{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:01Z","timestamp":1772138041592,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T00:00:00Z","timestamp":1610928000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"HARVEST collaboration supported by the Research Council of Norway","award":["229624"],"award-info":[{"award-number":["229624"]}]},{"name":"Center for Diabetes Research"},{"DOI":"10.13039\/501100005036","name":"University of Bergen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005036","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERC AdG project SELECTionPREDISPOSED","award":["293574"],"award-info":[{"award-number":["293574"]}]},{"name":"Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation"},{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","award":["240413"],"award-info":[{"award-number":["240413"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Novo Nordisk Distinguished Award","award":["NNF19OC0054741"],"award-info":[{"award-number":["NNF19OC0054741"]}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF19OC0057445"],"award-info":[{"award-number":["NNF19OC0057445"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Bergen and the Western Norway Health Authorities (Helse Vest","award":["F-12144"],"award-info":[{"award-number":["F-12144"]}]},{"name":"University of Bergen and the Western Norway Health Authorities (Helse Vest","award":["F-11528"],"award-info":[{"award-number":["F-11528"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting cohorts with trios available (e.g. nuclear family) to assist in quality control and downstream analyses following the calling.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed SeeCiTe (Seeing CNVs in Trios), a novel CNV-quality control tool that postprocesses output from current CNV-calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. We apply it to the Norwegian Mother, Father and Child Cohort Study (MoBa) and show that SeeCiTe improves the specificity and sensitivity compared to the common empiric filtering strategies. To our knowledge, it is the first tool that utilizes probe-level CNV data in trios (and singletons) to systematically highlight potential artifacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The software is implemented in R with the source code freely available at https:\/\/github.com\/aksenia\/SeeCiTe<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab028","type":"journal-article","created":{"date-parts":[[2021,1,13]],"date-time":"2021-01-13T00:22:32Z","timestamp":1610497352000},"page":"1876-1883","source":"Crossref","is-referenced-by-count":8,"title":["SeeCiTe: a method to assess CNV calls from SNP arrays using trio data"],"prefix":"10.1093","volume":"37","author":[{"given":"Ksenia","family":"Lavrichenko","sequence":"first","affiliation":[{"name":"Computational Biology Unit, Department of Informatics, University of Bergen , Bergen, Norway"},{"name":"Department of Clinical Science, University of Bergen , Bergen, Norway"}]},{"given":"\u00d8yvind","family":"Helgeland","sequence":"additional","affiliation":[{"name":"Department of Clinical Science, University of Bergen , Bergen, Norway"},{"name":"Department of Genetics and Bioinformatics, Norwegian Institute of Public Health , Oslo, Norway"}]},{"given":"P\u00e5l R","family":"Nj\u00f8lstad","sequence":"additional","affiliation":[{"name":"Department of Clinical Science, University of Bergen , Bergen, Norway"},{"name":"Department of Pediatrics and Adolescents, Haukeland University Hospital , Bergen, Norway"}]},{"given":"Inge","family":"Jonassen","sequence":"additional","affiliation":[{"name":"Computational Biology Unit, Department of Informatics, University of Bergen , Bergen, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2298-7008","authenticated-orcid":false,"given":"Stefan","family":"Johansson","sequence":"additional","affiliation":[{"name":"Department of Clinical Science, University of Bergen , Bergen, Norway"},{"name":"Department of Medical Genetics, Haukeland University Hospital , Bergen, Norway"}]}],"member":"286","published-online":{"date-parts":[[2021,1,18]]},"reference":[{"key":"2023051611465719000_btab028-B1","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg1895","article-title":"Primate segmental duplications: crucibles of evolution, diversity and disease","volume":"7","author":"Bailey","year":"2006","journal-title":"Nat. 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