TECHNOLOGY AND CODE article
Front. Bioinform.
Sec. Genomic Analysis
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1615834
Frontiers in Bioinformatics Genomic Analysis Technology and Code GenoPath: A pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data
Provisionally accepted
- 1Temple University, Philadelphia, Pennsylvania, United States
- 2University of Mississippi, Oxford, United States
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DNA sequencing technologies are widely used to study tumor evolution within a cancer patient.However, analyses require various computational methods, including those to infer clone sequences (genotypes of cancer cell populations), clone frequencies within each tumor sample, clone phylogeny, mutational tree, dynamics of mutational signatures, and metastatic cell migration events. Therefore, we developed GenoPath, a streamlined pipeline of existing tools to perform tumor evolution analysis.We also developed and added tools to visualize results to assist interpretation and derive biological insights.We have illustrated GenoPath's utility through a case study of tumor evolution using metastatic prostate cancer data. By reducing computational barriers, GenoPath broadens access to tumor evolution analysis. The software is available at https://github.com/SayakaMiura/GP.
Keywords: evolution, Cancer, Sequencing, somatic mutation, tumor, Phylogency, Mutational process, metastasis
Received: 21 Apr 2025; Accepted: 19 Jun 2025.
Copyright: © 2025 Tobin, Singh, Kumar and Miura. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Sayaka Miura, University of Mississippi, Oxford, United States
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.