{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:14:36Z","timestamp":1775981676170,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T00:00:00Z","timestamp":1661299200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["310030_179518"],"award-info":[{"award-number":["310030_179518"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patient\u2019s tumour composition and evolutionary history is key for personalized therapies. Single-cell sequencing (SCS) now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the complexity of the underlying evolutionary process.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>By modelling the noise processes and allowing mutations to be lost or to reoccur during tumour evolution, we present a method to jointly call mutations in each cell, reconstruct the phylogenetic relationship between cells, and determine the locations of mutational losses and recurrences. Our Bayesian approach allows us to accurately call mutations as well as to quantify our certainty in such predictions. We show the advantages of allowing mutational loss or recurrence with simulated data and present its application to tumour SCS data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SCI\u03a6N is available at https:\/\/github.com\/cbg-ethz\/SCIPhIN.<\/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\/btac577","type":"journal-article","created":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T09:35:41Z","timestamp":1661333741000},"page":"4713-4719","source":"Crossref","is-referenced-by-count":15,"title":["Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence"],"prefix":"10.1093","volume":"38","author":[{"given":"Jack","family":"Kuipers","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland"}]},{"given":"Jochen","family":"Singer","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0573-6119","authenticated-orcid":false,"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2022,8,24]]},"reference":[{"key":"2022101415193730100_btac577-B2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.trecan.2016.04.002","article-title":"Re-evaluating clonal dominance in cancer evolution","volume":"2","author":"Burrell","year":"2016","journal-title":"Trends Cancer"},{"key":"2022101415193730100_btac577-B3","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nature12625","article-title":"The causes and consequences of genetic heterogeneity in cancer evolution","volume":"501","author":"Burrell","year":"2013","journal-title":"Nature"},{"key":"2022101415193730100_btac577-B4","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nrclinonc.2017.166","article-title":"Tumour heterogeneity and resistance to cancer therapies","volume":"15","author":"Dagogo-Jack","year":"2018","journal-title":"Nat. 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