Functional & Integrative Genomics

, Volume 12, Issue 4, pp 609–624 | Cite as

Copy number variation in the cattle genome

Review

Abstract

Copy number variations (CNVs) are gains and losses of genomic sequence greater than 50 bp between two individuals of a species. While single nucleotide polymorphisms (SNPs) are more frequent, CNVs impact a higher percentage of genomic sequence and have potentially greater effects, including the changing of gene structure and dosage, altering gene regulation and exposing recessive alleles. In particular, segmental duplications (SDs) were shown to be one of the catalysts and hotspots for CNV formation. Substantial progress has been made in understanding CNVs in mammals, especially in humans and rodents. CNVs have been shown to be important in both normal phenotypic variability and disease susceptibility. Recently, interest in CNV study has extended into domesticated animals, including cattle. Multiple genome-wide cattle CNV studies have been carried out using both microarray and next generation sequencing technologies. Integration of SD and CNV results with SNP and other datasets are beginning to reveal impacts of CNVs on cattle domestication, health, and production traits.

Keywords

Cattle genome Breed Copy number variation Segmental duplication Array comparative genomic hybridization Next-generation sequencing 

References

  1. Agam A, Yalcin B, Bhomra A, Cubin M, Webber C, Holmes C, Flint J, Mott R (2010) Elusive copy number variation in the mouse genome. PLoS One 5:9CrossRefGoogle Scholar
  2. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 19:1622–1629PubMedCrossRefGoogle Scholar
  3. Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E, Hodges MD, Bhangal G, Patel SG, Sheehan-Rooney K, Duda M, Cook PR, Evans DJ, Domin J, Flint J, Boyle JJ, Pusey CD, Cook HT (2006) Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439:851–855PubMedCrossRefGoogle Scholar
  4. 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 (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41:1061–1067PubMedCrossRefGoogle Scholar
  5. Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363–375PubMedCrossRefGoogle Scholar
  6. Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu FL, Bonnen PE, de Bakker PIW, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia XM, Palotie A, Parkin M, Whittaker P, Chang K, Hawes A, Lewis LR, Ren YR, Wheeler D, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarroll SA, Nemesh J, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Gonzaga-Jauregui C, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Zhang QR, Ghori MJR, McGinnis R, McLaren W, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng CQ, Brooks LD, Mcewen JE (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467:52–58PubMedCrossRefGoogle Scholar
  7. Alvarez CE, Akey JM (2012) Copy number variation in the domestic dog. Mamm Genome 23:144–163PubMedCrossRefGoogle Scholar
  8. Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, Chun JY, Kim JY, Pasaje CF, Lee JS, Shin HD (2010) Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 11:232PubMedCrossRefGoogle Scholar
  9. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 11:1005–1017PubMedCrossRefGoogle Scholar
  10. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE (2002) Recent segmental duplications in the human genome. Science 297:1003–1007PubMedCrossRefGoogle Scholar
  11. 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 CR, 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, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E, Catenazzi S, Chang CR, Neil NR, Crake OO, Dada KD, Diakoumakos B, Dominguez-Fernandez DJ, Earnshaw UC, Egbujor DW, Elmore SS, Etchin MR, Ewan M, Fedurco LJ, Fraser KV, Fuentes Fajardo FW, Scott D, George KJ, Gietzen CP, Goddard GS, Golda PA, Granieri DE, Green DL, Gustafson NF, Hansen K, Harnish CD, Haudenschild NI, Heyer MM, Hims JT, Ho AM, Horgan K, Hoschler S, Hurwitz DV, Ivanov MQ, Johnson T, James TA, Huw Jones GD, Kang TH, Kerelska AD, Kersey I, Khrebtukova AP, Kindwall Z, Kingsbury PI, Kokko-Gonzales A, Kumar MA, Laurent CT, Lawley SE, Lee X, Lee AK, Liao JA, Loch M, Lok S, Luo RM, Mammen JW, Martin PG, McCauley P, McNitt P, Mehta KW, Moon JW, Mullens T, Newington Z, Ning NB, Ling SM, Novo MJ, O'Neill MA, Osborne A, Osnowski O, Ostadan LL, Paraschos L, Pickering AC, Pike AC, Pike PD, Chris DP, Pliskin J, Podhasky VJ, Quijano C, Raczy VH, Rae SR, Rawlings RA, Chiva PM, Roe J, Rogers MC, Rogert Bacigalupo N, Romanov A, Romieu RK, Roth NJ, Rourke ST, Ruediger E, Rusman RM, Sanches-Kuiper MR, Schenker JM, Seoane RJ, Shaw MK, Shiver SW, Short NL, Sizto JP, Sluis MA, Smith SJ, Ernest Sohna EJ, Spence K, Stevens N, Sutton L, Szajkowski CL, Tregidgo G, Turcatti S, Vandevondele Y, Verhovsky SM, Virk S, Wakelin GC, Walcott J, Wang GJ, Worsley J, Yan L, Yau M, Zuerlein J, Rogers JC, Mullikin ME, Hurles NJ, McCooke JS, West FL, Oaks PL, Lundberg D, Klenerman RD, Smith AJ (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59PubMedCrossRefGoogle Scholar
