Journal Article

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

Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer and Vineet Bafna

in Bioinformatics

Volume 27, issue 8, pages 1068-1075
Published in print April 2011 | ISSN: 1367-4803
Published online February 2011 | e-ISSN: 1460-2059 | DOI:
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs

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Motivation: 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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6002 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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