ArticleBioinformatics (Oxford, England)2020
PathFinder: Bayesian inference of clone migration histories in cancer.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 17 citations in OpenAlex.
- Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.Cell genomics · 2026Article
- VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies.bioRxiv : the preprint server for biology · 2026Article
- Inferring cancer type-specific patterns of metastatic spread using Metient.Nature methods · 2026Article
- Evolutionary dynamics of early and late mutational signatures in metastatic cancer.Frontiers in bioinformatics · 2026Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- Single-cell RNA sequencing reveals different cellular states in malignant cells and the tumor microenvironment in primary and metastatic ER-positive breast cancer.NPJ breast cancer · 2025Article
- GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data.Frontiers in bioinformatics · 2025Article
- Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer.Cancer discovery · 2024Article
- Resolving tumor evolution: a phylogenetic approach.Journal of the National Cancer Center · 2024Review
- Improving cellular phylogenies through the integrated use of mutation order and optimality principles.Computational and structural biotechnology journal · 2023Article
- Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data.Frontiers in bioinformatics · 2023Article
- Article
- Tumors Are Evolutionary Island-Like Ecosystems.Genome biology and evolution · 2021Article
- The somatic molecular evolution of cancer: Mutation, selection, and epistasis.Progress in biophysics and molecular biology · 2021Article
- Migrations of cancer cells through the lens of phylogenetic biogeography.Scientific reports · 2021Article
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Authors and funding
8 authors at 2 institutions in 4 countries.
Funding
Abstract
summaryMetastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells. Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes.In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases. AVAILABILITY AND IMPLEMENTATION: PathFinder is available on the web at https://github.com/SayakaMiura/PathFinder.
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