tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes

Abstract Summary The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution...

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Bibliographic Details
Published in:Bioinformatics 2020-06, Vol.36 (11), p.3597-3599
Main Authors: Nagornov, Iurii S, Kato, Mamoru
Format: Article
Language:English
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Summary:Abstract Summary The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. Availability and implementation The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. Contact mamkato@ncc.go.jp Supplementary information Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btaa182