{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T07:02:41Z","timestamp":1781766161832,"version":"3.54.5"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,8,4]],"date-time":"2022-08-04T00:00:00Z","timestamp":1659571200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA211939"],"award-info":[{"award-number":["R01CA211939"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24CA264021"],"award-info":[{"award-number":["U24CA264021"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UG1CA233333"],"award-info":[{"award-number":["UG1CA233333"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24CA210988"],"award-info":[{"award-number":["U24CA210988"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DE025712"],"award-info":[{"award-number":["R01DE025712"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Somatic DNA copy number alterations (CNAs) arise in tumor tissue because of underlying genomic instability. Recurrent CNAs that occur in the same genomic region across multiple independent samples are of interest to researchers because they may contain genes that contribute to the cancer phenotype. However, differences in copy number states between cancers are also commonly of interest, for example when comparing tumors with distinct morphologies in the same anatomic location. Current methodologies are limited by their inability to perform direct comparisons of CNAs between tumor cohorts, and thus they cannot formally assess the statistical significance of observed copy number differences or identify regions of the genome where these differences occur.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We introduce the DiNAMIC.Duo R package that can be used to identify recurrent CNAs in a single cohort or recurrent copy number differences between two cohorts, including when neither cohort is copy neutral. The package utilizes Python scripts for computational efficiency and provides functionality for producing figures and summary output files.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The DiNAMIC.Duo R package is available from CRAN at https:\/\/cran.r-project.org\/web\/packages\/DiNAMIC.Duo\/index.html. This article uses publicly available data from the Broad Institute TCGA Genome Data Analysis Center, https:\/\/doi.org\/10.7908\/C11G0KM9.<\/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\/btac542","type":"journal-article","created":{"date-parts":[[2022,8,4]],"date-time":"2022-08-04T13:46:15Z","timestamp":1659620775000},"page":"4415-4417","source":"Crossref","is-referenced-by-count":4,"title":["DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6114-6714","authenticated-orcid":false,"given":"Vonn","family":"Walter","sequence":"first","affiliation":[{"name":"Department of Public Health Sciences, Penn State College of Medicine , Hershey, PA 17033, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyo Young","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, University of Tennessee Health Science Center , Memphis, TN 38163, USA"},{"name":"Department of Medicine, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobei","family":"Zhao","sequence":"additional","affiliation":[{"name":"Division of Hematology and Oncology, Department of Medicine, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6852-2038","authenticated-orcid":false,"given":"Yan","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremiah","family":"Holt","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D Neil","family":"Hayes","sequence":"additional","affiliation":[{"name":"Division of Hematology and Oncology, Department of Medicine, University of Tennessee Health Science Center , Memphis, TN 38163, USA"},{"name":"Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163, USA"},{"name":"Center for Cancer Research, University of Tennessee Health Science Center , Memphis, TN 38163, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,8,4]]},"reference":[{"key":"2023041408374956800_","doi-asserted-by":"crossref","first-page":"21128","DOI":"10.1038\/s41598-020-77284-8","article-title":"Lung squamous cell carcinoma and lung adenocarcinoma differential gene expression regulation through pathways of Notch, Hedgehog, Wnt, and ErbB signaling","volume":"10","author":"Anusewicz","year":"2020","journal-title":"Sci. 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