ウシのコピー数多型

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Published in動物遺伝育種研究 Vol. 44; no. 2; pp. 59 - 68
Main Author 佐々木, 慎二
Format Journal Article
LanguageJapanese
Published 日本動物遺伝育種学会 2016
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ISSN1345-9961
1884-3883
DOI10.5924/abgri.44.59

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Author 佐々木, 慎二
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  organization: 公益社団法人畜産技術協会附属動物遺伝研究所 福島県西白河郡西郷村大字小田倉字小田倉原1
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References Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H, Ding X, Liu J, Zhang Q. 2013. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics, 14:131.
Sasaki S, Watanabe T, Nishimura S, Sugimoto Y. 2016. Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle. BMC Genetics, 17:26.
Liu GE, Brown T, Hebert DA, Cardone MF, Hou Y, Choudhary RK, Shaffer J, Amazu C, Connor EE, Ventura M, Gasbarre LC. 2010. Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Mammalian Genome, 22:111-121.
Whale AS, Huggett JF, Cowen S, Speirs V, Shaw J, Ellison S, Foy CA, Scott DJ. 2012. Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation. Nucleic Acids Research, 40:e82.
Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. 2007. Diet and the evolution of human amylase gene copy number variation. Nature Genetics, 39:1256-1260.
Pausch H, Venhoranta H, Wurmser C, Hakala K, Iso-Touru T, Sironen A, Vingborg RK, Lohi H, Soderquist L, Fries R, Andersson M. 2016. A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle. BMC Genetics, 17:49.
McDaneld TG, Kuehn LA, Thomas MG, Pollak EJ, Keele JW. 2014. Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle. Journal of Animal Science, 92:1378-1384.
Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics, 156:297-304.
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, 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, 444:444-454.
Rubin CJ, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg O, Jern P, Jorgensen CB, Archibald AL, Fredholm M, Groenen MA, Andersson L. 2012. Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences of the United States of America, 109:19529-19536.
河合康洋 . 2016. ゲノム編集技術の現状と可能性 . The Journal of Animal Genetics, 44:23-34.
Hastings PJ, Lupski JR, Rosenberg SM, Ira G. 2009. Mechanisms of change in gene copy number. Nature Reviews: Genetics, 10:551-564.
Borge KS, Nord S, Van Loo P, Lingjaerde OC, Gunnes G, Alnaes GI, Solvang HK, Luders T, Kristensen VN, Borresen-Dale AL, Lingaas F. 2015. Canine Mammary Tumours Are Affected by Frequent Copy Number Aberrations, including Amplification of MYC and Loss of PTEN. PloS One, 10:e0126371.
Kondrashov AS. 2003. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation, 21:12-27.
Liburd N, Ghosh M, Riazuddin S, Naz S, Khan S, Ahmed Z, Liang Y, Menon PS, Smith T, Smith AC, Chen KS, Lupski JR, Wilcox ER, Potocki L, Friedman TB. 2001. Novel mutations of MYO15A associated with profound deafness in consanguineous families and moderately severe hearing loss in a patient with Smith-Magenis syndrome. Human Genetics, 109:535-541.
Hirano T, Hirotsune S, Sasaki S, Kikuchi T, Sugimoto Y. 2002. A new deletion mutation in bovine Claudin-16 (CL-16) deficiency and diagnosis. Animal Genetics, 33:118-122.
Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, Krauss RM, Myers RM, Ridker PM, Chasman DI, Mefford H, Ying P, Nickerson DA, Eichler EE. 2009. Population analysis of large copy number variants and hotspots of human genetic disease. American Journal of Human Genetics, 84:148-161.
Fridman C, Hosomi N, Varela MC, Souza AH, Fukai K, Koiffmann CP. 2003. Angelman syndrome associated with oculocutaneous albinism due to an intragenic deletion of the P gene. American Journal of Medical Genetics. Part A, 119A:180-183.
Feuk L, Carson AR, Scherer SW. 2006. Structural variation in the human genome. Nature Reviews: Genetics, 7:85-97.
Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vila C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. 2014. Genome sequencing highlights the dynamic early history of dogs. PLos Genetics, 10:e1004016.
Lupski JR. 2007. Genomic rearrangements and sporadic disease. Nature Genetics, 39:S43-47.
渡邊敏夫 . 2016. 黒毛和種経済形質のゲノム育種価評価 . The Journal of Animal Genetics, 44:3-10.
Gu W, Zhang F, Lupski JR. 2008. Mechanisms for human genomic rearrangements. Pathogenetics, 1:4.
Hou Y, Bickhart DM, Chung H, Hutchison JL, Norman HD, Connor EE, Liu GE. 2012a. Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake. Functional & Integrative Genomics, 12:717-723.
Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brondum RF, Liao X, Djari A, Rodriguez SC, Grohs C, Esquerre D, Bouchez O, Rossignol MN, Klopp C, Rocha D, Fritz S, Eggen A, Bowman PJ, Coote D, Chamberlain AJ, Anderson C, VanTassell CP, Hulsegge I, Goddard ME, Guldbrandtsen B, Lund MS, Veerkamp RF, Boichard DA, Fries R, Hayes BJ. 2014. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 46:858-865.