  12. 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 (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22:778–790PubMedCrossRefGoogle Scholar
  13. 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 (2009) Large, rare chromosomal deletions associated with severe early-onset obesity. Nature 463:666–670PubMedCrossRefGoogle Scholar
  14. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18:810–820PubMedCrossRefGoogle Scholar
  15. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722–729PubMedCrossRefGoogle Scholar
  16. Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, Vives L, Tsang P, Bruhn L, Eichler EE (2011) Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet 88:317–332PubMedCrossRefGoogle Scholar
  17. Chaisson MJ, Brinza D, Pevzner PA (2009) De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res 19:336–346PubMedCrossRefGoogle Scholar
  18. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER (2009a) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681PubMedCrossRefGoogle Scholar
  19. Chen WK, Swartz JD, Rush LJ, Alvarez CE (2009b) Mapping DNA structural variation in dogs. Genome Res 19:500–509PubMedCrossRefGoogle Scholar
  20. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, deJong P, Wilson RK, Paabo S, Rocchi M, Eichler EE (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437:88–93PubMedCrossRefGoogle Scholar
  21. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6:99–103PubMedCrossRefGoogle Scholar
  22. Church DM, Lappalainen I, Sneddon TP, Hinton J, Maguire M, Lopez J, Garner J, Paschall J, DiCuccio M, Yaschenko E, Scherer SW, Feuk L, Flicek P (2010) Public data archives for genomic structural variation. Nat Genet 42:813–814PubMedCrossRefGoogle Scholar
  23. 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 35:2013–2025PubMedCrossRefGoogle Scholar
  24. Conrad DF, Hurles ME (2007) The population genetics of structural variation. Nat Genet 39:S30–S36PubMedCrossRefGoogle Scholar
  25. 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 464:704–712PubMedCrossRefGoogle Scholar
  26. Cook EH Jr, Scherer SW (2008) Copy-number variations associated with neuropsychiatric conditions. Nature 455:919–923PubMedCrossRefGoogle Scholar
  27. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464:713–720PubMedCrossRefGoogle Scholar
  28. de Vries BBA, Pfundt R, Leisink M, Koolen DA, Vissers LELM, Janssen IM, van Reijmersdal S, Nillesen WM, Huys EHLP, De Leeuw N, Smeets D, Sistermans EA, Feuth T, Ravenswaaij-Arts CMA, van Kessel AG, Schoenmakers EFPM, Brunner HG, Veltman JA (2005) Diagnostic genome profiling in mental retardation. Am J Hum Genet 77:606–616PubMedCrossRefGoogle Scholar
  29. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464:999–1005PubMedCrossRefGoogle Scholar
  30. 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 459:987–991PubMedCrossRefGoogle Scholar
  31. Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17:1697–1706PubMedCrossRefGoogle Scholar
  32. Dreger DL, Schmutz SM (2010) The variant red coat colour phenotype of Holstein cattle maps to BTA27. Anim Genet 41:109–112PubMedCrossRefGoogle Scholar
  33. Drogemuller C, Distl O, Leeb T (2001) Partial deletion of the bovine ED1 gene causes anhidrotic ectodermal dysplasia in cattle. Genome Res 11:1699–1705PubMedCrossRefGoogle Scholar
  34. Durkin K, Coppieters W, Drogemuller C, Ahariz N, Cambisano N, Druet T, Fasquelle C, Haile A, Horin P, Huang L, Kamatani Y, Karim L, Lathrop M, Moser S, Oldenbroek K, Rieder S, Sartelet A, Solkner J, Stalhammar H, Zelenika D, Zhang Z, Leeb T, Georges M, Charlier C (2012) Serial translocation by means of circular intermediates underlies colour sidedness in cattle. Nature 482:81–84PubMedCrossRefGoogle Scholar
