{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:20:56Z","timestamp":1783488056245,"version":"3.55.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T00:00:00Z","timestamp":1590364800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100022011","name":"Cancer Research UK Cambridge Institute","doi-asserted-by":"crossref","award":["C14303\/A17197"],"award-info":[{"award-number":["C14303\/A17197"]}],"id":[{"id":"10.13039\/501100022011","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Francis Crick Institute with core funding from Cancer Research UK","award":["FC001202"],"award-info":[{"award-number":["FC001202"]}]},{"DOI":"10.13039\/501100000265","name":"UK Medical Research Council","doi-asserted-by":"crossref","award":["FC001202"],"award-info":[{"award-number":["FC001202"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["FC001202"],"award-info":[{"award-number":["FC001202"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Winton Group Leader"},{"name":"Royal Society Wolfson Research Merit"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present asmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>asmultipcf is available as part of the ASCAT R package (version \u22652.5) from github.com\/Crick-CancerGenomics\/ascat\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa538","type":"journal-article","created":{"date-parts":[[2020,5,19]],"date-time":"2020-05-19T12:41:42Z","timestamp":1589892102000},"page":"1909-1911","source":"Crossref","is-referenced-by-count":45,"title":["Allele-specific multi-sample copy number segmentation in ASCAT"],"prefix":"10.1093","volume":"37","author":[{"given":"Edith M.","family":"Ross","sequence":"first","affiliation":[{"name":"Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge CB2 0RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Haase","sequence":"additional","affiliation":[{"name":"The Francis Crick Institute , London NW1 1AT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Van Loo","sequence":"additional","affiliation":[{"name":"The Francis Crick Institute , London NW1 1AT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2784-5308","authenticated-orcid":false,"given":"Florian","family":"Markowetz","sequence":"additional","affiliation":[{"name":"Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge CB2 0RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,5,25]]},"reference":[{"key":"2023051611453255100_btaa538-B1","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1016\/j.celrep.2019.04.098","article-title":"The genomic and immune landscapes of lethal metastatic breast cancer","volume":"27","author":"De Mattos-Arruda","year":"2019","journal-title":"Cell Rep"},{"key":"2023051611453255100_btaa538-B2","doi-asserted-by":"crossref","first-page":"33918","DOI":"10.1038\/srep33918","article-title":"Comparing nodal versus bony metastatic spread using tumour phylogenies","volume":"6","author":"Mangiola","year":"2016","journal-title":"Sci. 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USA"},{"key":"2023051611453255100_btaa538-B6","doi-asserted-by":"crossref","DOI":"10.1101\/496174","article-title":"Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data","author":"Zaccaria","year":"2018"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa538\/38844082\/btaa538.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/13\/1909\/50340081\/btaa538.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/13\/1909\/50340081\/btaa538.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T11:46:40Z","timestamp":1684237600000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/13\/1909\/5843787"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,5,25]]},"references-count":6,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2021,7,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa538","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7,1]]},"published":{"date-parts":[[2021,5,25]]}}}