ArticleBioinformatics (Oxford, England)2022
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Trial
- Theoretical estimates on the expected number of mutations needed to reconstruct clonal lineage trees.Bioinformatics advances · 2026Article
- 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
- Marker selection strategies for circulating tumor DNA guided by phylogenetic inference.Bioinformatics (Oxford, England) · 2025Article
- Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- Deconvolution and phylogeny inference of diverse variant types integrating bulk DNA-seq with single-cell RNA-seq.Bioinformatics advances · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Computationally reconstructing the evolution of cancer progression risk.bioRxiv : the preprint server for biology · 2024Article
- Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationCancer develops through a process of clonal evolution in which an initially healthy cell gives rise to progeny gradually differentiating through the accumulation of genetic and epigenetic mutations. These mutations can take various forms, including single-nucleotide variants (SNVs), copy number alterations (CNAs) or structural variations (SVs), with each variant type providing complementary insights into tumor evolution as well as offering distinct challenges to phylogenetic inference.
resultsIn this work, we develop a tumor phylogeny method, TUSV-ext, which incorporates SNVs, CNAs and SVs into a single inference framework. We demonstrate on simulated data that the method produces accurate tree inferences in the presence of all three variant types. We further demonstrate the method through application to real prostate tumor data, showing how our approach to coordinated phylogeny inference and clonal construction with all three variant types can reveal a more complicated clonal structure than is suggested by prior work, consistent with extensive polyclonal seeding or migration. AVAILABILITY AND IMPLEMENTATION: https://github.com/CMUSchwartzLab/TUSV-ext. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.