ArticleNAR genomics and bioinformatics2020
Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed, 45 citations in OpenAlex.
- Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction.Scientific reports · 2026Article
- Development Process of a Clinical Decision Support System for Empiric Antibiotic Therapies in Patients With Sepsis: Case Study.JMIR medical informatics · 2026Article
- Rational engineering of the P5 TRS-mimic site and REP78/68 start codon yields promoter variants that improve rAAV purity while maintaining high titers.Molecular therapy. Advances · 2026Article
- Engineering of High-Yield Recombinant Adeno-Associated Virus Producer Plasmids.Biotechnology journal · 2026Article
- Characterization and quantitation of baculoviral DNA in rAAV vectors produced in Sf9 cells.Molecular therapy. Methods & clinical development · 2025Article
- Development of high-throughput analytical methods for characterization and quantitation of rAAV genome integrity.Molecular therapy. Methods & clinical development · 2025Article
- Quantifying DNA point mutations in commercially available AAV reporter vectors and plasmids.Molecular therapy. Methods & clinical development · 2025Article
- Orthogonal approaches to AAV vector characterization: Validating quantitative TEM for partially filled particles.Molecular therapy. Methods & clinical development · 2025Article
- Recombinant AAV batch profiling by nanopore sequencing elucidates product-related DNA impurities and vector genome length distribution.Molecular therapy. Methods & clinical development · 2025Article
- Degradation and stable maintenance of adeno-associated virus inverted terminal repeats in E. coli.Nucleic acids research · 2025Article
- Non-encapsidated miRNA contaminants found in AAV preparations.Molecular therapy. Methods & clinical development · 2024Article
- AAVolve: Concatenated long-read deep sequencing enables whole capsid tracking during shuffled AAV library selection.Molecular therapy. Methods & clinical development · 2024Article
- An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings.International journal of molecular sciences · 2024Article
- Article
- Characterization of AAV vectors: A review of analytical techniques and critical quality attributes.Molecular therapy. Methods & clinical development · 2024Review
- In-Depth Comparison of Adeno-Associated Virus Containing Fractions after CsCl Ultracentrifugation Gradient Separation.Viruses · 2024Article
- Computationally guided AAV engineering for enhanced gene delivery.Trends in biochemical sciences · 2024Review
- Thorough molecular configuration analysis of noncanonical AAV genomes in AAV vector preparations.Molecular therapy. Methods & clinical development · 2024Article
- A Comprehensive Study of the Effects by Sequence Truncation within Inverted Terminal Repeats (ITRs) on the Productivity, Genome Packaging, and Potency of AAV Vectors.Microorganisms · 2024Article
- An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings.medRxiv : the preprint server for health sciences · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing of single-stranded DNA (ssDNA) enables transgene characterization of gene therapy vectors such as adeno-associated virus (AAV), but current library generation uses complicated and potentially biased second-strand synthesis. We report that libraries for nanopore sequencing of ssDNA can be conveniently created without second-strand synthesis using a transposase-based protocol. We show for bacteriophage M13 ssDNA that the MuA transposase has unexpected residual activity on ssDNA, explained in part by transposase action on transient double-stranded hairpins. In case of AAV, library creation is additionally aided by genome hybridization. We demonstrate the power of direct sequencing combined with nanopore long reads by characterizing AAV vector transgenes. Sequencing yielded reads up to full genome length, including GC-rich inverted terminal repeats. Unlike short-read techniques, single reads covered genome-genome and genome-contaminant fusions and other recombination events, whilst additionally providing information on epigenetic methylation. Single-nucleotide variants across the transgene cassette were revealed and secondary genome packaging signals were readily identified. Moreover, comparison of sequence abundance with quantitative polymerase chain reaction results demonstrated the technique's future potential for quantification of DNA impurities in AAV vector stocks. The findings promote direct nanopore sequencing as a fast and versatile platform for ssDNA characterization, such as AAV ssDNA in research and clinical settings.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.