  35. Estivill X, Armengol L (2007) Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PLoS Genet 3:1787–1799PubMedCrossRefGoogle Scholar
  36. Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C (2008) A snapshot of CNVs in the pig genome. PLoS One 3:12CrossRefGoogle Scholar
  37. Fadista J, Thomsen B, Holm LE, Bendixen C (2010) Copy number variation in the bovine genome. BMC Genomics 11:284PubMedCrossRefGoogle Scholar
  38. Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SC, de Smith A, Blakemore AI, Froguel P, Owen CJ, Pearce SH, Teixeira L, Guillevin L, Graham DS, Pusey CD, Cook HT, Vyse TJ, Aitman TJ (2007) FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet 39:721–723PubMedCrossRefGoogle Scholar
  39. Fellermann K, Stange DE, Schaeffeler E, Schmalzl H, Wehkamp J, Bevins CL, Reinisch W, Teml A, Schwab M, Lichter P, Radlwimmer B, Stange EF (2006) A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to crohn disease of the colon. Am J Hum Genet 79:439–448PubMedCrossRefGoogle Scholar
  40. Flicek P, Birney E (2009) Sense from sequence reads: methods for alignment and assembly. Nat Methods 6:S6–S12PubMedCrossRefGoogle Scholar
  41. Flisikowski K, Venhoranta H, Nowacka-Woszuk J, McKay SD, Flyckt A, Taponen J, Schnabel R, Schwarzenbacher H, Szczerbal I, Lohi H, Fries R, Taylor JF, Switonski M, Andersson M (2010) 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 5:11CrossRefGoogle Scholar
  42. Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'olio S, Colombo M, Casadio R, Russo V, Portolano B (2010) An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics 11:639PubMedCrossRefGoogle Scholar
  43. Fontanesi L, Beretti F, Martelli PL, Colombo M, Dall'olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V (2011) A first comparative map of copy number variations in the sheep genome. Genomics 97:158–165PubMedCrossRefGoogle Scholar
  44. 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 459:569–573PubMedCrossRefGoogle Scholar
  45. Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ (2007) A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3:e3PubMedCrossRefGoogle Scholar
  46. Guryev V, Saar K, Adamovic T, Verheul M, van Heesch SA, Cook S, Pravenec M, Aitman T, Jacob H, Shull JD, Hubner N, Cuppen E (2008) Distribution and functional impact of DNA copy number variation in the rat. Nat Genet 40:538–545PubMedCrossRefGoogle Scholar
  47. Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC (2010) mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat methods 7:576–577PubMedCrossRefGoogle Scholar
  48. Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC (2010) Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26:1277–1283PubMedCrossRefGoogle Scholar
  49. Handsaker RE, Korn JM, Nemesh J, McCarroll SA (2011) Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet 43:269–276PubMedCrossRefGoogle Scholar
  50. Henrichsen CN, Chaignat E, Reymond A (2009) Copy number variants, diseases and gene expression. Hum Mol Genet 18:R1–R8PubMedCrossRefGoogle Scholar
  51. Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J (2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 18:802–809PubMedCrossRefGoogle Scholar
  52. Hillbertz NHCS, Isaksson M, Karlsson EK, Hellmen E, Pielberg GR, Savolainen P, Wade CM, Von Euler H, Gustafson U, Hedhammar K, Nilsson M, Lindblad-Toh K, Andersson L, Andersson G (2007) Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in ridgeback dogs. Nat Genet 39:1318–1320CrossRefGoogle Scholar
  53. Hirano T, Kobayashi N, Itoh T, Takasuga A, Nakamaru T, Hirotsune S, Sugimoto Y (2000) Null mutation of PCLN-1/Claudin-16 results in bovine chronic interstitial nephritis. Genome Res 10:659–663PubMedCrossRefGoogle Scholar
  54. Holt RA, Jones SJ (2008) The new paradigm of flow cell sequencing. Genome Res 18:839–846PubMedCrossRefGoogle Scholar
  55. Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC (2009) Combinatorial algorithms for structural variation detection in high throughput sequenced genomes. Genome Res 19:1270–1278PubMedCrossRefGoogle Scholar
  56. Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26:i350–i357PubMedCrossRefGoogle Scholar
  57. Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasberre LC, Van Tassell CP, Sonstegard TS (2011a) Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle. Funct Integr Genomics 12:81–92PubMedCrossRefGoogle Scholar
