ArticleCell genomics2023
Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox.
Article in Cell genomics, 2023. 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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Who cites it
14 citing papers in PubMed.
- A guide to understanding tumour evolution through the lens of population genetics.Nature reviews. Cancer · 2026Review
- Performance Evaluation of Whole-Genome Amplification Platforms for Clinical Next-Generation Sequencing with Minimal Nucleic Acid Input.Annals of laboratory medicine · 2026Article
- Single-cell whole-genome sequencing reveals convergent evolution in Burkitt lymphoma.Nature communications · 2026Article
- High-resolution single-cell mapping of clonal hematopoiesis and structural variation in aplastic anemia.Nature genetics · 2026Article
- Precise exome analysis of blastocyst biopsy scale samples using primary template-directed amplification.BMC genomics · 2026Article
- Reconstructing the lifelong history of cells and tissues via somatic mutation analysis.Cellular and molecular life sciences : CMLS · 2025Review
- Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive benchmarking of somatic mutation detection by the SMaHT Network.bioRxiv : the preprint server for biology · 2025Article
- Unraveling mutagenic processes influencing the tumor mutational patterns of individuals with constitutional mismatch repair deficiency.Nature communications · 2025Article
- Detecting somatic variants in purified brain DNA obtained from surgically implanted depth electrodes in epilepsy.Epilepsia · 2025Article
- Transient Differentiation-State Plasticity Occurs during Acute Lymphoblastic Leukemia Initiation.Cancer research · 2024Article
- Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms.Nature communications · 2024Article
- Mitochondrial HNature communications · 2024Article
- Stem cell mutations, associated cancer risk, and consequences for regenerative medicine.Cell stem cell · 2023Review
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
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