MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution
Authors
- T.L. Kaufmann
- M. Petkovic
- T.B.K. Watkins
- E.C. Colliver
- S. Laskina
- N. Thapa
- D.C. Minussi
- N. Navin
- C. Swanton
- P. Van Loo
- K. Haase
- M. Tarabichi
- R.F. Schwarz
Journal
- Genome Biology
Citation
- Genome Biol 23 (1): 241
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.