{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T22:12:01Z","timestamp":1759961521149,"version":"3.37.3"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T00:00:00Z","timestamp":1656115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>While the identification of small variants in panel sequencing data can be considered a solved problem, the identification of larger, multi-exon copy number variants (CNVs) still poses a considerable challenge. Thus, CNV calling has not been established in all laboratories performing panel sequencing. At the same time, such laboratories have accumulated large datasets and thus have the need to identify CNVs on their data to close the diagnostic gap.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this article, we present our method clearCNV that addresses this need in two ways. First, it helps laboratories to properly assign datasets to enrichment kits. Based on homogeneous subsets of data, clearCNV identifies CNVs affecting the targeted regions. Using real-world datasets and validation, we show that our method is highly competitive with previous methods and preferable in terms of specificity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The software is available for free under a permissible license at https:\/\/github.com\/bihealth\/clear-cnv.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac418","type":"journal-article","created":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T12:42:17Z","timestamp":1656160937000},"page":"3871-3876","source":"Crossref","is-referenced-by-count":4,"title":["ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise"],"prefix":"10.1093","volume":"38","author":[{"given":"Vinzenz","family":"May","sequence":"first","affiliation":[{"name":"Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin , Berlin 10117, Germany"}]},{"given":"Leonard","family":"Koch","sequence":"additional","affiliation":[{"name":"Institute of Medical Genetics and Human Genetics, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin , Berlin 13353, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1075-7571","authenticated-orcid":false,"given":"Bj\u00f6rn","family":"Fischer-Zirnsak","sequence":"additional","affiliation":[{"name":"Institute of Medical Genetics and Human Genetics, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin , Berlin 13353, Germany"},{"name":"FG Development and Disease, Max-Planck-Institut f\u00fcr Molekulare Genetik , Berlin 14195, Germany"}]},{"given":"Denise","family":"Horn","sequence":"additional","affiliation":[{"name":"Institute of Medical Genetics and Human Genetics, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin , Berlin 13353, Germany"}]},{"given":"Petra","family":"Gehle","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine\u2014Cardiology, Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin , Berlin 13353, Germany"},{"name":"DZHK (German Center for Cardiovascular Research) , Berlin, Germany"}]},{"given":"Uwe","family":"Kornak","sequence":"additional","affiliation":[{"name":"FG Development and Disease, Max-Planck-Institut f\u00fcr Molekulare Genetik , Berlin 14195, Germany"},{"name":"Institute of Human Genetics, University Medical Center G\u00f6ttingen , G\u00f6ttingen 37073, Germany"}]},{"given":"Dieter","family":"Beule","sequence":"additional","affiliation":[{"name":"Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin , Berlin 10117, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3051-1763","authenticated-orcid":false,"given":"Manuel","family":"Holtgrewe","sequence":"additional","affiliation":[{"name":"Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin , Berlin 10117, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,6,25]]},"reference":[{"key":"2023041408470470400_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023041408470470400_","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1093\/bioinformatics\/btx691","article-title":"Simulating the dynamics of targeted capture sequencing with CapSim","volume":"34","author":"Cao","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041408470470400_","first-page":"1","article-title":"Atlas-CNV: A validated approach to call single-exon CNVs in the eMERGESeq gene panel","volume":"0","author":"Chiang","year":"2019","journal-title":"Genet. 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