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Zolotovskaia MA, Sorokin MI, Roumiantsev SA, et al. Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers. Front Oncol. 2019;8:658doi: 10.3389/fonc.2018.00658.
Zolotovskaia, M. A., Sorokin, M. I., Roumiantsev, S. A., Borisov, N. M., & Buzdin, A. A. (2018). Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers. Frontiers in oncology, 8658. https://doi.org/10.3389/fonc.2018.00658
Zolotovskaia, Marianna A, et al. "Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers." Frontiers in oncology vol. 8 (2018): 658. doi: https://doi.org/10.3389/fonc.2018.00658
Zolotovskaia MA, Sorokin MI, Roumiantsev SA, Borisov NM, Buzdin AA. Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers. Front Oncol. 2019 Jan 04;8:658. doi: 10.3389/fonc.2018.00658. eCollection 2018. PMID: 30662873; PMCID: PMC6328788.
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Front Oncol. 2019 Jan 04;8:658. doi: 10.3389/fonc.2018.00658. eCollection 2018.

Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers.

Frontiers in oncology

Marianna A Zolotovskaia, Maxim I Sorokin, Sergey A Roumiantsev, Nikolay M Borisov, Anton A Buzdin

Affiliations

  1. Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia.
  2. Oncobox Ltd., Moscow, Russia.
  3. The Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
  4. Omicsway Corp., Walnut, CA, United States.
  5. The Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.

PMID: 30662873 PMCID: PMC6328788 DOI: 10.3389/fonc.2018.00658

Abstract

DNA mutations play a crucial role in cancer development and progression. Mutation profiles vary dramatically in different cancer types and between individual tumors. Mutations of several individual genes are known as reliable cancer biomarkers, although the number of such genes is tiny and does not enable differential diagnostics for most of the cancers. We report here a technique enabling dramatically increased efficiency of cancer biomarkers development using DNA mutations data. It includes a quantitative metric termed Pathway instability (PI) based on mutations enrichment of intracellular molecular pathways. This method was tested on 5,956 tumor mutation profiles of 15 cancer types from The Cancer Genome Atlas (TCGA) project. Totally, we screened 2,316,670 mutations in 19,872 genes and 1,748 molecular pathways. Our results demonstrated considerable advantage of pathway-based mutation biomarkers over individual gene mutation profiles, as reflected by more than two orders of magnitude greater numbers by high-quality [ROC area-under-curve (AUC)>0.75] biomarkers. For example, the number of such high-quality mutational biomarkers distinguishing between different cancer types was only six for the individual gene mutations, and already 660 for the pathway-based biomarkers. These results evidence that PI value can be used as a new generation of complex cancer biomarkers significantly outperforming the existing gene mutation biomarkers.

Keywords: DNA mutation; biomarker; cancer; molecular pathways; pathway instability

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