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

2014; Oxford University Press; Volume: 30; Issue: 23 Linguagem: Inglês

10.1093/bioinformatics/btu549

1367-4811

Aaron M. Newman, Scott V. Bratman, Henning Stehr, Luke J. Lee, Chih Long Liu, Maximilian Diehn, Ash A. Alizadeh,

Cholangiocarcinoma and Gallbladder Cancer Studies

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.