{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T19:54:46Z","timestamp":1777406086151,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T00:00:00Z","timestamp":1656288000000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004897","name":"Pennsylvania Department of Health","doi-asserted-by":"publisher","award":["FP00003273"],"award-info":[{"award-number":["FP00003273"]}],"id":[{"id":"10.13039\/100004897","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Human Genome Research Institute of the National Institutes of Health","award":["R01HG010589"],"award-info":[{"award-number":["R01HG010589"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004897","name":"The Pennsylvania Department of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100004897","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,24]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Cancer develops through a process of clonal evolution in which an initially healthy cell gives rise to progeny gradually differentiating through the accumulation of genetic and epigenetic mutations. These mutations can take various forms, including single-nucleotide variants (SNVs), copy number alterations (CNAs) or structural variations (SVs), with each variant type providing complementary insights into tumor evolution as well as offering distinct challenges to phylogenetic inference.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this work, we develop a tumor phylogeny method, TUSV-ext, which incorporates SNVs, CNAs and SVs into a single inference framework. We demonstrate on simulated data that the method produces accurate tree inferences in the presence of all three variant types. We further demonstrate the method through application to real prostate tumor data, showing how our approach to coordinated phylogeny inference and clonal construction with all three variant types can reveal a more complicated clonal structure than is suggested by prior work, consistent with extensive polyclonal seeding or migration.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/github.com\/CMUSchwartzLab\/TUSV-ext.<\/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\/btac253","type":"journal-article","created":{"date-parts":[[2022,4,15]],"date-time":"2022-04-15T19:20:39Z","timestamp":1650050439000},"page":"i125-i133","source":"Crossref","is-referenced-by-count":21,"title":["Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations"],"prefix":"10.1093","volume":"38","author":[{"given":"Xuecong","family":"Fu","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoyun","family":"Lei","sequence":"additional","affiliation":[{"name":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yifeng","family":"Tao","sequence":"additional","affiliation":[{"name":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4970-2252","authenticated-orcid":false,"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, PA 15213, USA"},{"name":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,6,27]]},"reference":[{"key":"2023041407571959300_","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.bbcan.2017.01.003","article-title":"Tumor evolution: linear, branching, neutral or punctuated?","volume":"1867","author":"Davis","year":"2017","journal-title":"Biochim. 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