ArticleNature communications2022
MQuad enables clonal substructure discovery using single cell mitochondrial variants.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Reconstruction of Cell Diversity and Cell Lineages from Somatic Mutations in Single-Cell Transcriptomic Data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Article
- Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives.Genomics, proteomics & bioinformatics · 2026Review
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- MiTo: tracing the phenotypic evolution of somatic cell lineages via mitochondrial single-cell multi-omics.Nature communications · 2026Article
- Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell mitochondrial lineage tracing: Opportunities and challenges.Quantitative biology (Beijing, China) · 2026Review
- A hierarchical Bayesian framework for inferring mitochondrial clonal selection from single-cell data.Research square · 2026Article
- Mitochondrial transfer in cancer: mechanisms, immune evasion, and therapeutic opportunities.Genomics & informatics · 2026Review
- Mapping NK cell diversity in response to COVID-19 and mRNA vaccination.Scientific reports · 2025Article
- TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations.bioRxiv : the preprint server for biology · 2025Article
- SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder.Genome biology · 2025Article
- MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data.BMC genomics · 2025Article
- CLADES: a hybrid NeuralODE-Gillespie approach for unveiling clonal cell fate and differentiation dynamics.Nature communications · 2025Article
- MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.PLoS computational biology · 2025Article
- De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.Genome research · 2025Article
- Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells.Genome biology · 2025Article
- ScLineageAtlas: a comprehensive single-cell genomics database for characterizing cellular clones in cancer.Database : the journal of biological databases and curation · 2025Article
- MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants.Genomics, proteomics & bioinformatics · 2024Article
- scMitoMut for calling mitochondrial lineage-related mutations in single cells.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mitochondrial mutations are increasingly recognised as informative endogenous genetic markers that can be used to reconstruct cellular clonal structure using single-cell RNA or DNA sequencing data. However, identifying informative mtDNA variants in noisy and sparse single-cell sequencing data is still challenging with few computation methods available. Here we present an open source computational tool MQuad that accurately calls clonally informative mtDNA variants in a population of single cells, and an analysis suite for complete clonality inference, based on single cell RNA, DNA or ATAC sequencing data. Through a variety of simulated and experimental single cell sequencing data, we showed that MQuad can identify mitochondrial variants with both high sensitivity and specificity, outperforming existing methods by a large extent. Furthermore, we demonstrate its wide applicability in different single cell sequencing protocols, particularly in complementing single-nucleotide and copy-number variations to extract finer clonal resolution.
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