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.
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Zechen
authors.initials: Z
authors.lastname: Chong
authors.affiliation: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
authors.forename: Jue
authors.initials: J
authors.lastname: Ruan
authors.affiliation: Department of Experimental Radiation Oncology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Gao
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Wanding
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Tenghui
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Xian
authors.initials: X
authors.lastname: Fan
authors.affiliation: McDonnell Genome Institute, Washington University, St. Louis, Missouri, USA.
authors.forename: Li
authors.identifier: 0000-0003-1517-2975
authors.initials: L
authors.lastname: Ding
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: Anna Y
authors.identifier: 0000-0001-8197-6272
authors.initials: AY
authors.lastname: Lee
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.|Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Paul
authors.identifier: 0000-0003-0553-7520
authors.initials: P
authors.lastname: Boutros
authors.affiliation: Department of Experimental Radiation Oncology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Junjie
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D056905:Chromosome Breakpoints; D019295:Computational Biology; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014407:Tumor Cells, Cultured