NovoBreak: Local assembly for breakpoint detection in cancer genomes

Zechen Chong; Jue Ruan; Min Gao; Wanding Zhou; Tenghui Chen; Xian Fan; Li Ding; Anna Y. Lee; Paul Boutros; Junjie Chen; Ken Chen

doi:10.1038/nmeth.4084

NovoBreak: Local assembly for breakpoint detection in cancer genomes

Zechen Chong, Jue Ruan, Min Gao, Wanding Zhou, Tenghui Chen, Xian Fan, Li Ding, Anna Y. Lee, Paul Boutros, Junjie Chen, Ken Chen

Research output: Contribution to journal › Article › peer-review

67 Scopus citations

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.

Original language	English (US)
Pages (from-to)	65-67
Number of pages	3
Journal	Nature Methods
Volume	14
Issue number	1
DOIs	https://doi.org/10.1038/nmeth.4084
State	Published - Dec 29 2016

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

MD Anderson CCSG core facilities

Bioinformatics Shared Resource

Access to Document

10.1038/nmeth.4084

Cite this

@article{2ac73e1b4492426580f25ef581c20c6e,

title = "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.",

author = "Zechen Chong and Jue Ruan and Min Gao and Wanding Zhou and Tenghui Chen and Xian Fan and Li Ding and Lee, {Anna Y.} and Paul Boutros and Junjie Chen and Ken Chen",

year = "2016",

month = dec,

day = "29",

doi = "10.1038/nmeth.4084",

language = "English (US)",

volume = "14",

pages = "65--67",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Public Library of Science",

number = "1",

}

TY - JOUR

T1 - NovoBreak

T2 - Local assembly for breakpoint detection in cancer genomes

AU - Chong, Zechen

AU - Ruan, Jue

AU - Gao, Min

AU - Zhou, Wanding

AU - Chen, Tenghui

AU - Fan, Xian

AU - Ding, Li

AU - Lee, Anna Y.

AU - Boutros, Paul

AU - Chen, Junjie

AU - Chen, Ken

PY - 2016/12/29

Y1 - 2016/12/29

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84997610642&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84997610642&partnerID=8YFLogxK

U2 - 10.1038/nmeth.4084

DO - 10.1038/nmeth.4084

M3 - Article

C2 - 27892959

AN - SCOPUS:84997610642

SN - 1548-7091

VL - 14

SP - 65

EP - 67

JO - Nature Methods

JF - Nature Methods

IS - 1

ER -

NovoBreak: Local assembly for breakpoint detection in cancer genomes

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

Access to Document

Other files and links

Fingerprint

Cite this