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

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Item Type:	Article
Title:	MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Creators Name:	Kaufmann, T.L., Petkovic, M., Watkins, T.B.K., Colliver, E.C., Laskina, S., Thapa, N., Minussi, D.C., Navin, N., Swanton, C., Van Loo, P., Haase, K., Tarabichi, M. and Schwarz, R.F.
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.
Keywords:	Somatic Copy-Number Alterations, Chromosomal Instability, Aneuploidy, Whole-Genome Doubling, Intratumor Heterogeneity, Cancer Evolution, Phylogenetic, Reconstruction, Single-Cell Sequencing
Source:	Genome Biology
ISSN:	1474-760X
Publisher:	BMC
Volume:	23
Number:	1
Page Range:	241
Date:	14 November 2022
Official Publication:	https://doi.org/10.1186/s13059-022-02794-9
PubMed:	View item in PubMed

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