ArticleNucleic acids research2013
TrAp: a tree approach for fingerprinting subclonal tumor composition.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 140 citations in OpenAlex.
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.PLoS computational biology · 2024Article
- Resolving tumor evolution: a phylogenetic approach.Journal of the National Cancer Center · 2024Review
- 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
- Acute myeloid leukemia: from NGS, through scRNA-seq, to CAR-T. dissect cancer heterogeneity and tailor the treatment.Journal of experimental & clinical cancer research : CR · 2023Review
- Reconstructing Clonal Evolution-A Systematic Evaluation of Current Bioinformatics Approaches.International journal of environmental research and public health · 2023Article
- clevRvis: visualization techniques for clonal evolution.GigaScience · 2022Article
- Accurate Identification of Subclones in Tumor Genomes.Molecular biology and evolution · 2022Article
- Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree.Blood cancer discovery · 2022Article
- Parsimonious Clone Tree Integration in cancer.Algorithms for molecular biology : AMB · 2022Article
- Clonal evolution in chronic lymphocytic leukemia is scant in relapsed but accelerated in refractory cases after chemo(immune) therapy.Haematologica · 2022Article
- COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics.Zoological research · 2022Article
- Reconstruction of evolving gene variants and fitness from short sequencing reads.Nature chemical biology · 2021Article
- DEVOLUTION-A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data.Communications biology · 2021Article
- PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.BMC bioinformatics · 2021Article
- Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.Bioinformatics (Oxford, England) · 2021Article
- A practical guide to cancer subclonal reconstruction from DNA sequencing.Nature methods · 2021Review
- Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine.PLoS computational biology · 2021Article
9 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 at 3 institutions in 1 country.
Funding
Abstract
Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
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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.