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Updated: Mar 11, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
novoBreak: local assembly for breakpoint detection in cancer genomes
Zechen Chong1, Jue Ruan2, Min Gao3
1Department of Bioinformatics and Computational Biology, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA.
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.
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