ArticleCell reports2014
High-definition reconstruction of clonal composition in cancer.
Article in Cell reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers, 1 of them a synthesis that pooled it.
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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
106 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Trans-ethnic meta-analysis identifies common and rare variants associated with hepatocyte growth factor levels in the Multi-Ethnic Study of Atherosclerosis (MESA).Annals of human genetics · 2015Pooled it
- Trial
- Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies.Blood · 2016Trial
- Molecular effects of Lapatinib in the treatment of HER2 overexpressing oesophago-gastric adenocarcinoma.British journal of cancer · 2015Trial
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.Virus evolution · 2026Article
- Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.Bioinformatics (Oxford, England) · 2025Article
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.Nature biotechnology · 2025Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- Article
- Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.Genome biology · 2024Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Reconstructing Clonal Evolution-A Systematic Evaluation of Current Bioinformatics Approaches.International journal of environmental research and public health · 2023Article
- Reconstructing Phylogenetic Relationship in Bladder Cancer: A Methodological Overview.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Bulk segregant linkage mapping for rodent and human malaria parasites.Parasitology international · 2022Review
- CONET: copy number event tree model of evolutionary tumor history for single-cell data.Genome biology · 2022Article
46 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
4 authors.
Funding
Abstract
The extensive genetic heterogeneity of cancers can greatly affect therapy success due to the existence of subclonal mutations conferring resistance. However, the characterization of subclones in mixed-cell populations is computationally challenging due to the short length of sequence reads that are generated by current sequencing technologies. Here, we report cloneHD, a probabilistic algorithm for the performance of subclone reconstruction from data generated by high-throughput DNA sequencing: read depth, B-allele counts at germline heterozygous loci, and somatic mutation counts. The algorithm can exploit the added information present in correlated longitudinal or multiregion samples and takes into account correlations along genomes caused by events such as copy-number changes. We apply cloneHD to two case studies: a breast cancer sample and time-resolved samples of chronic lymphocytic leukemia, where we demonstrate that monitoring the response of a patient to therapy regimens is feasible. Our work provides new opportunities for tracking cancer development.
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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.