MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Aneuploidy
Cancer evolution
Chromosomal instability
Intratumor heterogeneity
Phylogenetic reconstruction
Single-cell sequencing
Somatic copy-number alterations
Whole-genome doubling
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
14 11 2022
14 11 2022
Historique:
received:
15
11
2021
accepted:
12
10
2022
entrez:
15
11
2022
pubmed:
16
11
2022
medline:
18
11
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 36376909
doi: 10.1186/s13059-022-02794-9
pii: 10.1186/s13059-022-02794-9
pmc: PMC9661799
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
241Subventions
Organisme : Cancer Research UK
ID : FC001169
Pays : United Kingdom
Organisme : Cancer Research UK
ID : FC001202
Pays : United Kingdom
Organisme : Medical Research Council
ID : FC001169
Pays : United Kingdom
Organisme : Medical Research Council
ID : FC001202
Pays : United Kingdom
Organisme : Wellcome Trust
ID : FC001169
Pays : United Kingdom
Organisme : Wellcome Trust
ID : FC001202
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/L016311/1
Pays : United Kingdom
Informations de copyright
© 2022. The Author(s).
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