Lupski JR, Stankiewicz P. 2005. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLos Genetics, 1:e49.
Ragoussis J. 2006. Genotyping technologies for all. Drug Discovery Today: Technologies, 3:115-122.
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science, 305:525-528.
Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP, Liu GE. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics, 15:683.
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 Research, 17:1665-1674.
Lee ST, Nicholls RD, Bundey S, Laxova R, Musarella M, Spritz RA. 1994. Mutations of the P gene in oculocutaneous albinism, ocular albinism, and Prader-Willi syndrome plus albinism. New England Journal of Medicine, 330:529-534.
Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, DeNise S, Wiggans GR, Sonstegard TS, Van Tassell CP, Liu GE. 2012b. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics, 13:376.
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. American Journal of Human Genetics, 77:78-88.
Zhao M, Wang Q, Jia P, Zhao Z. 2014. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics, 14 Suppl 11:S1.
Lynch M. 2010. Rate, molecular spectrum, and consequences of human mutation. Proceedings of the National Academy of Sciences of the United States of America, 107:961-968.
Flipsen-ten Berg K, van Hasselt PM, Eleveld MJ, van der Wijst SE, Hol FA, de Vroede MA, Beemer FA, Hochstenbach PF, Poot M. 2007. Unmasking of a hemizygous WFS1 gene mutation by a chromosome 4p deletion of 8.3 Mb in a patient with Wolf-Hirschhorn syndrome. European Journal of Human Genetics, 15:1132-1138.
Kunz E, Rothammer S, Pausch H, Schwarzenbacher H, Seefried FR, Matiasek K, Seichter D, Russ I, Fries R, Medugorac I. 2016. Confirmation of a non-synonymous SNP in PNPLA8 as a candidate causal mutation for Weaver syndrome in Brown Swiss cattle. Genetics Selection Evolution, 48:21.
Alkan C, Coe BP, Eichler EE. 2011. Genome structural variation discovery and genotyping. Nature Reviews: Genetics, 12:363-376.
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 Research, 10:659-663.
Zhang Q, Ma Y, Wang X, Zhang Y, Zhao X. 2015. Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. Molecular Genetics and Genomics, 290:319-327.
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. Nature Genetics, 36:949-951.
Zhang F, Gu W, Hurles ME, Lupski JR. 2009. Copy number variation in human health, disease, and evolution. Annual Review of Genomics and Human Genetics, 10:451-481.
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, 68:229-236.
References_xml – reference: Lynch M. 2010. Rate, molecular spectrum, and consequences of human mutation. Proceedings of the National Academy of Sciences of the United States of America, 107:961-968.
– reference: Pausch H, Venhoranta H, Wurmser C, Hakala K, Iso-Touru T, Sironen A, Vingborg RK, Lohi H, Soderquist L, Fries R, Andersson M. 2016. A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle. BMC Genetics, 17:49.
– reference: Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, Krauss RM, Myers RM, Ridker PM, Chasman DI, Mefford H, Ying P, Nickerson DA, Eichler EE. 2009. Population analysis of large copy number variants and hotspots of human genetic disease. American Journal of Human Genetics, 84:148-161.
– reference: Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP, Liu GE. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics, 15:683.
– reference: Sasaki S, Watanabe T, Nishimura S, Sugimoto Y. 2016. Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle. BMC Genetics, 17:26.
– reference: Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. 2007. Diet and the evolution of human amylase gene copy number variation. Nature Genetics, 39:1256-1260.
– reference: Kondrashov AS. 2003. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation, 21:12-27.
– reference: Fridman C, Hosomi N, Varela MC, Souza AH, Fukai K, Koiffmann CP. 2003. Angelman syndrome associated with oculocutaneous albinism due to an intragenic deletion of the P gene. American Journal of Medical Genetics. Part A, 119A:180-183.
– reference: Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics, 156:297-304.
– reference: Feuk L, Carson AR, Scherer SW. 2006. Structural variation in the human genome. Nature Reviews: Genetics, 7:85-97.
– reference: Zhao M, Wang Q, Jia P, Zhao Z. 2014. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics, 14 Suppl 11:S1.
– reference: Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H, Ding X, Liu J, Zhang Q. 2013. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics, 14:131.
– reference: Lupski JR, Stankiewicz P. 2005. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLos Genetics, 1:e49.
– reference: 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 Research, 17:1665-1674.
– reference: Lupski JR. 2007. Genomic rearrangements and sporadic disease. Nature Genetics, 39:S43-47.
– reference: Rubin CJ, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg O, Jern P, Jorgensen CB, Archibald AL, Fredholm M, Groenen MA, Andersson L. 2012. Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences of the United States of America, 109:19529-19536.
