MEDALT: single-cell copy number lineage tracing enabling gene discovery.
Copy number alteration
Driver discovery
Lineage tracing
Single-cell
Tumor evolution
scDNA-seq
scRNA-seq
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
23 02 2021
23 02 2021
Historique:
received:
25
08
2020
accepted:
09
02
2021
entrez:
24
2
2021
pubmed:
25
2
2021
medline:
13
1
2022
Statut:
epublish
Résumé
We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine named lineage speciation analysis (LSA), whichty facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees. MEDALT appears more accurate than phylogenetics approaches in reconstructing copy number lineage. From data from 20 triple-negative breast cancer patients, our approaches effectively prioritize genes that are essential for breast cancer cell fitness and predict patient survival, including those implicating convergent evolution.The source code of our study is available at https://github.com/KChen-lab/MEDALT .
Identifiants
pubmed: 33622385
doi: 10.1186/s13059-021-02291-5
pii: 10.1186/s13059-021-02291-5
pmc: PMC7901082
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
70Subventions
Organisme : NIH HHS
ID : R01CA172652
Pays : United States
Organisme : NIH HHS
ID : U01CA211006
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA247760
Pays : United States
Organisme : NIH HHS
ID : U01CA247760
Pays : United States
Organisme : University of Texas MD Anderson Cancer Center
ID : U54CA112970
Organisme : NCI NIH HHS
ID : P30 CA016672
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA217842
Pays : United States
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