MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
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Tom L Kaufmann Marina Petkovic Tom Watkins Emma C Colliver Sofya Laskina Nisha Thapa Darlan C Minussi Nicholas Navin Charles Swanton Peter Van Loo Kerstin Haase Maxime Tarabichi Roland F SchwarzAbstract
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.
Journal details
Journal Genome Biology
Volume 23
Issue number 1
Pages 241
Available online
Publication date
Full text links
Publisher website (DOI) 10.1186/s13059-022-02794-9
Europe PubMed Central 36376909
Pubmed 36376909