Clonality inference in multiple tumor samples using phylogeny.
Bioinformatics
; 31(9): 1349-56, 2015 May 01.
Article
en En
| MEDLINE
| ID: mdl-25568283
ABSTRACT
MOTIVATION Intra-tumor heterogeneity presents itself through the evolution of subclones during cancer progression. Although recent research suggests that this heterogeneity has clinical implications, in silico determination of the clonal subpopulations remains a challenge. RESULTS:
We address this problem through a novel combinatorial method, named clonality inference in tumors using phylogeny (CITUP), that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and deep sequencing data from two cancer studies, we show that CITUP predicts clonal frequencies and the underlying phylogeny with high accuracy. AVAILABILITY AND IMPLEMENTATION CITUP is freely available at http//sourceforge.net/projects/citup/. CONTACT cenk@sfu.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Filogenia
/
Algoritmos
/
Evolución Clonal
/
Neoplasias
Tipo de estudio:
Evaluation_studies
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2015
Tipo del documento:
Article
País de afiliación:
Estados Unidos