MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Year: 2022
Type: article
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.
Institutions: Max Delbrück Center, Berlin Institute for the Foundations of Learning and Data, Technische Universität Berlin, Humboldt-Universität zu Berlin, Charité – Universitätsmedizin Berlin, The Francis Crick Institute, Freie Universität Berlin, University College London, The University of Texas MD Anderson Cancer Center, University College Hospital, German Cancer Research Center, Deutsches Konsortium für Translationale Krebsforschung, Université Libre de Bruxelles
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: green
Funders: Breast Cancer Research Foundation, Cancer Prevention and Research Institute of Texas, Wellcome Trust, Francis Crick Institute, Cancer Research UK, Foulkes Foundation, Fonds De La Recherche Scientifique - FNRS, Berlin Institute of Health, Medical Research Council, FP7 People: Marie-Curie Actions
OpenAlex ID: W3196894178