar
Gokcumen O, Babb PL, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark AG, Johnson WE, Lee C: Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. Genome Biol. 2011, 12 (5): R52-10.1186/gb-2011-12-5-r52.
Article
PubMed Central
PubMed
Google Scholar
Patel RK, Jain M: NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012, 7 (2): e30619-10.1371/journal.pone.0030619.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ: The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014, 42 (Database issue): D764-770-
Google Scholar
Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009, 4 (1): 44-57.
Article
CAS
Google Scholar
Hu ZL, Park CA, Wu XL, Reecy JM: Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res. 2013, 41 (Database issue): D871-D879.
Article
CAS
PubMed Central
PubMed
Google Scholar