  58. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim ES, Matukumalli LK, Ventura M, Song J, Vanradan PM, Sonstegard TS, Van Tassell CP (2011b) Genomic characteristics of cattle copy number variations. BMC Genomics 12:127PubMedCrossRefGoogle Scholar
  59. 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 36:949–951PubMedCrossRefGoogle Scholar
  60. Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23:2942–2944PubMedCrossRefGoogle Scholar
  61. Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA, Eichler EE (2011) Detection of structural variants and indels within exome data. Nat Meth 9:176–178CrossRefGoogle Scholar
  62. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453:56–64PubMedCrossRefGoogle Scholar
  63. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, Kallicki J, Anderson P, Tsalenko A, Yamada NA, Tsang P, Kaul R, Wilson RK, Bruhn L, Eichler EE (2010) Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods 7:365–371PubMedCrossRefGoogle Scholar
  64. Kijas JW, Barendse W, Barris W, Harrison B, McCulloch R, McWilliam S, Whan V (2011) Analysis of copy number variants in the cattle genome. Gene 482:73–77PubMedCrossRefGoogle Scholar
  65. 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, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, 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, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011–1015PubMedGoogle Scholar
  66. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318:420–426PubMedCrossRefGoogle Scholar
  67. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol 10:R23PubMedCrossRefGoogle Scholar
  68. LaFramboise T (2009) Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 37:4181–4193PubMedCrossRefGoogle Scholar
  69. Lai WR, Johnson MD, Kucherlapati R, Park PJ (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21:3763–3770PubMedCrossRefGoogle Scholar
  70. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25PubMedCrossRefGoogle Scholar
  71. Le Marechal C, Masson E, Chen JM, Morel F, Ruszniewski P, Levy P, Ferec C (2006) Hereditary pancreatitis caused by triplication of the trypsinogen locus. Nat Genet 38:1372–1374PubMedCrossRefGoogle Scholar
  72. Le Scouarnec S, Gribble SM (2012) Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity (Edinb) 108:75–85CrossRefGoogle Scholar
  73. Lee S, Hormozdiari F, Alkan C, Brudno M (2009) MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods 6:473–474PubMedCrossRefGoogle Scholar
  74. 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:e254PubMedCrossRefGoogle Scholar
  75. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456:66–72PubMedCrossRefGoogle Scholar
  76. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858PubMedCrossRefGoogle Scholar
  77. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967PubMedCrossRefGoogle Scholar
  78. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272PubMedCrossRefGoogle Scholar
  79. Lindsay SJ, Khajavi M, Lupski JR, Hurles ME (2006) A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am J Hum Genet 79:890–902PubMedCrossRefGoogle Scholar
  80. Liu GE, Van Tassell CP, Sonstegard TS, Li RW, Alexander LJ, Keele JW, Matukumalli LK, Smith TP, Gasbarre LC (2008) Detection of germline and somatic copy number variations in cattle. Dev Biol 132:231–237Google Scholar
  81. Liu GE, Ventura M, Cellamare A, Chen L, Cheng Z, Zhu B, Li C, Song J, Eichler EE (2009) Analysis of recent segmental duplications in the bovine genome. BMC Genomics 10:571PubMedCrossRefGoogle Scholar
  82. 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 LCD, Smith TPL, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res 20:693–703PubMedCrossRefGoogle Scholar
  83. Liu GE, Brown T, Hebert DA, Cardone MF, Hou YL, Choudhary RK, Shaffer J, Amazu C, Connor EE, Ventura M, Gasbarre LC (2011) Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Mamm Genome 22:111–121PubMedCrossRefGoogle Scholar
  84. Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM, Eichler EE (2006) Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet 79:275–290PubMedCrossRefGoogle Scholar
  85. 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 461:747–753PubMedCrossRefGoogle Scholar
  86. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141PubMedCrossRefGoogle Scholar
  87. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361:1058–1066PubMedCrossRefGoogle Scholar
  88. Marques-Bonet T, Girirajan S, Eichler EE (2009) The origins and impact of primate segmental duplications. Trends Genet 25:443–454PubMedCrossRefGoogle Scholar
