FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution

Bioinformatics. 2014 Dec 1;30(23):3390-3. doi: 10.1093/bioinformatics/btu549. Epub 2014 Aug 20.


For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment/Map file and produces easily interpretable output. We demonstrate FACTERA's ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets.

Availability and implementation: http://factera.stanford.edu.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Carcinoma, Non-Small-Cell Lung / genetics
  • Chromosome Aberrations*
  • Chromosome Breakpoints*
  • Chromosome Mapping
  • Gene Fusion*
  • Genomics / methods
  • Humans
  • Lung Neoplasms / genetics
  • Sequence Analysis, DNA
  • Software
  • Translocation, Genetic