ArticleBMC bioinformatics2017
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Tumor-targeted interferon-α gene therapy for glioblastoma: a phase 1 trial.Nature medicine · 2026Trial
- Hematopoietic reconstitution dynamics of mobilized- and bone marrow-derived human hematopoietic stem cells after gene therapy.Nature communications · 2023Trial
- Sleeping Beauty-engineered CAR T cells achieve antileukemic activity without severe toxicities.The Journal of clinical investigation · 2020Trial
- Double activation and low IL-2 manufacturing protocol increase expansion of healthy and patient-derived CAR-Tregs.Molecular therapy. Advances · 2026Article
- Ex vivo expansion of hematopoietic stem and progenitor cells from human mobilized peripheral blood for gene therapy applications.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- intmap: fast and flexible mapping of mobile DNA integration for basic and translational research.Bioinformatics (Oxford, England) · 2026Article
- Nanoengineered 3D culture substrate enables superior persistence and polyclonal engraftment of genetically engineered hematopoietic stem cells.Cell stem cell · 2026Article
- Article
- Enhancing the potency of in vivo lentiviral vector mediated gene therapy to hepatocytes.Nature communications · 2025Article
- A case of T-cell acute lymphoblastic leukemia in retroviral gene therapy for ADA-SCID.Nature communications · 2024Article
- Removal of innate immune barriers allows efficient transduction of quiescent human hematopoietic stem cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- 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
- 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
- Clonal reconstruction from co-occurrence of vector integration sites accurately quantifies expanding clones in vivo.Nature communications · 2022Article
- Normalization of clonal diversity in gene therapy studies using shape constrained splines.Scientific reports · 2022Article
- Efficient and safe correction of hemophilia A by lentiviral vector-transduced BOECs in an implantable device.Molecular therapy. Methods & clinical development · 2021Article
- Challenges in estimating numbers of vectors integrated in gene-modified cells using DNA sequence information.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- Retrieval of vector integration sites from cell-free DNA.Nature medicine · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundBioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution. The increasing number of gene therapy clinical trials combined with the increasing amount of Next Generation Sequencing data, aimed at identifying integration sites, require both highly accurate and efficient computational software able to correctly process "big data" in a reasonable computational time.
resultsHere we present VISPA2 (Vector Integration Site Parallel Analysis, version 2), the latest optimized computational pipeline for integration site identification and analysis with the following features: (1) the sequence analysis for the integration site processing is fully compliant with paired-end reads and includes a sequence quality filter before and after the alignment on the target genome; (2) an heuristic algorithm to reduce false positive integration sites at nucleotide level to reduce the impact of Polymerase Chain Reaction or trimming/alignment artifacts; (3) a classification and annotation module for integration sites; (4) a user friendly web interface as researcher front-end to perform integration site analyses without computational skills; (5) the time speedup of all steps through parallelization (Hadoop free).
conclusionsWe tested VISPA2 performances using simulated and real datasets of lentiviral vector integration sites, previously obtained from patients enrolled in a hematopoietic stem cell gene therapy clinical trial and compared the results with other preexisting tools for integration site analysis. On the computational side, VISPA2 showed a > 6-fold speedup and improved precision and recall metrics (1 and 0.97 respectively) compared to previously developed computational pipelines. These performances indicate that VISPA2 is a fast, reliable and user-friendly tool for integration site analysis, which allows gene therapy integration data to be handled in a cost and time effective fashion. Moreover, the web access of VISPA2 ( http://openserver.itb.cnr.it/vispa/ ) ensures accessibility and ease of usage to researches of a complex analytical tool. We released the source code of VISPA2 in a public repository ( https://bitbucket.org/andreacalabria/vispa2 ).
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Registered trials
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