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.
Original language | English (US) |
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Article number | 241 |
Journal | Genome biology |
Volume | 23 |
Issue number | 1 |
DOIs | |
State | Published - Dec 2022 |
Keywords
- Aneuploidy
- Cancer evolution
- Chromosomal instability
- Intratumor heterogeneity
- Phylogenetic reconstruction
- Single-cell sequencing
- Somatic copy-number alterations
- Whole-genome doubling
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
- Cell Biology