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NovoBreak: local assembly for breakpoint detection in cancer genomes.

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.

SUBMITTER: Chong Z

PROVIDER: S-EPMC5199621 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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novoBreak: local assembly for breakpoint detection in cancer genomes.

Chong Zechen Z Ruan Jue J Gao Min M Zhou Wanding W Chen Tenghui T Fan Xian X Ding Li L Lee Anna Y AY Boutros Paul P Chen Junjie J Chen Ken K

Nature methods 20161128 1

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. ...[more]

PMID: 27892959

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