ArticleNature communications2023
COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Phylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA.Genome biology · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Theoretical estimates on the expected number of mutations needed to reconstruct clonal lineage trees.Bioinformatics advances · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- scDNA: Single Cell DNA analysis software toolkit for subclonality discovery and assessment.bioRxiv : the preprint server for biology · 2025Article
- Resolving intra-tumor heterogeneity and clonal evolution of core-binding factor acute myeloid leukemia patients with single-cell resolution.Experimental hematology & oncology · 2025Article
- Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants.Journal of computational biology : a journal of computational molecular cell biology · 2025Article
- Bayesian inference of fitness landscapes via tree-structured branching processes.Bioinformatics (Oxford, England) · 2025Article
- Single-cell copy number calling and event history reconstruction.Bioinformatics (Oxford, England) · 2025Article
- DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.Life science alliance · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Whole exome sequencing and single-cell DNA sequencing for assessment of clonal heterogeneity and evolution in acute myeloid leukemia.Computational and structural biotechnology journal · 2025Article
- Oncotree2vec - a method for embedding and clustering of tumor mutation trees.Bioinformatics (Oxford, England) · 2024Article
- Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data.Genome research · 2023Article
- ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model.Genome biology · 2023Article
- Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer.Nature communications · 2023Article
- ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including a cohort of 123 patients with acute myeloid leukemia. COMPASS detected clonal CNAs that could be orthogonally validated with bulk data, in addition to subclonal ones that require single-cell resolution, some of which point toward convergent evolution.
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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.