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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution

Kaufmann, Tom L; Petkovic, Marina; Watkins, Thomas BK; Colliver, Emma C; Laskina, Sofya; Thapa, Nisha; Minussi, Darlan C; ... Schwarz, Roland F; + view all (2022) MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biology volume , 23 , Article 241. 10.1186/s13059-022-02794-9. Green open access

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Abstract

Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events. Using simulations and multiple data types from 2780 tumors, we use MEDICC2 to demonstrate accurate inference of phylogenies, clonal and subclonal WGD, and ancestral copy-number states.

Type: Article
Title: MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s13059-022-02794-9
Publisher version: https://doi.org/10.1186/s13059-022-02794-9
Language: English
Additional information: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Keywords: Aneuploidy, Cancer evolution, Chromosomal instability, Intratumor heterogeneity, Phylogenetic reconstruction, Single-cell sequencing, Somatic copy-number alterations, Whole-genome doubling, Humans, Phylogeny, Neoplasms, DNA Copy Number Variations, Exome, Genome, Human
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology
URI: https://discovery.ucl.ac.uk/id/eprint/10160816
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