ArticleBMC bioinformatics2020
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- Clinical application of tumour-in-normal contamination assessment from whole genome sequencing.Nature communications · 2024Pooled it
- Mosaic Accumulation of Somatic Genetic Variation and Estimates of Age in the Long-Lived Reef-Building Coral Acropora palmata.Molecular ecology · 2026Article
- Dissecting cancer in a non-mammalian model: genomic insights from lemon frost geckos.BMC biology · 2026Article
- Competing subclones and fitness diversity shape tumor evolution across cancer types.Bioinformatics (Oxford, England) · 2026Article
- Antimutator and Mutational Spectrum Effects Can Combine to Reduce Evolutionary Potential in Escherichia coli ΔnudJ.Molecular biology and evolution · 2025Article
- Article
- Advancing precision oncology with AI-powered genomic analysis.Frontiers in pharmacology · 2025Review
- The Evolutionary Interplay of Somatic and Germline Mutation Rates.Annual review of biomedical data science · 2024Review
- Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.Genome biology · 2024Article
- Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of oesophagael adenocarcinoma.Research square · 2023Article
- Bioinformatics roadmap for therapy selection in cancer genomics.Molecular oncology · 2022Review
- J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments.BMC bioinformatics · 2022Article
- Measuring competitive exclusion in non-small cell lung cancer.Science advances · 2022Article
- Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin.Nature biotechnology · 2022Article
- DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy.Signal transduction and targeted therapy · 2021Review
- Computational Reconstruction of Clonal Hierarchies From Bulk Sequencing Data of Acute Myeloid Leukemia Samples.Frontiers in physiology · 2021Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution methods are used to determine the composition of cancer subpopulations in the biopsy sample, a fundamental step to determine clonal expansions and their evolutionary trajectories.
resultsIn a recent work we have developed a new model-based approach to carry out subclonal deconvolution from the site frequency spectrum of somatic mutations. This new method integrates, for the first time, an explicit model for neutral evolutionary forces that participate in clonal expansions; in that work we have also shown that our method improves largely over competing data-driven methods. In this Software paper we present mobster, an open source R package built around our new deconvolution approach, which provides several functions to plot data and fit models, assess their confidence and compute further evolutionary analyses that relate to subclonal deconvolution.
conclusionsWe present the mobster package for tumour subclonal deconvolution from bulk sequencing, the first approach to integrate Machine Learning and Population Genetics which can explicitly model co-existing neutral and positive selection in cancer. We showcase the analysis of two datasets, one simulated and one from a breast cancer patient, and overview all package functionalities.
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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.