Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization

Jan Budczies, Frederick Klauschen, Bruno V. Sinn, Balázs Gyorffy, Wolfgang D. Schmitt, Silvia Darb-Esfahani, Carsten Denkert

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527 Citations (Scopus)

Abstract

Gene or protein expression data are usually represented by metric or at least ordinal variables. In order to translate a continuous variable into a clinical decision, it is necessary to determine a cutoff point and to stratify patients into two groups each requiring a different kind of treatment. Currently, there is no standard method or standard software for biomarker cutoff determination. Therefore, we developed Cutoff Finder, a bundle of optimization and visualization methods for cutoff determination that is accessible online. While one of the methods for cutoff optimization is based solely on the distribution of the marker under investigation, other methods optimize the correlation of the dichotomization with respect to an outcome or survival variable. We illustrate the functionality of Cutoff Finder by the analysis of the gene expression of estrogen receptor (ER) and progesterone receptor (PgR) in breast cancer tissues. This distribution of these important markers is analyzed and correlated with immunohistologically determined ER status and distant metastasis free survival. Cutoff Finder is expected to fill a relevant gap in the available biometric software repertoire and will enable faster optimization of new diagnostic biomarkers. The tool can be accessed at http://molpath.charite.de/cutoff.

Original languageEnglish
Article numbere51862
JournalPloS one
Volume7
Issue number12
DOIs
Publication statusPublished - Dec 14 2012

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Budczies, J., Klauschen, F., Sinn, B. V., Gyorffy, B., Schmitt, W. D., Darb-Esfahani, S., & Denkert, C. (2012). Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization. PloS one, 7(12), [e51862]. https://doi.org/10.1371/journal.pone.0051862