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

par Kaufmann, Tom;Petkovic, Marina;Watkins, Thomas B K;Colliver, Emma;Laskina, Sofya;Thapa, Nisha;Minussi, Darlan;Navin, Nicholas;Swanton, Charles;Van Loo, Peter;Haase, Kerstin;Tarabichi, Maxime ;Schwarz, Roland F.
Référence Genome biology, 23, 1
Publication Publié, 2022-12

Article révisé par les pairs

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Résumé :

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.