– reference: Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brondum RF, Liao X, Djari A, Rodriguez SC, Grohs C, Esquerre D, Bouchez O, Rossignol MN, Klopp C, Rocha D, Fritz S, Eggen A, Bowman PJ, Coote D, Chamberlain AJ, Anderson C, VanTassell CP, Hulsegge I, Goddard ME, Guldbrandtsen B, Lund MS, Veerkamp RF, Boichard DA, Fries R, Hayes BJ. 2014. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 46:858-865.
– reference: Hirano T, Hirotsune S, Sasaki S, Kikuchi T, Sugimoto Y. 2002. A new deletion mutation in bovine Claudin-16 (CL-16) deficiency and diagnosis. Animal Genetics, 33:118-122.
– reference: 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. Nature Genetics, 36:949-951.
– reference: Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, DeNise S, Wiggans GR, Sonstegard TS, Van Tassell CP, Liu GE. 2012b. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics, 13:376.
– reference: Zhang Q, Ma Y, Wang X, Zhang Y, Zhao X. 2015. Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. Molecular Genetics and Genomics, 290:319-327.
– reference: Hou Y, Bickhart DM, Chung H, Hutchison JL, Norman HD, Connor EE, Liu GE. 2012a. Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake. Functional & Integrative Genomics, 12:717-723.
– reference: Lee ST, Nicholls RD, Bundey S, Laxova R, Musarella M, Spritz RA. 1994. Mutations of the P gene in oculocutaneous albinism, ocular albinism, and Prader-Willi syndrome plus albinism. New England Journal of Medicine, 330:529-534.
– reference: Gu W, Zhang F, Lupski JR. 2008. Mechanisms for human genomic rearrangements. Pathogenetics, 1:4.
– reference: Ragoussis J. 2006. Genotyping technologies for all. Drug Discovery Today: Technologies, 3:115-122.
– reference: Whale AS, Huggett JF, Cowen S, Speirs V, Shaw J, Ellison S, Foy CA, Scott DJ. 2012. Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation. Nucleic Acids Research, 40:e82.
– reference: 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, 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, 444:444-454.
– reference: Flipsen-ten Berg K, van Hasselt PM, Eleveld MJ, van der Wijst SE, Hol FA, de Vroede MA, Beemer FA, Hochstenbach PF, Poot M. 2007. Unmasking of a hemizygous WFS1 gene mutation by a chromosome 4p deletion of 8.3 Mb in a patient with Wolf-Hirschhorn syndrome. European Journal of Human Genetics, 15:1132-1138.
– reference: Kunz E, Rothammer S, Pausch H, Schwarzenbacher H, Seefried FR, Matiasek K, Seichter D, Russ I, Fries R, Medugorac I. 2016. Confirmation of a non-synonymous SNP in PNPLA8 as a candidate causal mutation for Weaver syndrome in Brown Swiss cattle. Genetics Selection Evolution, 48:21.
– reference: Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science, 305:525-528.
– reference: 河合康洋 . 2016. ゲノム編集技術の現状と可能性 . The Journal of Animal Genetics, 44:23-34.
– reference: McDaneld TG, Kuehn LA, Thomas MG, Pollak EJ, Keele JW. 2014. Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle. Journal of Animal Science, 92:1378-1384.
– reference: Liburd N, Ghosh M, Riazuddin S, Naz S, Khan S, Ahmed Z, Liang Y, Menon PS, Smith T, Smith AC, Chen KS, Lupski JR, Wilcox ER, Potocki L, Friedman TB. 2001. Novel mutations of MYO15A associated with profound deafness in consanguineous families and moderately severe hearing loss in a patient with Smith-Magenis syndrome. Human Genetics, 109:535-541.
– reference: Hastings PJ, Lupski JR, Rosenberg SM, Ira G. 2009. Mechanisms of change in gene copy number. Nature Reviews: Genetics, 10:551-564.
– reference: Liu GE, Brown T, Hebert DA, Cardone MF, Hou Y, Choudhary RK, Shaffer J, Amazu C, Connor EE, Ventura M, Gasbarre LC. 2010. Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Mammalian Genome, 22:111-121.
– reference: Borge KS, Nord S, Van Loo P, Lingjaerde OC, Gunnes G, Alnaes GI, Solvang HK, Luders T, Kristensen VN, Borresen-Dale AL, Lingaas F. 2015. Canine Mammary Tumours Are Affected by Frequent Copy Number Aberrations, including Amplification of MYC and Loss of PTEN. PloS One, 10:e0126371.
– reference: 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. American Journal of Human Genetics, 77:78-88.
– reference: 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 Research, 10:659-663.
– reference: Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vila C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. 2014. Genome sequencing highlights the dynamic early history of dogs. PLos Genetics, 10:e1004016.
– reference: 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, 68:229-236.
– reference: Zhang F, Gu W, Hurles ME, Lupski JR. 2009. Copy number variation in human health, disease, and evolution. Annual Review of Genomics and Human Genetics, 10:451-481.
– reference: 渡邊敏夫 . 2016. 黒毛和種経済形質のゲノム育種価評価 . The Journal of Animal Genetics, 44:3-10.
– reference: Alkan C, Coe BP, Eichler EE. 2011. Genome structural variation discovery and genotyping. Nature Reviews: Genetics, 12:363-376.
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