Discovery of predictive biomarkers for cancer therapy through computational approaches.

Journal: Nature reviews. Clinical oncology
Published Date:

Abstract

Precision oncology involves the use of predictive biomarkers to personalize treatment. However, for most cancer therapeutics or combination regimens, effective biomarkers have been elusive. This challenge has fuelled efforts to interrogate increasingly diverse and complex clinical and molecular determinants of treatment response. Some molecular predictors have been identified (for example, based on analysis of transcriptomic or imaging data), although the limited reproducibility and robustness of many of these candidate biomarkers make them difficult to apply in clinical practice. Moreover, different types of predictor must often be combined to optimize treatment selection (for example, gene signatures plus patient characteristics). Computational methods, including machine learning and artificial intelligence approaches, provide opportunities to identify predictive patterns in both clinical data and preclinical datasets and to predict treatment response for individual patients. Such approaches also offer opportunities to predict the efficacy or synergy of drug combinations, for example, via extrapolation from correlations of monotherapy responses or by linking the cellular responses observed in preclinical drug screens with molecular and clinical data from patients. In this Review, we describe the application of computational methods to predictive biomarker discovery, including current progress, key challenges facing this field, and future opportunities.

Authors

  • Xin Wang
    Key Laboratory of Bio-based Material Science & Technology (Northeast Forestry University), Ministry of Education, Harbin 150040, China.
  • Julia Nguyen
    University of Toronto, Toronto, Canada.
  • Kristen Nader
    University of Helsinki, Helsinki, Finland.
  • Mitro Miihkinen
    Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland.
  • Patrick Wall
    UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, and School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
  • Akshat Singhal
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
  • Philippe L Bedard
    Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
  • Trey Ideker
  • Tero Aittokallio
    Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00290 Helsinki, Finland.
  • Benjamin Haibe-Kains
    Princess Margaret Cancer Centre, University Health Network, Canada, Toronto, ON, Canada.

Keywords

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