title: Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
abstract: BACKGROUND
  Paired-end whole transcriptome sequencing provides evidence for fusion transcripts. However, due to the repetitiveness of the transcriptome, many reads have multiple high-quality mappings. Previous methods to find gene fusions either ignored these reads or required additional longer single reads. This can obscure up to 30% of fusions and unnecessarily discards much of the data.
  
  
  RESULTS
  We present a method for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing. Using simulated data and data from tumors and cell lines, we show that our method can find fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.
  
  
  BACKGROUND
  A C++ and Python implementation of the method demonstrated in this article is available at http://exon.ucsd.edu/ShortFuse.
  
  
  BACKGROUND
  mckinsel@ucsd.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics and Systems Biology Program, Moores UCSD Cancer Center, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA. mckinsel@ucsd.edu
authors.forename: Marcus
authors.initials: M
authors.lastname: Kinsella
authors.forename: Olivier
authors.initials: O
authors.lastname: Harismendy
authors.forename: Masakazu
authors.initials: M
authors.lastname: Nakano
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
mesh_terms: D002460:Cell Line; D020869:Gene Expression Profiling; D050939:Gene Fusion; D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger