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Research Article

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

  • Andrew McPherson,

    Affiliations: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada, School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada

    X
  • Fereydoun Hormozdiari,

    Affiliation: School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada

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  • Abdalnasser Zayed,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Ryan Giuliany,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Gavin Ha,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Mark G. F. Sun,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Malachi Griffith,

    Affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Alireza Heravi Moussavi,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Janine Senz,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Nataliya Melnyk,

    Affiliation: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Marina Pacheco,

    Affiliation: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada

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  • Marco A. Marra,

    Affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Martin Hirst,

    Affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada

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  • Torsten O. Nielsen,

    Affiliation: Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada

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  • S. Cenk Sahinalp,

    Affiliation: School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada

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  • David Huntsman,

    Affiliations: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada

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  • Sohrab P. Shah mail

    sshah@bccrc.ca

    Affiliations: Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada, Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada

    X
  • Published: May 19, 2011
  • DOI: 10.1371/journal.pcbi.1001138

About the Authors

Andrew McPherson, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, David Huntsman, Sohrab P. Shah
Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
Andrew McPherson, Fereydoun Hormozdiari, S. Cenk Sahinalp
School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
Malachi Griffith, Marco A. Marra, Martin Hirst
Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
Marina Pacheco, Torsten O. Nielsen, David Huntsman, Sohrab P. Shah
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
Sohrab P. Shah
Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada

Corresponding Author

Email: sshah@bccrc.ca

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: AM AZ MAM MH TON SCS DH SPS. Performed the experiments: AM. Analyzed the data: AM. Contributed reagents/materials/analysis tools: AM. Wrote the paper: AM SPS. Assisted with algorithm development: FH. Software development: RG MGFS. Copy number variation analysis: GH. Development of precursor software: MG. Gene expression analysis: AHM. RT-PCR validation: JS. FISH validation: NM MP.