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Selecting predictive biomarkers from genomic data

Author

Listed:
  • Florian Frommlet
  • Piotr Szulc
  • Franz König
  • Malgorzata Bogdan

Abstract

Recently there have been tremendous efforts to develop statistical procedures which allow to determine subgroups of patients for which certain treatments are effective. This article focuses on the selection of prognostic and predictive genetic biomarkers based on a relatively large number of candidate Single Nucleotide Polymorphisms (SNPs). We consider models which include prognostic markers as main effects and predictive markers as interaction effects with treatment. We compare different high-dimensional selection approaches including adaptive lasso, a Bayesian adaptive version of the Sorted L-One Penalized Estimator (SLOBE) and a modified version of the Bayesian Information Criterion (mBIC2). These are compared with classical multiple testing procedures for individual markers. Having identified predictive markers we consider several different approaches how to specify subgroups susceptible to treatment. Our main conclusion is that selection based on mBIC2 and SLOBE has similar predictive performance as the adaptive lasso while including substantially fewer biomarkers.

Suggested Citation

  • Florian Frommlet & Piotr Szulc & Franz König & Malgorzata Bogdan, 2022. "Selecting predictive biomarkers from genomic data," PLOS ONE, Public Library of Science, vol. 17(6), pages 1-21, June.
    • Handle: RePEc:plo:pone00:0269369
    DOI: 10.1371/journal.pone.0269369
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    References listed on IDEAS

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