ArticleBioinformatics (Oxford, England)2018
Predicting clone genotypes from tumor bulk sequencing of multiple samples.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 36 citations in OpenAlex.
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- Evolutionary dynamics of early and late mutational signatures in metastatic cancer.Frontiers in bioinformatics · 2026Article
- Whole exome sequencing and single-cell DNA sequencing for assessment of clonal heterogeneity and evolution in acute myeloid leukemia.Computational and structural biotechnology journal · 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
- Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data.Frontiers in bioinformatics · 2023Article
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- Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution.Molecular biology and evolution · 2022Article
- Accurate Identification of Subclones in Tumor Genomes.Molecular biology and evolution · 2022Article
- A phylogenetic approach to study the evolution of somatic mutational processes in cancer.Communications biology · 2022Article
- COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics.Zoological research · 2022Article
- Tumors Are Evolutionary Island-Like Ecosystems.Genome biology and evolution · 2021Article
- Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.Nature communications · 2021Article
- PathFinder: Bayesian inference of clone migration histories in cancer.Bioinformatics (Oxford, England) · 2020Article
- Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo.Cancers · 2020Article
- Molecular Biology and Evolution of Cancer: From Discovery to Action.Molecular biology and evolution · 2020Article
- Algorithmic approaches to clonal reconstruction in heterogeneous cell populations.Quantitative biology (Beijing, China) · 2019Article
- Article
- Rapid evolution and biogeographic spread in a colorectal cancer.Nature communications · 2019Article
- Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology.Cancers · 2019Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Motivation: Analyses of data generated from bulk sequencing of tumors have revealed extensive genomic heterogeneity within patients. Many computational methods have been developed to enable the inference of genotypes of tumor cell populations (clones) from bulk sequencing data. However, the relative and absolute accuracy of available computational methods in estimating clone counts and clone genotypes is not yet known. Results: We have assessed the performance of nine methods, including eight previously-published and one new method (CloneFinder), by analyzing computer simulated datasets. CloneFinder, LICHeE, CITUP and cloneHD inferred clone genotypes with low error (<5% per clone) for a majority of datasets in which the tumor samples contained evolutionarily-related clones. Computational methods did not perform well for datasets in which tumor samples contained mixtures of clones from different clonal lineages. Generally, the number of clones was underestimated by cloneHD and overestimated by PhyloWGS, and BayClone2, Canopy and Clomial required prior information regarding the number of clones. AncesTree and Canopy did not produce results for a large number of datasets. Overall, the deconvolution of clone genotypes from single nucleotide variant (SNV) frequency differences among tumor samples remains challenging, so there is a need to develop more accurate computational methods and robust software for clone genotype inference. Availability and implementation: CloneFinder is implemented in Python and is available from https://github.com/gstecher/CloneFinderAPI. Supplementary information: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.