ArticleFrontiers in oncology2018
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers.
Article in Frontiers in oncology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Forced Overexpression and Knockout Analysis of SLC30A and SLC39A Family Genes Suggests Their Involvement in Establishing Resistance to Cisplatin in Human Cancer Cells.International journal of molecular sciences · 2024Article
- Genomic events stratifying prognosis of early gastric cancer.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2024Article
- Quantified pathway mutations associate epithelial-mesenchymal transition and immune escape with poor prognosis and immunotherapy resistance of head and neck squamous cell carcinoma.BMC medical genomics · 2024Article
- Underexploited Brazilian Cerrado fruits as sources of phenolic compounds for diseases management: A review.Food chemistry. Molecular sciences · 2022Article
- Personalized targeted therapy prescription in colorectal cancer using algorithmic analysis of RNA sequencing data.BMC cancer · 2022Article
- OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization.Computational and structural biotechnology journal · 2022Article
- Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles.Frontiers in oncology · 2021Article
- System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation.International journal of molecular sciences · 2020Article
- Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments.BMC medical genomics · 2020Article
- RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens.Biomedicines · 2020Article
- RNA sequencing profiles and diagnostic signatures linked with response to ramucirumab in gastric cancer.Cold Spring Harbor molecular case studies · 2020Article
- Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology.International journal of molecular sciences · 2020Article
- Article
- Molecular heterogeneity in breast carcinoma cells with increased invasive capacities.Radiology and oncology · 2020Article
- Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer.Cancers · 2020Article
- Article
- Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small-Cell Lung Cancer.Molecular diagnosis & therapy · 2019Article
- High-Throughput Mutation Data Now Complement Transcriptomic Profiling: Advances in Molecular Pathway Activation Analysis Approach in Cancer Biology.Cancer informatics · 2019Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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