ReviewNature methods2021
A practical guide to cancer subclonal reconstruction from DNA sequencing.
Review in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
117 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The influence of socio-demographics and clinical characteristics on coping strategies in cancer patients: a systematic review.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2022Pooled it
- Machine learning uncovers previously undetectable genetic deletions in cancer panel sequencing.NPJ precision oncology · 2026Article
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- Review
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Exploring copy number alterations (CNAs) to gain new insight into SCLC heterogeneity.Molecular biology reports · 2026Review
- 3D pathology-guided microdissection.Nature methods · 2026Article
- Accurate detection of tumor clonality and ongoing expansion mode from genomic data.bioRxiv : the preprint server for biology · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.Briefings in bioinformatics · 2026Article
- Whole-genome sequencing of cell-free DNA for assessment of minimal residual disease in high-risk smoldering multiple myeloma.HemaSphere · 2026Article
- Competing subclones and fitness diversity shape tumor evolution across cancer types.Bioinformatics (Oxford, England) · 2026Article
- LINE-1 retrotransposition is a recurrent cause ofbioRxiv : the preprint server for biology · 2026Article
- Article
- SHISMA: SHape-driven inference of significant cell type-specific subnetworks from tiMe series single-cell trAnscriptomics.Bioinformatics advances · 2026Article
- GATES: A Lightweight Tool Automating Pathogenic Variant Discovery From Raw Whole-Exome Sequencing Data.Cancer informatics · 2026Article
- A comprehensive analysis of the impact of genomic imbalance on gene expression in a poplar aneuploidy population.Communications biology · 2025Article
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
- Loss of IDH1 and IDH2 mutations during the evolution of metastatic chondrosarcoma.Genome biology · 2025Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.
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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.