ArticleBriefings in bioinformatics2022
BiTSC 2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data.
Article in Briefings in bioinformatics, 2022. 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, 31 citations in OpenAlex.
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 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
- DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.Life science alliance · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Single-Cell Transcriptomics Applied in Plants.Cells · 2024Review
- Overexpression of SYNGAP1 suppresses the proliferation of rectal adenocarcinoma via Wnt/β-Catenin signaling pathway.Discover oncology · 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
- COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data.Nature communications · 2023Article
- Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees.Nature communications · 2023Article
- ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model.bioRxiv : the preprint server for biology · 2023Article
- RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data.Frontiers in genetics · 2023Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid development of single-cell DNA sequencing (scDNA-seq) technology has greatly enhanced the resolution of tumor cell profiling, providing an unprecedented perspective in characterizing intra-tumoral heterogeneity and understanding tumor progression and metastasis. However, prominent algorithms for constructing tumor phylogeny based on scDNA-seq data usually only take single nucleotide variations (SNVs) as markers, failing to consider the effect caused by copy number alterations (CNAs). Here, we propose BiTSC$^2$, Bayesian inference of Tumor clonal Tree by joint analysis of Single-Cell SNV and CNA data. BiTSC$^2$ takes raw reads from scDNA-seq as input, accounts for the overlapping of CNA and SNV, models allelic dropout rate, sequencing errors and missing rate, as well as assigns single cells into subclones. By applying Markov Chain Monte Carlo sampling, BiTSC$^2$ can simultaneously estimate the subclonal scCNA and scSNV genotype matrices, subclonal assignments and tumor subclonal evolutionary tree. In comparison with existing methods on synthetic and real tumor data, BiTSC$^2$ shows high accuracy in genotype recovery, subclonal assignment and tree reconstruction. BiTSC$^2$ also performs robustly in dealing with scDNA-seq data with low sequencing depth and variant missing rate. BiTSC$^2$ software is available at https://github.com/ucasdp/BiTSC2.
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