ArticleNature communications2021
Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- Gemogenovatucel-T Advantage in Clonal Tumor Mutation Burden-High Ovarian Cancer.JCO precision oncology · 2026Trial
- Exome sequencing shows same pattern of clonal tumor mutational burden, intratumor heterogenicity and clonal neoantigen between autologous tumor and Vigil product.Scientific reports · 2025Trial
- Machine learning uncovers previously undetectable genetic deletions in cancer panel sequencing.NPJ precision oncology · 2026Article
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Multi-omic analysis identifies a multi-step pathology in a case of multiple chorangioma syndrome in monochorionic twins.Orphanet journal of rare diseases · 2026Article
- Identification and prognostic assessment of clonal and functional heterogeneity in head and neck squamous cell carcinoma.Translational cancer research · 2025Article
- Article
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Detecting and quantifying clonal selection in somatic stem cells.Nature genetics · 2025Article
- 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
- The evolutionary theory of cancer: challenges and potential solutions.Nature reviews. Cancer · 2024Review
- The Evolutionary Interplay of Somatic and Germline Mutation Rates.Annual review of biomedical data science · 2024Review
- Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer.Nature communications · 2024Article
- Computational immunogenomic approaches to predict response to cancer immunotherapies.Nature reviews. Clinical oncology · 2024Review
- Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression.Cancer cell · 2023Article
- Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti-PD-1 Immunotherapy in Endometrial Carcinoma.Cancer discovery · 2023Article
- Phasing analysis of lung cancer genomes using a long read sequencer.Nature communications · 2022Article
- Comprehensive Analysis of the Immunogenomics of Triple-Negative Breast Cancer Brain Metastases From LCCC1419.Frontiers in oncology · 2022Article
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Authors and funding
4 authors.
Funding
Abstract
Intratumour heterogeneity provides tumours with the ability to adapt and acquire treatment resistance. The development of more effective and personalised treatments for cancers, therefore, requires accurate characterisation of the clonal architecture of tumours, enabling evolutionary dynamics to be tracked. Many methods exist for achieving this from bulk tumour sequencing data, involving identifying mutations and performing subclonal deconvolution, but there is a lack of systematic benchmarking to inform researchers on which are most accurate, and how dataset characteristics impact performance. To address this, we use the most comprehensive tumour genome simulation tool available for such purposes to create 80 bulk tumour whole exome sequencing datasets of differing depths, tumour complexities, and purities, and use these to benchmark subclonal deconvolution pipelines. We conclude that i) tumour complexity does not impact accuracy, ii) increasing either purity or purity-corrected sequencing depth improves accuracy, and iii) the optimal pipeline consists of Mutect2, FACETS and PyClone-VI. We have made our benchmarking datasets publicly available for future use.
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Registered trials
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.