IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0051862.html
   My bibliography  Save this article

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

Author

Listed:
  • Jan Budczies
  • Frederick Klauschen
  • Bruno V Sinn
  • Balázs Győrffy
  • Wolfgang D Schmitt
  • Silvia Darb-Esfahani
  • Carsten Denkert

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.

Suggested Citation

  • Jan Budczies & Frederick Klauschen & Bruno V Sinn & Balázs Győrffy & Wolfgang D Schmitt & Silvia Darb-Esfahani & Carsten Denkert, 2012. "Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-7, December.
    • Handle: RePEc:plo:pone00:0051862
    DOI: 10.1371/journal.pone.0051862
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051862
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0051862&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0051862?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. B Rey deCastro, 2019. "Cumulative ROC curves for discriminating three or more ordinal outcomes with cutpoints on a shared continuous measurement scale," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-16, August.
    2. Claudia Bühnemann & Simon Li & Haiyue Yu & Harriet Branford White & Karl L Schäfer & Antonio Llombart-Bosch & Isidro Machado & Piero Picci & Pancras C W Hogendoorn & Nicholas A Athanasou & J Alison No, 2014. "Quantification of the Heterogeneity of Prognostic Cellular Biomarkers in Ewing Sarcoma Using Automated Image and Random Survival Forest Analysis," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-14, September.
    3. Jin Sheng & Yun-Peng Yang & Yu-Xiang Ma & Tao Qin & Zhi-Huang Hu & Shao-Dong Hong & Ting Zhou & Yan Huang & Hong-Yun Zhao & Li Zhang, 2016. "Low Prognostic Nutritional Index Correlates with Worse Survival in Patients with Advanced NSCLC following EGFR-TKIs," PLOS ONE, Public Library of Science, vol. 11(1), pages 1-12, January.
    4. Hyungjin Kim & Chang Min Park & Bhumsuk Keam & Sang Joon Park & Miso Kim & Tae Min Kim & Dong-Wan Kim & Dae Seog Heo & Jin Mo Goo, 2017. "The prognostic value of CT radiomic features for patients with pulmonary adenocarcinoma treated with EGFR tyrosine kinase inhibitors," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-13, November.
    5. Eike Steidl & Ulrich Pilatus & Elke Hattingen & Joachim P Steinbach & Friedhelm Zanella & Michael W Ronellenfitsch & Oliver Bähr, 2016. "Myoinositol as a Biomarker in Recurrent Glioblastoma Treated with Bevacizumab: A 1H-Magnetic Resonance Spectroscopy Study," PLOS ONE, Public Library of Science, vol. 11(12), pages 1-15, December.
    6. Özge Özgüç & Ludmilla de Plater & Varun Kapoor & Anna Francesca Tortorelli & Andrew G Clark & Jean-Léon Maître, 2022. "Cortical softening elicits zygotic contractility during mouse preimplantation development," PLOS Biology, Public Library of Science, vol. 20(3), pages 1-23, March.
    7. Douglas Adamoski & Larissa M. dos Reis & Ana Carolina Paschoalini Mafra & Felipe Corrêa-da-Silva & Pedro Manoel Mendes de Moraes-Vieira & Ioana Berindan-Neagoe & George A. Calin & Sandra Martha Gomes , 2024. "HuR controls glutaminase RNA metabolism," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    8. Elisa I. Rivas & Jenniffer Linares & Melissa Zwick & Andrea Gómez-Llonin & Marc Guiu & Anna Labernadie & Jordi Badia-Ramentol & Anna Lladó & Lídia Bardia & Iván Pérez-Núñez & Carolina Martínez-Ciarpag, 2022. "Targeted immunotherapy against distinct cancer-associated fibroblasts overcomes treatment resistance in refractory HER2+ breast tumors," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0051862. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.