Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

TitleSensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Publication TypeJournal Article
Year of Publication2011
AuthorsKinsella, M, Harismendy, O, Nakano, M, Frazer, KA, Bafna, V
JournalBioinformatics
Volume27
Issue8
Pagination1068-75
Date Published2011 Apr 15
ISSN1367-4811
iDASH CategoryGenomics
AbstractMOTIVATION: 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. AVAILABILITY: A C++ and Python implementation of the method demonstrated in this article is available at http://exon.ucsd.edu/ShortFuse. CONTACT: mckinsel@ucsd.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
DOI10.1093/bioinformatics/btr085
Alternate JournalBioinformatics
PubMed ID21330288