{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T13:56:48Z","timestamp":1756994208743,"version":"3.37.3"},"reference-count":25,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T00:00:00Z","timestamp":1652659200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011724","name":"Muscular Dystrophy UK","doi-asserted-by":"publisher","award":["16NEB-PG36-0094"],"award-info":[{"award-number":["16NEB-PG36-0094"]}],"id":[{"id":"10.13039\/100011724","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015736","name":"Folkh\u00e4lsan Research Foundation","doi-asserted-by":"crossref","award":["101003"],"award-info":[{"award-number":["101003"]}],"id":[{"id":"10.13039\/100015736","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004155","name":"Magnus Ehrnroothin S\u00e4\u00e4ti\u00f6","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010135","name":"Finska L\u00e4kares\u00e4llskapet","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010135","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010116","name":"Medicinska Underst\u00f6dsf\u00f6reningen Liv och H\u00e4lsa","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010116","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The human genome contains repetitive regions, such as segmental duplications, known to be prone to copy number variation. Segmental duplications are highly identical and homologous sequences, posing a specific challenge for most mutation detection methods. The giant nebulin gene is expressed in skeletal muscle. It harbors a large segmental duplication region composed of eight exons repeated three times, the so-called triplicate region. Mutations in nebulin are known to cause nemaline myopathy and other congenital myopathies. Using our custom targeted Comparative Genomic Hybridization arrays, we have previously shown that copy number variations in the nebulin triplicate region are pathogenic when the copy number of the segmental duplication block deviates two or more copies from the normal number, which is three per allele. To complement our Comparative Genomic Hybridization arrays, we have established a custom Droplet Digital PCR method for the detection of copy number variations within the nebulin triplicate region. The custom Droplet Digital PCR assays allow sensitive, rapid, high-throughput, and cost-effective detection of copy number variations within this region and is ready for implementation a screening method for disease-causing copy number variations of the nebulin triplicate region. We suggest that Droplet Digital PCR may also be used in the study and diagnostics of other segmental duplication regions of the genome.<\/jats:p>","DOI":"10.1371\/journal.pone.0267793","type":"journal-article","created":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T17:24:23Z","timestamp":1652721863000},"page":"e0267793","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6754-3830","authenticated-orcid":true,"given":"Lydia","family":"Sagath","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vilma-Lotta","family":"Lehtokari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carina","family":"Wallgren-Pettersson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katarina","family":"Pelin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirsi","family":"Kiiski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,5,16]]},"reference":[{"issue":"6","key":"pone.0267793.ref001","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1101\/gr.187101","article-title":"Segmental duplications: organization and impact within the current human genome project assembly","volume":"11","author":"JA Bailey","year":"2001","journal-title":"Genome Res"},{"issue":"11","key":"pone.0267793.ref002","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/S0168-9525(01)02492-1","article-title":"Recent duplication, domain accretion and the dynamic mutation of the human genome","volume":"17","author":"EE Eichler","year":"2001","journal-title":"Trends Genet"},{"issue":"6","key":"pone.0267793.ref003","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1101\/gr.228718.117","article-title":"Detection and analysis of ancient segmental duplications in mammalian genomes","volume":"28","author":"L Pu","year":"2018","journal-title":"Genome res"},{"issue":"5583","key":"pone.0267793.ref004","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1126\/science.1072047","article-title":"Recent segmental duplications in the human genome","volume":"297","author":"JA Bailey","year":"2002","journal-title":"Science"},{"issue":"2","key":"pone.0267793.ref005","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.nmd.2018.12.007","article-title":"Dominantly inherited distal nemaline\/cap myopathy caused by a large deletion in the nebulin gene","volume":"29","author":"KJ Kiiski","year":"2019","journal-title":"Neuromuscul Disord"},{"key":"pone.0267793.ref006","article-title":"Congenital asymmetric distal myopathy with hemifacial weakness caused by a heterozygous large de novo mosaic deletion in nebulin","author":"L Sagath","year":"2021","journal-title":"Neuromuscular disorders: NMD"},{"issue":"9","key":"pone.0267793.ref007","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/sj.ejhg.5201242","article-title":"Complete genomic structure of the human nebulin gene and identification of alternatively spliced transcripts","volume":"12","author":"K Donner","year":"2004","journal-title":"Eur J Hum Genet"},{"issue":"4","key":"pone.0267793.ref008","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1038\/ejhg.2015.166","article-title":"A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array","volume":"24","author":"K Kiiski","year":"2016","journal-title":"Eur J Hum Genet"},{"issue":"6","key":"pone.0267793.ref009","doi-asserted-by":"crossref","first-page":"e204","DOI":"10.1212\/NXG.0000000000000204","article-title":"Copy number variation analysis increases the diagnostic yield in muscle diseases","volume":"3","author":"S V\u00e4lipakka","year":"2017","journal-title":"Neurol Genet"},{"issue":"1","key":"pone.0267793.ref010","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.nmd.2012.07.007","article-title":"Targeted array comparative genomic hybridization\u2013a new diagnostic tool for the detection of large copy number variations in nemaline myopathy-causing genes","volume":"23","author":"K Kiiski","year":"2013","journal-title":"Neuromuscul Disord"},{"issue":"3","key":"pone.0267793.ref011","doi-asserted-by":"crossref","first-page":"307","DOI":"10.3233\/JND-170298","article-title":"An Extended Targeted Copy Number Variation Detection Array Including 187 Genes for the Diagnostics of Neuromuscular Disorders","volume":"5","author":"L Sagath","year":"2018","journal-title":"J Neuromuscul Dis"},{"issue":"2","key":"pone.0267793.ref012","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1142\/S021972001000480X","article-title":"Detecting copy number variations from array CGH data based on a conditional random field model","volume":"8","author":"XL Yin","year":"2010","journal-title":"J Bioinform Comput Biol"},{"issue":"15","key":"pone.0267793.ref013","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1002\/ajmg.a.31740","article-title":"Microarray-based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics","volume":"143a","author":"SW Cheung","year":"2007","journal-title":"Am J Med Genet"},{"issue":"8","key":"pone.0267793.ref014","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/ejhg.2013.285","article-title":"Somatic mosaicism detected by exon-targeted, high-resolution aCGH in 10,362 consecutive cases","volume":"22","author":"J Pham","year":"2014","journal-title":"Eur J Hum Genet"},{"key":"pone.0267793.ref015","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/j.cca.2020.09.024","article-title":"Analytical validation of the droplet digital PCR assay for diagnosis of spinal muscular atrophy","volume":"510","author":"S Park","year":"2020","journal-title":"Clin Chim Acta"},{"issue":"9","key":"pone.0267793.ref016","doi-asserted-by":"crossref","first-page":"e0162467","DOI":"10.1371\/journal.pone.0162467","article-title":"Digital Droplet PCR for the Absolute Quantification of Exon Skipping Induced by Antisense Oligonucleotides in (Pre-)Clinical Development for Duchenne Muscular Dystrophy","volume":"11","author":"RC Verheul","year":"2016","journal-title":"PLoS ONE"},{"key":"pone.0267793.ref017","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.cca.2020.12.001","article-title":"Droplet digital PCR for large genomic rearrangements detection: A promising strategy in tissue BRCA1 testing","volume":"513","author":"E De Paolis","year":"2021","journal-title":"Clin Chim Acta"},{"issue":"8","key":"pone.0267793.ref018","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1093\/clinchem\/hvaa125","article-title":"The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020","volume":"66","author":"The dMIQE Group","year":"2020","journal-title":"Clin Chem"},{"issue":"6","key":"pone.0267793.ref019","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1373\/clinchem.2013.206375","article-title":"The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments","volume":"59","author":"JF Huggett","year":"2013","journal-title":"Clin chem"},{"issue":"4","key":"pone.0267793.ref020","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1037\/h0026256","article-title":"Weighted kappa: nominal scale agreement with provision for scaled disagreement or partial credit","volume":"70","author":"J Cohen","year":"1968","journal-title":"Psychological Bull"},{"issue":"12","key":"pone.0267793.ref021","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1002\/humu.22693","article-title":"Mutation update: the spectra of nebulin variants and associated myopathies","volume":"35","author":"VL Lehtokari","year":"2014","journal-title":"Human mutat"},{"issue":"1","key":"pone.0267793.ref022","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.jmb.2010.07.011","article-title":"Nebulin: a study of protein repeat evolution","volume":"402","author":"AK Bj\u00f6rklund","year":"2010","journal-title":"J Mol Biol"},{"issue":"3","key":"pone.0267793.ref023","doi-asserted-by":"crossref","DOI":"10.1085\/jgp.202012783","article-title":"The number of Z-repeats and super-repeats in nebulin greatly varies across vertebrates and scales with animal size","volume":"153","author":"J Gohlke","year":"2021","journal-title":"J Gen Physiol"},{"key":"pone.0267793.ref024","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/0065-227X(96)81668-6","article-title":"Titin\/connectin and nebulin: giant protein rulers of muscle structure and function","volume":"33","author":"K Wang","year":"1996","journal-title":"Adv Biophys"},{"key":"pone.0267793.ref025","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1007\/978-3-319-49674-0_10","article-title":"Titin and Nebulin in Thick and Thin Filament Length Regulation","volume":"82","author":"L Tskhovrebova","year":"2017","journal-title":"Subcell Biochem"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0267793","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T17:24:57Z","timestamp":1652721897000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0267793"}},"subtitle":[],"editor":[{"given":"Ricardo","family":"Santos","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,5,16]]},"references-count":25,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2022,5,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0267793","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2022,5,16]]}}}