{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T23:14:38Z","timestamp":1788304478353,"version":"build-2803163510"},"publisher-location":"New York, NY","reference-count":35,"publisher":"Springer US","isbn-type":[{"value":"9781071652831","type":"print"},{"value":"9781071652848","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-1-0716-5284-8_13","type":"book-chapter","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T22:25:29Z","timestamp":1788301529000},"page":"243-259","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Copy Number Variation Analysis"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1585-5488","authenticated-orcid":false,"given":"Haydee","family":"Artaza","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"13_CR1","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/nrg2593","volume":"10","author":"PJ Hastings","year":"2009","unstructured":"Hastings PJ, Lupski JR, Rosenberg SM, Ira G (2009) Mechanisms of change in gene copy number. Nat Rev Genet 10:551\u2013564. https:\/\/doi.org\/10.1038\/nrg2593","journal-title":"Nat Rev Genet"},{"key":"13_CR2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13624-1","volume":"11","author":"YR Li","year":"2020","unstructured":"Li YR, Glessner JT, Coe BP, Li J, Mohebnasab M, Chang X, Connolly J, Kao C, Wei Z, Bradfield J et al  (2020) Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations. Nat Commun 11:255. https:\/\/doi.org\/10.1038\/s41467-019-13624-1","journal-title":"Nat Commun"},{"key":"13_CR3","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt0993-1026","volume":"11","author":"R Higuchi","year":"1993","unstructured":"Higuchi R, Fockler C, Dollinger G, Watson R (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnol 11:1026\u20131030. https:\/\/doi.org\/10.1038\/nbt0993-1026","journal-title":"Biotechnol"},{"key":"13_CR4","doi-asserted-by":"publisher","first-page":"e57","DOI":"10.1093\/nar\/gnf056","volume":"30","author":"JP Schouten","year":"2002","unstructured":"Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G (2002) Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30:e57. https:\/\/doi.org\/10.1093\/nar\/gnf056","journal-title":"Nucleic Acids Res"},{"key":"13_CR5","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1038\/nrg3871","volume":"16","author":"M Zarrei","year":"2015","unstructured":"Zarrei M, MacDonald JR, Merico D, Scherer SW (2015) A copy number variation map of the human genome. Nat Rev Genet 16:172\u2013183. https:\/\/doi.org\/10.1038\/nrg3871","journal-title":"Nat Rev Genet"},{"key":"13_CR6","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-021-08082-3","volume":"22","author":"K Lavrichenko","year":"2021","unstructured":"Lavrichenko K, Johansson S, Jonassen I (2021) Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data. BMC Genom 22: 826. https:\/\/doi.org\/10.1186\/s12864-021-08082-3","journal-title":"BMC Genom"},{"key":"13_CR7","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1802-x","volume":"18","author":"L de Ara\u00fajo Lima","year":"2017","unstructured":"de Ara\u00fajo Lima L, Wang K (2017) PennCNV in whole-genome sequencing data. BMC Bioinform 18: 383. https:\/\/doi.org\/10.1186\/s12859-017-1802-x","journal-title":"BMC Bioinform"},{"key":"13_CR8","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-015-0047-8","volume":"4","author":"CC Chang","year":"2015","unstructured":"Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4: 7. https:\/\/doi.org\/10.1186\/s13742-015-0047-8","journal-title":"Gigascience"},{"key":"13_CR9","doi-asserted-by":"publisher","first-page":"1374499","DOI":"10.3389\/fimmu.2024.1374499","volume":"15","author":"H Artaza","year":"2024","unstructured":"Artaza H, Eriksson D, Lavrichenko K, Aranda-Guill\u00e9n M, Bratland E, Vaudel M, Knappskog P, Husebye ES, Bensing S, Wolff ASB et al  (2024) Rare copy number variation in autoimmune Addison\u2019s