{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:23:23Z","timestamp":1765232603481,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2018,7,2]],"date-time":"2018-07-02T00:00:00Z","timestamp":1530489600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"St. Baldrick\u2019s Foundation"},{"name":"Robert J. Arceci Innovation Award","award":["National Cancer Institute"],"award-info":[{"award-number":["National Cancer Institute"]}]},{"name":"Outstanding Investigator Award","award":["R35 CA197695"],"award-info":[{"award-number":["R35 CA197695"]}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P50 GM115279"],"award-info":[{"award-number":["P50 GM115279"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["P30 CA021765"],"award-info":[{"award-number":["P30 CA021765"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single nucleotide polymorphism (SNP) array is the most widely used platform to assess somatic copy number variations (CNVs) in cancer studies. Many SNP data-based CNV callers are available, however, the false positive rates from automated calling are commonly high, and reported breakpoints can be inaccurate. Manual review for each reported CNV by visualizing the SNP data is important, but is challenging for users lacking computational experience. To address this, we present a Shiny\/R application ShinyCNV, an interactive graphical user interface to view and annotate CNVs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>With this application, normalized SNP data, which includes log R ratio (LRR) and B allele frequency, can be plotted against the reported CNVs, and users can visually check the reliability of CNVs per se or adjust the incorrectly assigned breakpoints. Further, the interactive LRR spectrum panel within ShinyCNV can facilitate the process to identify commonly affected CNV regions from a group of samples, and to visually check if important focal gains\/losses are missing from reported CNVs. ShinyCNV is designed to be intuitive for cancer researchers and can be easily installed for either personal use or deployed on servers to provide online service.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ShinyCNV and the tutorial are freely available from https:\/\/github.com\/gzhmat\/ShinyCNV.<\/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\/bty546","type":"journal-article","created":{"date-parts":[[2018,6,29]],"date-time":"2018-06-29T03:10:31Z","timestamp":1530241831000},"page":"126-129","source":"Crossref","is-referenced-by-count":8,"title":["ShinyCNV: a Shiny\/R application to view and annotate DNA copy number variations"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1581-1327","authenticated-orcid":false,"given":"Zhaohui","family":"Gu","sequence":"first","affiliation":[{"name":"Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles G","family":"Mullighan","sequence":"additional","affiliation":[{"name":"Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,7,2]]},"reference":[{"key":"2023013107214258400_bty546-B1","doi-asserted-by":"crossref","first-page":"4323","DOI":"10.1073\/pnas.0910684107","article-title":"High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset","volume":"107","author":"Caren","year":"2010","journal-title":"Proc. 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