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Nat Methods. 2017 Jan;14(1):65-67. doi: 10.1038/nmeth.4084. Epub 2016 Nov 28.

novoBreak: local assembly for breakpoint detection in cancer genomes.

Author information

1
Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
2
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
3
Department of Experimental Radiation Oncology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
4
McDonnell Genome Institute, Washington University, St. Louis, Missouri, USA.
5
Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
6
Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
7
Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.

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.

PMID:
27892959
PMCID:
PMC5199621
DOI:
10.1038/nmeth.4084
[Indexed for MEDLINE]
Free PMC Article

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