  89. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TP, Sonstegard TS, Van Tassell CP (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4:e5350PubMedCrossRefGoogle Scholar
  90. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40:1166–1174PubMedCrossRefGoogle Scholar
  91. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:1527–1541PubMedCrossRefGoogle Scholar
  92. Medvedev P, Stanciu M, Brudno M (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat Meth 6:S13–S20CrossRefGoogle Scholar
  93. Meyers SN, McDaneld TG, Swist SL, Marron BM, Steffen DJ, O'Toole D, O'Connell JR, Beever JE, Sonstegard TS, Smith TPL (2010) A deletion mutation in bovine SLC4A2 is associated with osteopetrosis in Red Angus cattle. BMC Genomics 11:337PubMedCrossRefGoogle Scholar
  94. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HYK, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker J, Wu J, Zhang Y, Zhang ZD, Batzer M, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll S, Korbel JO (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470:59–65PubMedCrossRefGoogle Scholar
  95. Moller MJ, Chaudhary R, Hellmen E, Hoyheim B, Chowdhary B, Andersson L (1996) Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor. Mamm Genome 7:822–830CrossRefGoogle Scholar
  96. Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM (2009) The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res 19:491–499PubMedCrossRefGoogle Scholar
  97. Nicholas TJ, Baker C, Eichler EE, Akey JM (2011) A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog. BMC Genomics 12:414PubMedCrossRefGoogle Scholar
  98. Norris BJ, Whan VA (2008) A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Res 18:1282–1293PubMedCrossRefGoogle Scholar
  99. Ohba Y, Kitagawa H, Kitoh K, Sasaki Y, Takami M, Shinkai Y, Kunieda T (2000) A deletion of the paracellin-1 gene is responsible for renal tubular dysplasia in cattle. Genomics 68:229–236PubMedCrossRefGoogle Scholar
  100. Olsson M, Meadows JRS, Truve K, Pielberg GR, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K (2011) A Novel unstable duplication upstream of has2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs. PLoS genetics 7:3CrossRefGoogle Scholar
  101. Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad D, Park H, Hurles M, Lee C, Venter JC, Kirkness E, Levy S, Feuk L, Scherer SW (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11:R52PubMedCrossRefGoogle Scholar
  102. Park CC, Ahn S, Bloom JS, Lin A, Wang RT, Wu T, Sekar A, Khan AH, Farr CJ, Lusis AJ, Leahy RM, Lange K, Smith DJ (2008) Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids. Nat Genet 40:421–429PubMedCrossRefGoogle Scholar
  103. 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, Kim H, 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 42:400–405PubMedCrossRefGoogle Scholar
  104. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL (2006) High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 16:1136–1148PubMedCrossRefGoogle Scholar
  105. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BHY, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang ZZ, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466:368–372PubMedCrossRefGoogle Scholar
  106. Pinto D, Darvishi K, Shi XH, 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 (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29:512–520PubMedCrossRefGoogle Scholar
  107. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordonez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR (2010a) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463:191–196PubMedCrossRefGoogle Scholar
  108. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordonez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ (2010b) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463:184–190PubMedCrossRefGoogle Scholar
  109. Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nat Biotechnol 27:847–852PubMedCrossRefGoogle Scholar
  110. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM (2010) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 20:623–635PubMedCrossRefGoogle Scholar
  111. Ramayo-Caldas Y, Castelló A, Pena RN, Alves E, Mercadé A, Souza CA, Fernández AI, Perez-Enciso M, Folch JM (2010) Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC. Genomics 11:593PubMedGoogle Scholar