disease. Front Immunol 15:1374499. https:\/\/doi.org\/10.3389\/fimmu.2024.1374499","journal-title":"Front Immunol"},{"key":"13_CR10","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1002\/humu.21398","volume":"32","author":"G Marenne","year":"2011","unstructured":"Marenne G, Rodr\u00edguez-Santiago B, Closas MG, P\u00e9rez-Jurado L, Rothman N, Rico D, Pita G, Pisano DG, Kogevinas M, Silverman DT et al  (2011) Assessment of copy number variation using the illumina infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer\/EPICURO study. Hum Mutat 32:240\u2013248. https:\/\/doi.org\/10.1002\/humu.21398","journal-title":"Hum Mutat"},{"key":"13_CR11","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1038\/nbt.1852","volume":"29","author":"D Pinto","year":"2011","unstructured":"Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, MacDonald JR, Mills R et al  (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29:512\u2013520. https:\/\/doi.org\/10.1038\/nbt.1852","journal-title":"Nat Biotechnol"},{"key":"13_CR12","doi-asserted-by":"publisher","first-page":"D986","DOI":"10.1093\/nar\/gkt958","volume":"42","author":"JR MacDonald","year":"2014","unstructured":"MacDonald JR, Ziman R, Yuen RKC, Feuk L, Scherer SW (2014) The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res 42:D986\u2013D992. https:\/\/doi.org\/10.1093\/nar\/gkt958","journal-title":"Nucleic Acids Res"},{"key":"13_CR13","doi-asserted-by":"publisher","first-page":"D993","DOI":"10.1093\/nar\/gkt937","volume":"42","author":"E Bragin","year":"2014","unstructured":"Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, Swaminathan GJ (2014) DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res 42:D993\u2013D1000. https:\/\/doi.org\/10.1093\/nar\/gkt937","journal-title":"Nucleic Acids Res"},{"key":"13_CR14","doi-asserted-by":"publisher","first-page":"W216","DOI":"10.1093\/nar\/gkac194","volume":"50","author":"BT Sherman","year":"2022","unstructured":"Sherman BT, Hao M, Qiu J, Jiao X, Baseler MW, Lane HC, Imamichi T, Chang W (2022) DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res 50:W216\u2013W221. https:\/\/doi.org\/10.1093\/nar\/gkac194","journal-title":"Nucleic Acids Res"},{"key":"13_CR15","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28:27\u201330","journal-title":"Nucleic Acids Res"},{"key":"13_CR16","doi-asserted-by":"publisher","first-page":"1179877","DOI":"10.3389\/fimmu.2023.1179877","volume":"14","author":"L Peng","year":"2023","unstructured":"Peng L, Chen L, Wan J, Liu W, Lou S, Shen Z (2023) Single-cell transcriptomic landscape of immunometabolism reveals intervention candidates of ascorbate and aldarate metabolism, fatty-acid degradation and PUFA metabolism of T-cell subsets in healthy controls, psoriasis and psoriatic arthritis. Front Immunol 14:1179877. https:\/\/doi.org\/10.3389\/fimmu.2023.1179877","journal-title":"Front Immunol"},{"key":"13_CR17","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1038\/nature08979","volume":"464","author":"The Wellcome Trust Case Control Consortium","year":"2010","unstructured":"The Wellcome Trust Case Control Consortium (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464:713\u2013720. https:\/\/doi.org\/10.1038\/nature08979","journal-title":"Nature"},{"key":"13_CR18","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/ng.2607","volume":"45","author":"E Wheeler","year":"2013","unstructured":"Wheeler E, Huang N, Bochukova EG, Keogh JM, Lindsay S, Garg S, Henning E, Blackburn H, Loos RJF, Wareham NJ et al  (2013) Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. Nat Genet 45:513\u2013517. https:\/\/doi.org\/10.1038\/ng.2607","journal-title":"Nat Genet"},{"key":"13_CR19","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.ajhg.2019.07.001","volume":"105","author":"M Aguirre","year":"2019","unstructured":"Aguirre M, Rivas MA, Priest J (2019) Phenome-wide burden of