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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

    X
  • Abdalnasser Zayed,

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

    X
  • Ryan Giuliany,

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

    X
  • Gavin Ha,

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

    X
  • 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

    X
  • 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

    X
  • 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

    X
  • 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

Reader Comments (3)

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Definition of Specificity at Table 4

Posted by nlsim on 08 Sep 2011 at 07:18 GMT

Greetings,

Just wondering if Specificity should be TN / (TN + FP) instead of TP / (TP + FP)? If the former is correct, then the Specificity values for deFuse-Threshold, deFuse-Classifier and FusionSeq should be 4/7, 3/4 and 0 respectively, instead of 100%, 94% and 76.5%...

No competing interests declared.

RE: Definition of Specificity at Table 4

sohrab replied to nlsim on 13 Sep 2011 at 20:48 GMT

Hello nlsim -
Thank you for pointing this out. You are correct that the numbers reported are not specificity. Rather they are positive predictive value (PPV). The Table 4 column header for the last column should therefore instead be PPV. It is also true that the actual specificity values should be: 4/7, 3/4 and 0 respectively as you state in your comment.

No competing interests declared.