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However, computational tools to maximize the use of scarce tissues combining distinct molecular layers are needed. Here we present a refined strategy, based on the R-package \u2018conumee\u2019, to better predict somatic copy number alterations (SCNA) from deoxyribonucleic acid (DNA) methylation arrays. Our approach, termed hereafter as \u2018conumee-KCN\u2019, improves SCNA prediction by incorporating tumor purity and dynamic thresholding. We trained our algorithm using paired DNA methylation and SNP Array 6.0 data from The Cancer Genome Atlas samples and confirmed its performance in cancer cell lines. Most importantly, the application of our approach in cancers of unknown primary identified amplified potentially actionable targets that were experimentally validated by Fluorescence in situ hybridization and immunostaining, reaching 100% specificity and 93.3% sensitivity.<\/jats:p>","DOI":"10.1093\/bib\/bbac161","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T11:16:25Z","timestamp":1649934985000},"source":"Crossref","is-referenced-by-count":2,"title":["Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary"],"prefix":"10.1093","volume":"23","author":[{"given":"Pedro","family":"Blecua","sequence":"first","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"}]},{"given":"Veronica","family":"Davalos","sequence":"additional","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"}]},{"given":"Izar","family":"de Villasante","sequence":"additional","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"}]},{"given":"Angelika","family":"Merkel","sequence":"additional","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"}]},{"given":"Eva","family":"Musulen","sequence":"additional","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"},{"name":"Department of Pathology, Hospital Universitari General de Catalunya-Grupo Quir\u00f3nsalud, Sant Cugat del Vall\u00e8s , Barcelona, Catalonia, Spain"}]},{"given":"Laia","family":"Coll-SanMartin","sequence":"additional","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4490-6093","authenticated-orcid":false,"given":"Manel","family":"Esteller","sequence":"additional","affiliation":[{"name":"Josep Carreras Leukaemia Research Institute (IJC) , Badalona, Barcelona, Catalonia, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Cancer (CIBERONC) , Madrid, Spain"},{"name":"Institucio Catalana de Recerca i Estudis Avan\u00e7ats (ICREA) , Barcelona, Catalonia, Spain"},{"name":"Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB) , Catalonia, Spain"}]}],"member":"286","published-online":{"date-parts":[[2022,5,6]]},"reference":[{"issue":"2","key":"2022092013200842400_ref1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41576-018-0074-2","article-title":"Clinical epigenetics: seizing opportunities for translation","volume":"20","author":"Berdasco","year":"2019","journal-title":"Nat Rev 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