copy-number variation in the UK Biobank. Am J Hum Genet 105:373\u2013383. https:\/\/doi.org\/10.1016\/j.ajhg.2019.07.001","journal-title":"Am J Hum Genet"},{"issue":"Unit-1","key":"13_CR20","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1002\/0471142905.hg0127s79","volume":"79","author":"C-F Lin","year":"2013","unstructured":"Lin C-F, Naj AC, Wang L-S (2013) Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests. Curr Protoc Hum Genet 79(Unit-1):27. https:\/\/doi.org\/10.1002\/0471142905.hg0127s79","journal-title":"Curr Protoc Hum Genet"},{"key":"13_CR21","doi-asserted-by":"publisher","unstructured":"Artaza H, Lavrichenko K, Wolff ASB, R\u00f8yrvik EC, Vaudel M, Johansson S (2024) Rare Copy Number Variant analysis in case-control studies using SNP Array Data: a scalable and automated data analysis pipeline. 2024.03.13.584428. https:\/\/doi.org\/10.1101\/2024.03.13.584428","DOI":"10.1101\/2024.03.13.584428"},{"key":"13_CR22","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3658-x","volume":"18","author":"RR Haraksingh","year":"2017","unstructured":"Haraksingh RR, Abyzov A, Urban AE (2017) Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. BMC Genom 18: 321. https:\/\/doi.org\/10.1186\/s12864-017-3658-x","journal-title":"BMC Genom"},{"key":"13_CR23","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1038\/s41436-020-0759-8","volume":"22","author":"E Zampaglione","year":"2020","unstructured":"Zampaglione E, Kinde B, Place EM, Navarro-Gomez D, Maher M, Jamshidi F, Nassiri S, Mazzone JA, Finn C, Schlegel D et al  (2020) Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations. Genet Med 22:1079\u20131087. https:\/\/doi.org\/10.1038\/s41436-020-0759-8","journal-title":"Genet Med"},{"key":"13_CR24","doi-asserted-by":"publisher","first-page":"110962","DOI":"10.1016\/j.ygeno.2024.110962","volume":"116","author":"MN van Baardwijk","year":"2024","unstructured":"van Baardwijk MN, Heijnen LSEM, Zhao H, Baudis M, Stubbs AP (2024) A systematic benchmark of copy number variation detection tools for high density SNP genotyping arrays. Genomics 116:110962. https:\/\/doi.org\/10.1016\/j.ygeno.2024.110962","journal-title":"Genomics"},{"key":"13_CR25","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson JT, Thorvaldsd\u00f3ttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative Genomics Viewer. Nat Biotechnol 29:24. https:\/\/doi.org\/10.1038\/nbt.1754","journal-title":"Nat Biotechnol"},{"key":"13_CR26","doi-asserted-by":"publisher","first-page":"D1243","DOI":"10.1093\/nar\/gkae974","volume":"53","author":"G Perez","year":"2024","unstructured":"Perez G, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM et al (2024) The UCSC Genome Browser database: 2025 update. Nucleic Acids Res 53:D1243\u2013D1249. https:\/\/doi.org\/10.1093\/nar\/gkae974","journal-title":"Nucleic Acids Res"},{"key":"13_CR27","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1038\/s41588-019-0528-2","volume":"51","author":"AR Martin","year":"2019","unstructured":"Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E et al  (2019) PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet 51:1560\u20131565. https:\/\/doi.org\/10.1038\/s41588-019-0528-2","journal-title":"Nat Genet"},{"key":"13_CR28","doi-asserted-by":"publisher","first-page":"1588","DOI":"10.1038\/s41431-018-0189-0","volume":"26","author":"T Selvanayagam","year":"2018","unstructured":"Selvanayagam T, Walker S, Gazzellone MJ, Kellam B, Cytrynbaum C, Stavropoulos DJ, Li P, Birken CS, Hamilton J, Weksberg R et al  (2018) Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity. Eur J Hum Genet 26:1588\u20131596. https:\/\/doi.org\/10.1038\/s41431-018-0189-0","journal-title":"Eur J Hum Genet"},{"key":"13_CR29","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1086\/378818","volume":"73","author":"RE Ensenauer","year":"2003","unstructured":"Ensenauer RE, Adeyinka A, Flynn