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Technical and logistical issues, however, make it challenging to accurately detect abnormal copy number events in a cost-effective manner in clinical studies.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here we present CNV Radar, a software tool that utilizes next-generation sequencing read depth information and variant allele frequency patterns, to infer the true copy number status of genes and genomic regions from whole exome sequencing data. Evaluation of CNV Radar in a public multiple myeloma dataset demonstrated that CNV Radar was able to detect a variety of CNVs associated with risk of progression, and we observed &gt;\u200970% concordance with fluorescence in situ hybridization (FISH) results. Compared to other CNV callers, CNV Radar showed high sensitivity and specificity. Similar results were observed when comparing CNV Radar calls to single nucleotide polymorphism array results from acute myeloid leukemia and prostate cancer datasets available on TCGA. More importantly, CNV Radar demonstrated its utility in the clinical trial setting: in POLLUX and CASTOR, two phase 3 studies in patients with relapsed or refractory multiple myeloma, we observed a high concordance rate with FISH for del17p, a risk defining CNV event (88% in POLLUX and 90% in CASTOR), therefore allowing for efficacy assessments in clinically relevant disease subgroups. Our case studies also showed that CNV Radar is capable of detecting abnormalities such as copy-neutral loss of heterozygosity that elude other approaches.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We demonstrated that CNV Radar is more sensitive than other CNV detection methods, accurately detects clinically important cytogenetic events, and allows for further interrogation of novel disease biology. Overall, CNV Radar exhibited high concordance with standard methods such as FISH, and its success in the POLLUX and CASTOR clinical trials demonstrated its potential utility for informing clinical and therapeutic decisions.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-020-3397-x","type":"journal-article","created":{"date-parts":[[2020,3,6]],"date-time":"2020-03-06T13:02:52Z","timestamp":1583499772000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["CNV Radar: an improved method for somatic copy number alteration characterization in oncology"],"prefix":"10.1186","volume":"21","author":[{"given":"David","family":"Soong","sequence":"first","affiliation":[]},{"given":"Jeran","family":"Stratford","sequence":"additional","affiliation":[]},{"given":"Herve","family":"Avet-Loiseau","sequence":"additional","affiliation":[]},{"given":"Nizar","family":"Bahlis","sequence":"additional","affiliation":[]},{"given":"Faith","family":"Davies","sequence":"additional","affiliation":[]},{"given":"Angela","family":"Dispenzieri","sequence":"additional","affiliation":[]},{"given":"A. 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EA genomic services https:\/\/github.com\/ExpressionAnalysis (accessed January 26, 2018)."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-3397-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-020-3397-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-020-3397-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,3,6]],"date-time":"2021-03-06T00:20:24Z","timestamp":1614990024000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-020-3397-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,6]]},"references-count":59,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["3397"],"URL":"https:\/\/doi.org\/10.1186\/s12859-020-3397-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,6]]},"assertion":[{"value":"28 June 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 February 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 March 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Patient-level data from publicly available datasets (MMRF CoMMpass, TCGA prostate, TCGA AML) were analyzed. For POLLUX and CASTOR studies, all patients provided written consent and the trial protocols were approved by independent ethics committees or institutional review boards at each study center.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"HA-L received honoraria from and served on a speakers bureau for Celgene, Amgen, Bristol-Myers Squibb, Sanofi, and Janssen; and received research funding from Celgene and Janssen. NB received honoraria and travel expenses from Celgene, Takeda, Janssen, and Amgen; served on advisory boards for Celgene, Takeda, Janssen, and Amgen; served on speakers bureaus for Celgene, Janssen, and Amgen; and received research funding from and provided expert testimony to Celgene and Janssen. FD received research funding from Janssen, and served on advisory boards for Amgen, Celgene, AbbVie, Novartis, and Bristol-Myers Squibb. AD received research funding from Celgene, Takeda, Pfizer, Alnylam, and Prothena. AKS is a former employee of Janssen and is currently employed at Genmab. DS, MS, JMS, MQ, and CC are employees of Janssen. DS and JMS hold stock and\/or stock options in Johnson & Johnson. WJ, JP, and JS are employees of Q<sup>2<\/sup> Solutions, EA Genomics. CB is a former employee of Q<sup>2<\/sup> Solutions, EA Genomics and a current employee of Align Technology. JJK and DA do not have any competing interests to report.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"98"}}