CoNCoS: copy number estimation in cancer with controlled support.
J Bioinform Comput Biol
; 13(5): 1550027, 2015 Oct.
Article
en En
| MEDLINE
| ID: mdl-26449175
ABSTRACT
Somatic copy number (CN) alterations are major drivers of tumorigenesis and growth. Although next-generation sequencing (NGS) technologies enable a deep genomic analysis of cancers, the analysis of the data remains subject to biases and multiple sources of error, including varying local read coverage. The currently existing algorithms for NGS-based detection of CN abberations do not incorporate information on the local coverage quality. We have developed a new algorithm, copy number estimation with controlled support (CoNCoS) that increases the accuracy of CN estimation in paired tumor/normal exome sequencing data sets by assessing and optimizing the support for a site-specific CN estimate. We show by simulations and in a benchmarking study against single nucleotide polymorphism (SNP) microarray data that our approach outperforms the commonly used methods CNAnorm and VarScan2. Our algorithm is suitable to increase the accuracy of somatic CN analysis by a support-optimized estimation approach.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Contexto en salud:
1_ASSA2030
/
2_ODS3
Problema de salud:
1_doencas_nao_transmissiveis
/
2_muertes_prematuras_enfermedades_notrasmisibles
Asunto principal:
Algoritmos
/
Variaciones en el Número de Copia de ADN
/
Neoplasias
Tipo de estudio:
Evaluation_studies
Límite:
Humans
Idioma:
En
Revista:
J Bioinform Comput Biol
Asunto de la revista:
BIOLOGIA
/
INFORMATICA MEDICA
Año:
2015
Tipo del documento:
Article
País de afiliación:
Alemania