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. and Petkovic, M. and Watkins, T.B.K. and Colliver, E.C. and Laskina, S. and Thapa, N. and Minussi, D.C. and Navin, N. and Swanton, C. and Van Loo, P. and Haase, K. and 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:

Number:

Page Range:

241

Date:

14 November 2022