  112. 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, Zhang J, 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 444:444–454PubMedCrossRefGoogle Scholar
  113. Rincon G, Weber KL, Van Eenennaam AL, Golden BL, Medrano JF (2011) Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 94:6116–6121PubMedCrossRefGoogle Scholar
  114. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328:636–639PubMedCrossRefGoogle Scholar
  115. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Mar+ºais G, Pop M, Yorke JA (2012) GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22:557–567PubMedCrossRefGoogle Scholar
  116. Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L (2007) Challenges and standards in integrating surveys of structural variation. Nat Genet 39:S7–S15PubMedCrossRefGoogle Scholar
  117. Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO (2011) Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Genome Res 21:2004–2013PubMedCrossRefGoogle Scholar
  118. 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 316:445–449PubMedCrossRefGoogle Scholar
  119. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, Nair P, Brothman AR, Stallings RL (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes chromosomes Cancer 44:305–319PubMedCrossRefGoogle Scholar
  120. Seroussi E, Glick G, Shirak A, Yakobson E, Weller JI, Ezra E, Zeron Y (2010) Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genomics 11:673PubMedCrossRefGoogle Scholar
  121. 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 (2005) Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77:78–88PubMedCrossRefGoogle Scholar
  122. Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJL, Eichler EE (2006) Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet 38:1038–1042PubMedCrossRefGoogle Scholar
  123. She X, Cheng Z, Zollner S, Church DM, Eichler EE (2008) Mouse segmental duplication and copy number variation. Nat Genet 40:909–914PubMedCrossRefGoogle Scholar
  124. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Crowe RR, Oksenberg JR, Mirel DB, Kendler KS, Freedman R, Gejman PV (2009) Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature 460:753–757PubMedGoogle Scholar
  125. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123PubMedCrossRefGoogle Scholar
  126. Sindi S, Helman E, Bashir A, Raphael BJ (2009) A geometric approach for classification and comparison of structural variants. Bioinformatics 25:i222–i230PubMedCrossRefGoogle Scholar
  127. Sjodin P, Jakobsson M (2012) Population genetic nature of copy number variation. Methods Mol Biol 838:209–223PubMedCrossRefGoogle Scholar
  128. Snyder M, Du J, Gerstein M (2010) Personal genome sequencing: current approaches and challenges. Genes Dev 24:423–431PubMedCrossRefGoogle Scholar
  129. Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437–455PubMedCrossRefGoogle Scholar
  130. Stefansson H, Ophoff RA, Steinberg S, Andreassen OA, Cichon S, Rujescu D, Werge T, Pietilainen OP, Mors O, Mortensen PB, Sigurdsson E, Gustafsson O, Nyegaard M, Tuulio-Henriksson A, Ingason A, Hansen T, Suvisaari J, Lonnqvist J, Paunio T, Borglum AD, Hartmann A, Fink-Jensen A, Nordentoft M, Hougaard D, Norgaard-Pedersen B, Bottcher Y, Olesen J, Breuer R, Moller HJ, Giegling I, Rasmussen HB, Timm S, Mattheisen M, Bitter I, Rethelyi JM, Magnusdottir BB, Sigmundsson T, Olason P, Masson G, Gulcher JR, Haraldsson M, Fossdal R, Thorgeirsson TE, Thorsteinsdottir U, Ruggeri M, Tosato S, Franke B, Strengman E, Kiemeney LA, Melle I, Djurovic S, Abramova L, Kaleda V, Sanjuan J, de Frutos R, Bramon E, Vassos E, Fraser G, Ettinger U, Picchioni M, Walker N, Toulopoulou T, Need AC, Ge D, Yoon JL, Shianna KV, Freimer NB, Cantor RM, Murray R, Kong A, Golimbet V, Carracedo A, Arango C, Costas J, Jonsson EG, Terenius L, Agartz I, Petursson H, Nothen MM, Rietschel M, Matthews PM, Muglia P, Peltonen L, St Clair D, Goldstein DB, Stefansson K, Collier DA (2009) Common variants conferring risk of schizophrenia. Nature 460:744–747PubMedGoogle Scholar
  131. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerod A, Russnes HE, Foekens JA, Reis-Filho JS, van Richardson VAL, Borresen-Dale AL, Campbell PJ, Futreal PA, Stratton MR (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462:1005–1010PubMedCrossRefGoogle Scholar
  132. Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao XP, Moore SS (2011) Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559PubMedCrossRefGoogle Scholar
