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TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

Daehwan Kim1* and Steven L Salzberg123

Author Affiliations

1 Center for Bioinformatics and Computational Biology, 3115 Biomolecular Sciences Building #296, University of Maryland, College Park, MD 20742, USA

2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Broadway Research Building, 733 N Broadway, Baltimore, MD 21205, USA

3 Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA

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Genome Biology 2011, 12:R72  doi:10.1186/gb-2011-12-8-r72

Published: 11 August 2011

Abstract

TopHat-Fusion is an algorithm designed to discover transcripts representing fusion gene products, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. TopHat-Fusion is an enhanced version of TopHat, an efficient program that aligns RNA-seq reads without relying on existing annotation. Because it is independent of gene annotation, TopHat-Fusion can discover fusion products deriving from known genes, unknown genes and unannotated splice variants of known genes. Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/. webcite