FusionHunter: Identifying fusion transcripts in cancer using paired-end RNA-seq

Yang Li, Jeremy Chien, David I Smith, Jian Ma

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Motivation: Fusion transcripts can be created as a result of genome rearrangement in cancer. Some of them play important roles in carcinogenesis, and can serve as diagnostic and therapeutic targets. With more and more cancer genomes being sequenced by next-generation sequencing technologies, we believe an efficient tool for reliably identifying fusion transcripts will be desirable for many groups.Results: We designed and implemented an open-source software tool, called FusionHunter, which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. We show that FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory.

Original languageEnglish (US)
Article numberbtr265
Pages (from-to)1708-1710
Number of pages3
JournalBioinformatics
Volume27
Issue number12
DOIs
StatePublished - Jun 2011

Fingerprint

RNA
Cancer
Fusion
Fusion reactions
Genome
Neoplasms
Carcinogenesis
Software
Technology
Sensitivity and Specificity
Polymerase Chain Reaction
Genes
Genome Rearrangement
Open Source Software
Software Tools
Sequencing
Specificity
Diagnostics
Therapeutics
Target

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

FusionHunter : Identifying fusion transcripts in cancer using paired-end RNA-seq. / Li, Yang; Chien, Jeremy; Smith, David I; Ma, Jian.

In: Bioinformatics, Vol. 27, No. 12, btr265, 06.2011, p. 1708-1710.

Research output: Contribution to journalArticle

Li, Yang ; Chien, Jeremy ; Smith, David I ; Ma, Jian. / FusionHunter : Identifying fusion transcripts in cancer using paired-end RNA-seq. In: Bioinformatics. 2011 ; Vol. 27, No. 12. pp. 1708-1710.
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