  133. 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 315:848–853PubMedCrossRefGoogle Scholar
  134. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE (2010) Diversity of human copy number variation and multicopy genes. Science 330:641–646PubMedCrossRefGoogle Scholar
  135. Sugimoto M, Furuoka H, Sugimoto Y (2003) Deletion of one of the duplicated Hsp70 genes causes hereditary myopathy of diaphragmatic muscles in Holstein-Friesian cattle. Anim Genet 34:191–197Google Scholar
  136. The Bovine Genome Sequencing and Analysis Consortium (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522–528CrossRefGoogle Scholar
  137. The Bovine HapMap Consortium (2009) Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528–532CrossRefGoogle Scholar
  138. Turner DJ, Miretti M, Rajan D, Fiegler H, Carter NP, Blayney ML, Beck S, Hurles ME (2008) Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat Genet 40:90–95PubMedCrossRefGoogle Scholar
  139. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE (2005) Fine-scale structural variation of the human genome. Nat Genet 37:727–732PubMedCrossRefGoogle Scholar
  140. Volker M, Backstrom N, Skinner BM, Langley EJ, Bunzey SK, Ellegren H, Griffin DK (2010) Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res 20:503–511PubMedCrossRefGoogle Scholar
  141. 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 17:1665–1674PubMedCrossRefGoogle Scholar
  142. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang 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, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J (2008) The diploid genome sequence of an Asian individual. Nature 456:60–65PubMedCrossRefGoogle Scholar
  143. Wang XF, Nahashon S, Feaster TK, Bohannon-Stewart A, Adefope N (2010) An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 11:351PubMedCrossRefGoogle Scholar
  144. Welz-Voegele C, Jinks-Robertson S (2008) Sequence divergence impedes crossover more than noncrossover events during mitotic gap repair in yeast. Genetics 179:1251–1262PubMedCrossRefGoogle Scholar
  145. 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 452:872–876PubMedCrossRefGoogle Scholar
  146. Winchester L, Yau C, Ragoussis J (2009) Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic 8:353–366PubMedCrossRefGoogle Scholar
  147. Wong K, Keane TM, Stalker J, Adams DJ (2010) Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol 11:12CrossRefGoogle Scholar
  148. Wright D, Boije H, Meadows JRS, Bed'hom B, Gourichon D, Vieaud A, Tixier-Boichard Ml, Rubin CJ, Imsland F, Hallböök F, Andersson L (2009) Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS genetics 5:e1000512PubMedCrossRefGoogle Scholar
  149. Xie C, Tammi MT (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinforma 10:80CrossRefGoogle Scholar
  150. Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan XC, 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 (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477:326–329PubMedCrossRefGoogle Scholar
  151. Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, Hebert M, Jones KN, Shu Y, Kitzmiller K, Blanchong CA, McBride KL, Higgins GC, Rennebohm RM, Rice RR, Hackshaw KV, Roubey RA, Grossman JM, Tsao BP, Birmingham DJ, Rovin BH, Hebert LA, Yu CY (2007) 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 80:1037–1054PubMedCrossRefGoogle Scholar
  152. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865–2871PubMedCrossRefGoogle Scholar
  153. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19:1586–1592PubMedCrossRefGoogle Scholar
  154. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829PubMedCrossRefGoogle Scholar
  155. Zhan BJ, Fadista J, Thomsen B, Hedegaard J, Panitz F, Bendixen C (2011) Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics 12:557PubMedCrossRefGoogle Scholar
  156. Zhang F, Gu W, Hurles ME, Lupski JR (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10:451–481PubMedCrossRefGoogle Scholar
  157. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marcais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL (2009) A whole-genome assembly of the domestic cow. Bos Taurus Genome Biol 10:R42CrossRefGoogle Scholar

Copyright information

© Springer-Verlag (outside the USA) 2012

Authors and Affiliations

  1. 1.Bovine Functional Genomics LaboratoryUSDA-ARS, ANRIBeltsvilleUSA
  2. 2.GEL: Bovine Functional Genomics LaboratoryUSDA-ARSBeltsvilleUSA

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