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novoBreak: local assembly for breakpoint detection in cancer genomes.
Chong, Zechen; Ruan, Jue; Gao, Min; Zhou, Wanding; Chen, Tenghui; Fan, Xian; Ding, Li; Lee, Anna Y; Boutros, Paul; Chen, Junjie; Chen, Ken.
  • Chong Z; Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
  • Ruan J; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
  • Gao M; Department of Experimental Radiation Oncology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
  • Zhou W; Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
  • Chen T; Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
  • Fan X; Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
  • Ding L; McDonnell Genome Institute, Washington University, St. Louis, Missouri, USA.
  • Lee AY; Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Boutros P; Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Chen J; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
  • Chen K; Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.
Nat Methods ; 14(1): 65-67, 2017 01.
Article en En | MEDLINE | ID: mdl-27892959
ABSTRACT
We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Análisis de Secuencia de ADN / Secuenciación de Nucleótidos de Alto Rendimiento / Mutación / Neoplasias Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Año: 2017 Tipo del documento: Article
Texto completo
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Análisis de Secuencia de ADN / Secuenciación de Nucleótidos de Alto Rendimiento / Mutación / Neoplasias Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Año: 2017 Tipo del documento: Article