ArticleNature communications2020
Quantifying the influence of mutation detection on tumour subclonal reconstruction.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The trial behind it
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
14 citing papers in PubMed, 20 citations in OpenAlex.
- Single-cell genomic analysis of cancer cells from one treatment-naïve patient with metastatic prostate cancer.BMC genomic data · 2026Article
- The Germline and Somatic Origins of Prostate Cancer Heterogeneity.Cancer discovery · 2025Article
- Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.Nature biotechnology · 2025Article
- Comprehensive assessment of computational methods for cancer immunoediting.Cell reports methods · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Basket Trials: Past, Present, and Future.Annual review of cancer biology · 2024Article
- Understanding and targeting prostate cancer cell heterogeneity and plasticity.Seminars in cancer biology · 2022Review
- Quenching Epigenetic Drug Resistance Using Antihypoxic Microparticles in Glioblastoma Patient-Derived Chips.Advanced healthcare materials · 2022Article
- In vivo growth of subclones derived from Lewis lung carcinoma is determined by the tumor microenvironment.American journal of cancer research · 2022Article
- Clone decomposition based on mutation signatures provides novel insights into mutational processes.NAR genomics and bioinformatics · 2021Article
- Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.Nature communications · 2021Article
- Aging of the progenitor cells that initiate prostate cancer.Cancer letters · 2021Review
- A practical guide to cancer subclonal reconstruction from DNA sequencing.Nature methods · 2021Review
- Inferring structural variant cancer cell fraction.Nature communications · 2020Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Whole-genome sequencing can be used to estimate subclonal populations in tumours and this intra-tumoural heterogeneity is linked to clinical outcomes. Many algorithms have been developed for subclonal reconstruction, but their variabilities and consistencies are largely unknown. We evaluate sixteen pipelines for reconstructing the evolutionary histories of 293 localized prostate cancers from single samples, and eighteen pipelines for the reconstruction of 10 tumours with multi-region sampling. We show that predictions of subclonal architecture and timing of somatic mutations vary extensively across pipelines. Pipelines show consistent types of biases, with those incorporating SomaticSniper and Battenberg preferentially predicting homogenous cancer cell populations and those using MuTect tending to predict multiple populations of cancer cells. Subclonal reconstructions using multi-region sampling confirm that single-sample reconstructions systematically underestimate intra-tumoural heterogeneity, predicting on average fewer than half of the cancer cell populations identified by multi-region sequencing. Overall, these biases suggest caution in interpreting specific architectures and subclonal variants.
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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.