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
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author Chong, Zechen
Ruan, Jue
Gao, Min
Zhou, Wanding
Chen, Tenghui
Fan, Xian
Ding, Li
Lee, Anna Y.
Boutros, Paul
Chen, Junjie
Chen, Ken
author_facet Chong, Zechen
Ruan, Jue
Gao, Min
Zhou, Wanding
Chen, Tenghui
Fan, Xian
Ding, Li
Lee, Anna Y.
Boutros, Paul
Chen, Junjie
Chen, Ken
author_sort Chong, Zechen
collection PubMed
description 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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spelling pubmed-51996212017-05-28 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 Nat Methods Article 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/. 2016-11-28 2017-01 /pmc/articles/PMC5199621/ /pubmed/27892959 http://dx.doi.org/10.1038/nmeth.4084 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Chong, Zechen
Ruan, Jue
Gao, Min
Zhou, Wanding
Chen, Tenghui
Fan, Xian
Ding, Li
Lee, Anna Y.
Boutros, Paul
Chen, Junjie
Chen, Ken
novoBreak: local assembly for breakpoint detection in cancer genomes
title novoBreak: local assembly for breakpoint detection in cancer genomes
title_full novoBreak: local assembly for breakpoint detection in cancer genomes
title_fullStr novoBreak: local assembly for breakpoint detection in cancer genomes
title_full_unstemmed novoBreak: local assembly for breakpoint detection in cancer genomes
title_short novoBreak: local assembly for breakpoint detection in cancer genomes
title_sort novobreak: local assembly for breakpoint detection in cancer genomes
topic Article
url 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
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