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novoBreak: local assembly for breakpoint detection in cancer genomes.

  • Author(s): Chong, Zechen;
  • Ruan, Jue;
  • Gao, Min;
  • Zhou, Wanding;
  • Chen, Tenghui;
  • Fan, Xian;
  • Ding, Li;
  • Lee, Anna Y;
  • Boutros, Paul;
  • Chen, Junjie;
  • Chen, Ken
  • et al.
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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