HC, Michels VV, Lindor NM, Dawson DB, Thorland EC, Lorentz CP, Goldstein JL, McDonald MT et al  (2003) Microduplication 22q11.2, an emerging syndrome: clinical, cytogenetic, and molecular analysis of thirteen patients. Am J Hum Genet 73:1027\u20131040","journal-title":"Am J Hum Genet"},{"key":"13_CR30","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1007\/s10875-023-01443-5","volume":"43","author":"D Bhattarai","year":"2023","unstructured":"Bhattarai D, McGinn DE, Crowley TB, Giunta V, Gaiser K, Zackai EH, Emanuel BS, Heimall J, Jyonouchi S, Lee J et al  (2023) Immunologic, Molecular, and Clinical Profile of Patients with Chromosome 22q11.2 Duplications. J Clin Immunol 43:794\u2013807. https:\/\/doi.org\/10.1007\/s10875-023-01443-5","journal-title":"J Clin Immunol"},{"key":"13_CR31","doi-asserted-by":"publisher","first-page":"344","DOI":"10.2174\/157015912804143496","volume":"10","author":"E Gyengesi","year":"2012","unstructured":"Gyengesi E, Paxinos G, Andrews ZB (2012) Oxidative stress in the hypothalamus: the importance of calcium signaling and mitochondrial ROS in body weight regulation. Curr Neuropharmacol 10:344\u2013353. https:\/\/doi.org\/10.2174\/157015912804143496","journal-title":"Curr Neuropharmacol"},{"key":"13_CR32","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1007\/s00125-011-2221-6","volume":"54","author":"T Cai","year":"2011","unstructured":"Cai T, Hirai H, Zhang G, Zhang M, Takahashi N, Kasai H, Satin LS, Leapman RD, Notkins AL (2011) Deletion of IA-2 and\/or IA-2\u03b2 decreases insulin secretion by reducing the number of dense core vesicles. Diabetologia 54:2347\u20132357. https:\/\/doi.org\/10.1007\/s00125-011-2221-6","journal-title":"Diabetologia"},{"key":"13_CR33","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1177\/1933719117716779","volume":"25","author":"P-Y Chen","year":"2018","unstructured":"Chen P-Y, Chu A, Liao W-W, Rubbi L, Janzen C, Hsu F-M, Thamotharan S, Ganguly A, Lam L, Montoya D et al  (2018) Prenatal growth patterns and birthweight are associated with differential DNA methylation and gene expression of cardiometabolic risk genes in human placentas: a discovery-based approach. Reprod Sci 25:523\u2013539. https:\/\/doi.org\/10.1177\/1933719117716779","journal-title":"Reprod Sci"},{"key":"13_CR34","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/j.bbrc.2009.11.049","volume":"391","author":"T Yamakawa","year":"2010","unstructured":"Yamakawa T, Sugimoto K, Whitson RH, Itakura K (2010) Modulator recognition factor-2 regulates triglyceride metabolism in adipocytes. Biochem Biophys Res Commun 391:277\u2013281. https:\/\/doi.org\/10.1016\/j.bbrc.2009.11.049","journal-title":"Biochem Biophys Res Commun"},{"key":"13_CR35","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1056\/NEJMoa1502214","volume":"373","author":"M Claussnitzer","year":"2015","unstructured":"Claussnitzer M, Dankel SN, Kim K-H, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V et al  (2015) FTO obesity variant circuitry and adipocyte browning in humans. N Engl J Med 373:895\u2013907. https:\/\/doi.org\/10.1056\/NEJMoa1502214","journal-title":"N Engl J Med"}],"container-title":["Methods in Molecular Biology","AI\/ML-Driven Gene Analysis"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5284-8_13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T22:25:30Z","timestamp":1788301530000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-5284-8_13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9781071652831","9781071652848"],"references-count":35,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5284-8_13","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"2 September 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"The authors have no conflicts of interest to declare that are relevant to the content of this chapter.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}}]}}