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https://www.nature.com/articles/s41467-023-36202-y
QT:{{” Though each cell is fundamentally distinct in cancer, there typically exist groups of cells that are genomically nearly identical, so-called clonal populations1. The evolutionary relationship between clones can be represented by a phylogenetic tree or clonal tree. Inferring clonal population structure, genotypes, and trees from sequence data has been an active area of research in the past decade with implications for cancer treatment2,3,4. Early approaches used bulk sequence data coupled with computational deconvolution to address the admixed nature of bulk data5,6,7,8,9. The limitations of clonal analysis using only the bulk method is well documented in the literature (e.g., refs. 10,11). Recent advances in single-cell DNA sequencing (scDNA-seq) technologies have prompted the development of approaches better tailored to these data types12,13,14 as well as methods that integrate scDNA-seq data with the bulk data for joint analysis for improved accuracy15,16. “}}
Posts Tagged ‘spvar’
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics | Nature Communications
June 7, 2026Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data | Scientific Reports
June 7, 2026https://www.nature.com/articles/s41598-020-59006-2
QT:{{” Though each cell is fundamentally distinct in cancer, there typically exist groups of cells that are genomically nearly identical, so-called clonal populations1. The evolutionary relationship between clones can be represented by a phylogenetic tree or clonal tree. Inferring clonal population structure, genotypes, and trees from sequence data has been an active area of research in the past decade with implications for cancer treatment2,3,4. Early approaches used bulk sequence data coupled with computational deconvolution to address the admixed nature of bulk data5,6,7,8,9. The limitations of clonal analysis using only the bulk method is well documented in the literature (e.g., refs. 10,11). “}}
how is the word clone used in tumor phylogenetic analysis
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