{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T19:25:32Z","timestamp":1774725932581,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called \u2018Clonality\u2019. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results.<\/jats:p>\n               <jats:p>Availability: Bioconductor (http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/Clonality.html) and http:\/\/www.mskcc.org\/mskcc\/html\/13287.cfm.<\/jats:p>\n               <jats:p>Contact: \u00a0ostrovni@mskcc.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr267","type":"journal-article","created":{"date-parts":[[2011,5,6]],"date-time":"2011-05-06T02:18:24Z","timestamp":1304648304000},"page":"1698-1699","source":"Crossref","is-referenced-by-count":44,"title":["Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic\nprofiles"],"prefix":"10.1093","volume":"27","author":[{"given":"Irina","family":"Ostrovnaya","sequence":"first","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 and 2Department of Epidemiology and Biostatistics and Helen Diller Family Comprehensive Cancer Center, University of California\u2014San Francisco, San Francisco, CA 94158, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Venkatraman E.","family":"Seshan","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 and 2Department of Epidemiology and Biostatistics and Helen Diller Family Comprehensive Cancer Center, University of California\u2014San Francisco, San Francisco, CA 94158, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam B.","family":"Olshen","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 and 2Department of Epidemiology and Biostatistics and Helen Diller Family Comprehensive Cancer Center, University of California\u2014San Francisco, San Francisco, CA 94158, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin B.","family":"Begg","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 and 2Department of Epidemiology and Biostatistics and Helen Diller Family Comprehensive Cancer Center, University of California\u2014San Francisco, San Francisco, CA 94158, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,5,5]]},"reference":[{"key":"2023012511151146500_B1","first-page":"522","article-title":"Statistical tests for clonality","author":"Begg","year":"2007"},{"key":"2023012511151146500_B2","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics 2004","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023012511151146500_B3","doi-asserted-by":"crossref","first-page":"2562","DOI":"10.1002\/cncr.20273","article-title":"Clonality of lobular carcinoma in situ and synchronous invasive lobular cancer","volume":"100","author":"Hwang","year":"2004","journal-title":"Cancer"},{"key":"2023012511151146500_B4","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics"},{"key":"2023012511151146500_B5","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1111\/j.1541-0420.2008.00988.x","article-title":"Comparison of properties of tests for assessing tumor clonality","volume":"68","author":"Ostrovnaya","year":"2008","journal-title":"Biometrics"},{"key":"2023012511151146500_B6","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1002\/sim.3866","article-title":"A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data","volume":"29","author":"Ostrovnaya","year":"2010","journal-title":"Stat. Med."},{"key":"2023012511151146500_B7","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1158\/1078-0432.CCR-09-2398","article-title":"Testing clonal relatedness of tumors using array comparative genomic hybridization: a statistical challenge","volume":"16","author":"Ostrovnaya","year":"2010","journal-title":"Clin. Cancer Res."},{"key":"2023012511151146500_B8","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1186\/1471-2105-11-297","article-title":"A classification model for distinguishing copy number variants from cancer-related alterations","volume":"11","author":"Ostrovnaya","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012511151146500_B9","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2010"},{"key":"2023012511151146500_B10","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1093\/bioinformatics\/btl646","article-title":"A faster circular binary segmentation algorithm for the analysis of array CGH data","volume":"23","author":"Venkatraman","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1698\/48862238\/bioinformatics_27_12_1698.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/12\/1698\/48862238\/bioinformatics_27_12_1698.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:20:54Z","timestamp":1674645654000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/12\/1698\/258712"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,5]]},"references-count":10,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2011,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr267","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,6,15]]},"published":{"date-parts":[[2011,5,5]]}}}