ArticleHuman gene therapy methods2012
Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites.
Article in Human gene therapy methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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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.
- 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
- Retroviral gene therapy in Germany with a view on previous experience and future perspectives.Gene therapy · 2021Review
- Multiplexed clonality verification of cell lines for protein biologic production.Biotechnology progress · 2020Article
- VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy.Molecular therapy. Methods & clinical development · 2020Article
- Therapeutic expression of human clotting factors IX and X following adeno-associated viral vector-mediated intrauterine gene transfer in early-gestation fetal macaques.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- Preclinical Development of a Hematopoietic Stem and Progenitor Cell Bioengineered Factor VIII Lentiviral Vector Gene Therapy for Hemophilia A.Human gene therapy · 2018Article
- VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.BMC bioinformatics · 2017Article
- VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.BMC bioinformatics · 2017Article
- In Utero Transfer of Adeno-Associated Viral Vectors Produces Long-Term Factor IX Levels in a Cynomolgus Macaque Model.Molecular therapy : the journal of the American Society of Gene Therapy · 2017Article
- The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome.Applied and environmental microbiology · 2017Article
- Genome-wide Specificity of Highly Efficient TALENs and CRISPR/Cas9 for T Cell Receptor Modification.Molecular therapy. Methods & clinical development · 2017Article
- GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.Molecular therapy. Nucleic acids · 2017Article
- Evaluation of TCR Gene Editing Achieved by TALENs, CRISPR/Cas9, and megaTAL Nucleases.Molecular therapy : the journal of the American Society of Gene Therapy · 2016Article
- Gene Therapy for X-Linked Severe Combined Immunodeficiency: Where Do We Stand?Human gene therapy · 2016Review
- VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.BMC bioinformatics · 2015Article
- Presence of a trs-Like Motif Promotes Rep-Mediated Wild-Type Adeno-Associated Virus Type 2 Integration.Journal of virology · 2015Article
- Cell cycle status of CD34(+) hemopoietic stem cells determines lentiviral integration in actively transcribed and development-related genes.Molecular therapy : the journal of the American Society of Gene Therapy · 2015Article
- Fanconi anemia gene editing by the CRISPR/Cas9 system.Human gene therapy · 2015Article
- Preclinical evaluation of efficacy and safety of an improved lentiviral vector for the treatment of β-thalassemia and sickle cell disease.Current gene therapy · 2015Article
- High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies.Molecular therapy. Methods & clinical development · 2015Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clonality analysis of viral vector-transduced cell populations represents a convincing approach to dissect the physiology of tissue and organ regeneration, to monitor the fate of individual gene-corrected cells in vivo, and to assess vector biosafety. With the decoding of mammalian genomes and the introduction of next-generation sequencing technologies, the demand for automated bioinformatic analysis tools that can rapidly process and annotate vector integration sites is rising. Here, we provide a publicly accessible, graphical user interface-guided automated bioinformatic high-throughput integration site analysis pipeline. Its performance and key features are illustrated on pyrosequenced linear amplification-mediated PCR products derived from one patient previously enrolled in the first lentiviral vector clinical gene therapy study. Analysis includes trimming of vector genome junctions, alignment of genomic sequence fragments to the host genome for the identification of integration sites, and the annotation of nearby genomic elements. Most importantly, clinically relevant features comprise the determination of identical integration sites with respect to different time points or cell lineages, as well as the retrieval of the most prominent cell clones and common integration sites. The resulting output is summarized in tables within a convenient spreadsheet and can be further processed by researchers without profound bioinformatic knowledge.
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