{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T05:32:44Z","timestamp":1774935164159,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"Supplement_2","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["LM013385-01"],"award-info":[{"award-number":["LM013385-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["LM012758-02"],"award-info":[{"award-number":["LM012758-02"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Metastases cause a vast majority of cancer morbidity and\u00a0mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells.<\/jats:p>\n                    <jats:p>Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes.<\/jats:p>\n                    <jats:p>In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and\/or existing metastases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PathFinder is available on the web at https:\/\/github.com\/SayakaMiura\/PathFinder.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa795","type":"journal-article","created":{"date-parts":[[2020,9,7]],"date-time":"2020-09-07T15:14:50Z","timestamp":1599491690000},"page":"i675-i683","source":"Crossref","is-referenced-by-count":19,"title":["PathFinder: Bayesian inference of clone migration histories in cancer"],"prefix":"10.1093","volume":"36","author":[{"given":"Sudhir","family":"Kumar","sequence":"first","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"},{"name":"Center\u00a0for Excellence in Genome Medicine and Research, King Abdulaziz University , Jeddah 21589, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonia","family":"Chroni","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koichiro","family":"Tamura","sequence":"additional","affiliation":[{"name":"Research Center for Genomics and Bioinformatics,"},{"name":"Department of Biological Sciences, Tokyo Metropolitan University , Hachioji, Tokyo 192-039, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maxwell","family":"Sanderford","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olumide","family":"Oladeinde","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vivian","family":"Aly","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tracy","family":"Vu","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sayaka","family":"Miura","sequence":"additional","affiliation":[{"name":"Institute for Genomics and Evolutionary Medicine"},{"name":"Department of Biology, Temple University , Philadelphia, PA 19122, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,12,29]]},"reference":[{"key":"2023062409315551900_btaa795-B1","doi-asserted-by":"crossref","first-page":"5139","DOI":"10.1038\/s41467-019-12926-8","article-title":"Rapid evolution and biogeographic spread in a colorectal cancer","volume":"10","author":"Alves","year":"2019","journal-title":"Nat. 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