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

• Published in: Bioinformatics Vol. 30; no. 23; pp. 3390 - 3393
• Main Authors: Newman, Aaron M, Bratman, Scott V, Stehr, Henning, Lee, Luke J, Liu, Chih Long, Diehn, Maximilian, Alizadeh, Ash A
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2014
• Subjects: Algorithms; Alignment; Applications Notes; Bioinformatics; Cancer; Carcinoma, Non-Small-Cell Lung - genetics; Chromosome Aberrations; Chromosome Breakpoints; Chromosome Mapping; Enumeration; Gene Fusion; Gene sequencing; Genomics - methods; Humans; Lung Neoplasms - genetics; Online; Patients; Sequence Analysis, DNA; Software; Translocation, Genetic
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btu549

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. http://factera.stanford.edu.