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RUBIC identifies driver genes by detecting recurrent DNA copy number breaks

Author

Listed:
  • Ewald van Dyk

    (The Netherlands Cancer Institute
    Delft University of Technology)

  • Marlous Hoogstraat

    (The Netherlands Cancer Institute)

  • Jelle ten Hoeve

    (The Netherlands Cancer Institute)

  • Marcel J. T. Reinders

    (Delft University of Technology)

  • Lodewyk F. A. Wessels

    (The Netherlands Cancer Institute
    Delft University of Technology)

Abstract

The frequent recurrence of copy number aberrations across tumour samples is a reliable hallmark of certain cancer driver genes. However, state-of-the-art algorithms for detecting recurrent aberrations fail to detect several known drivers. In this study, we propose RUBIC, an approach that detects recurrent copy number breaks, rather than recurrently amplified or deleted regions. This change of perspective allows for a simplified approach as recursive peak splitting procedures and repeated re-estimation of the background model are avoided. Furthermore, we control the false discovery rate on the level of called regions, rather than at the probe level, as in competing algorithms. We benchmark RUBIC against GISTIC2 (a state-of-the-art approach) and RAIG (a recently proposed approach) on simulated copy number data and on three SNP6 and NGS copy number data sets from TCGA. We show that RUBIC calls more focal recurrent regions and identifies a much larger fraction of known cancer genes.

Suggested Citation

  • Ewald van Dyk & Marlous Hoogstraat & Jelle ten Hoeve & Marcel J. T. Reinders & Lodewyk F. A. Wessels, 2016. "RUBIC identifies driver genes by detecting recurrent DNA copy number breaks," Nature Communications, Nature, vol. 7(1), pages 1-10, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12159
    DOI: 10.1038/ncomms12159
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