novoBreak: local assembly for breakpoint detection in cancer genomes

We present novoBreak, a novel genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole genome sequencing data. In the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge and real cancer genome data analysis, novoBreak consistently outperfo...

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Detalles Bibliográficos
Autores principales: Chong, Zechen, Ruan, Jue, Gao, Min, Zhou, Wanding, Chen, Tenghui, Fan, Xian, Ding, Li, Lee, Anna Y., Boutros, Paul, Chen, Junjie, Chen, Ken
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2016
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199621/
https://www.ncbi.nlm.nih.gov/pubmed/27892959
http://dx.doi.org/10.1038/nmeth.4084
Descripción
Sumario:We present novoBreak, a novel genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole genome sequencing data. In the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge and real cancer genome data analysis, novoBreak consistently outperformed existing algorithms due largely to more effective utilization of reads spanning breakpoints. NovoBreak also demonstrated great sensitivity in identifying short INDELs. The source code is available at http://sourceforge.net/projects/novobreak/.

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