title: FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.
abstract: 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.
  
  
  METHODS
  http://factera.stanford.edu.
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Newman
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Bratman
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Henning
authors.initials: H
authors.lastname: Stehr
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Lee
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Chih Long
authors.initials: CL
authors.lastname: Liu
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Diehn
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA Institute for Stem Cell Biology and Regenerative Medicine, Division of Oncology, Department of Medicine, Department of Radiation Oncology and Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
authors.forename: Ash A
authors.initials: AA
authors.lastname: Alizadeh
mesh_terms: D000465:Algorithms; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics; D002869:Chromosome Aberrations; D056905:Chromosome Breakpoints; D002874:Chromosome Mapping; D050939:Gene Fusion; D023281:Genomics / Q000379:methods; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D014178:Translocation, Genetic