ArticleProceedings of the National Academy of Sciences of the United States of America2016
Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
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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
132 citing papers in PubMed.
- Trial
- Inferring gene expression profiles of tumor clones.Bioinformatics (Oxford, England) · 2026Article
- Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor.Nature communications · 2026Article
- Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- CluVar: clustering of variants using autoencoder for inferring cancer subclones from single cell RNA sequencing data.Briefings in bioinformatics · 2025Article
- Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data.Nature methods · 2025Article
- A clinical solution for tracking clonal evolution of acute myeloid leukemia after allogeneic transplantation using bulk next generation sequencing.Bone marrow transplantation · 2025Article
- Genome-level selection in tumors as a universal marker of resistance to therapy.Nature communications · 2025Article
- Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort.Acta neuropathologica communications · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data.Frontiers in bioinformatics · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants.Genome biology · 2024Article
- Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.Nature communications · 2024Article
- A Functional Survey of the Regulatory Landscape of Estrogen Receptor-Positive Breast Cancer Evolution.Cancer discovery · 2024Article
- A Probabilistic Approach to Estimate the Temporal Order of Pathway Mutations Accounting for Intra-Tumor Heterogeneity.Cancers · 2024Article
- Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data.Bioinformatics (Oxford, England) · 2024Article
- Resolving tumor evolution: a phylogenetic approach.Journal of the National Cancer Center · 2024Review
72 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Cancer is a disease driven by evolutionary selection on somatic genetic and epigenetic alterations. Here, we propose Canopy, a method for inferring the evolutionary phylogeny of a tumor using both somatic copy number alterations and single-nucleotide alterations from one or more samples derived from a single patient. Canopy is applied to bulk sequencing datasets of both longitudinal and spatial experimental designs and to a transplantable metastasis model derived from human cancer cell line MDA-MB-231. Canopy successfully identifies cell populations and infers phylogenies that are in concordance with existing knowledge and ground truth. Through simulations, we explore the effects of key parameters on deconvolution accuracy and compare against existing methods. Canopy is an open-source R package available at https://cran.r-project.org/web/packages/Canopy/.
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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.