ArticleMolecular therapy. Methods & clinical development2020
VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy.
Article in Molecular therapy. Methods & clinical development, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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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
10 citing papers in PubMed.
- intmap: fast and flexible mapping of mobile DNA integration for basic and translational research.Bioinformatics (Oxford, England) · 2026Article
- RAAVioli: A comprehensive approach to characterizing AAV vector integrations and rearrangements.Molecular therapy. Advances · 2026Article
- PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites.bioRxiv : the preprint server for biology · 2026Article
- Virusplot: a web server for viral integration analysis and visualization.Frontiers in oncology · 2025Article
- InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration.Database : the journal of biological databases and curation · 2023Article
- IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods.BMC bioinformatics · 2023Article
- Article
- Meeting FDA Guidance recommendations for replication-competent virus and insertional oncogenesis testing.Molecular therapy. Methods & clinical development · 2023Review
- ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications.Briefings in bioinformatics · 2023Article
- Interrogation of clonal tracking data usingNature computational science · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral vector characterization and analysis are important components for the development of safe gene therapeutic products, elucidating the potential genotoxic and immunogenic effects of vectors and establishing their safety profiles. Here, we present VSeq-Toolkit, which offers varying analysis modes for viral gene therapy data. The first mode determines the undesirable known contaminants and their frequency in viral preparations or other sequencing data. The second mode is designed for the analysis of intra-vector fusion breakpoints and the third mode for unraveling the viral-host fusion events distribution. Analysis modes of our toolkit can be executed independently or together and allow the analysis of multiple viral vectors concurrently. It has been designed and evaluated for the analysis of short read high-throughput sequencing data, including whole-genome or targeted sequencing. VSeq-Toolkit is developed in Perl and Bash programming languages and is available at https://github.com/CompMeth/VSeq-Toolkit.
Identifiers
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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.