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

Daehwan Kim, Steven L. Salzberg

Research output: Contribution to journalArticlepeer-review

600 Scopus citations


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.

Original languageEnglish (US)
Article numberR72
JournalGenome biology
Issue number8
StatePublished - Aug 11 2011

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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