ArticleCommunications biology2021
DEVOLUTION-A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 25 citations in OpenAlex.
- Tracing metastatic spread in pediatric solid tumors using copy number and targeted deep sequencing.The Journal of pathology · 2025Article
- Bladder cancer subtypes exhibit limited plasticity across different microenvironments and in metastases.Experimental hematology & oncology · 2025Article
- Integrating model systems and genomic insights to decipher mechanisms of cancer metastasis.Nature reviews. Genetics · 2025Review
- The bile duct and liver cancer: ON-treatment surveillance of tumor evolution and response to systemic treatment (BILLIONSTARS) study.BMC cancer · 2025Observational
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.Nature communications · 2024Article
- Article
- Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.Bioinformatics advances · 2024Article
- Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples.Genome biology · 2023Article
- Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance.Nature communications · 2023Article
- Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.Science advances · 2022Article
- Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer.Molecular cancer research : MCR · 2022Article
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5 authors at 1 institution in 1 country.
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Abstract
Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations.
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