Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers
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...
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doaj-9d5a087202d843fda65d7799bc1bf3b52020-11-24T23:58:06ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2019-01-01810.3389/fonc.2018.00658431722Pathway Instability Is an Effective New Mutation-Based Type of Cancer BiomarkersMarianna A. Zolotovskaia0Marianna A. Zolotovskaia1Maxim I. Sorokin2Maxim I. Sorokin3Sergey A. Roumiantsev4Nikolay M. Borisov5Nikolay M. Borisov6Anton A. Buzdin7Anton A. Buzdin8Anton A. Buzdin9Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, RussiaOncobox Ltd., Moscow, RussiaThe Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, RussiaOmicsway Corp., Walnut, CA, United StatesDepartment of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, RussiaOncobox Ltd., Moscow, RussiaThe Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, RussiaThe Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, RussiaOmicsway Corp., Walnut, CA, United StatesThe Laboratory of Systems Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, RussiaDNA 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.https://www.frontiersin.org/article/10.3389/fonc.2018.00658/fullcancerDNA mutationmolecular pathwaysbiomarkerpathway instability |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Marianna A. Zolotovskaia Marianna A. Zolotovskaia Maxim I. Sorokin Maxim I. Sorokin Sergey A. Roumiantsev Nikolay M. Borisov Nikolay M. Borisov Anton A. Buzdin Anton A. Buzdin Anton A. Buzdin |
spellingShingle |
Marianna A. Zolotovskaia Marianna A. Zolotovskaia Maxim I. Sorokin Maxim I. Sorokin Sergey A. Roumiantsev Nikolay M. Borisov Nikolay M. Borisov Anton A. Buzdin Anton A. Buzdin Anton A. Buzdin Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers Frontiers in Oncology cancer DNA mutation molecular pathways biomarker pathway instability |
author_facet |
Marianna A. Zolotovskaia Marianna A. Zolotovskaia Maxim I. Sorokin Maxim I. Sorokin Sergey A. Roumiantsev Nikolay M. Borisov Nikolay M. Borisov Anton A. Buzdin Anton A. Buzdin Anton A. Buzdin |
author_sort |
Marianna A. Zolotovskaia |
title |
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers |
title_short |
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers |
title_full |
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers |
title_fullStr |
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers |
title_full_unstemmed |
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers |
title_sort |
pathway instability is an effective new mutation-based type of cancer biomarkers |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Oncology |
issn |
2234-943X |
publishDate |
2019-01-01 |
description |
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. |
topic |
cancer DNA mutation molecular pathways biomarker pathway instability |
url |
https://www.frontiersin.org/article/10.3389/fonc.2018.00658/full |
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