ArticleMolecular therapy. Nucleic acids2017
GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.
Article in Molecular therapy. Nucleic acids, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Severe hematopoietic stem cell inflammation compromises chronic granulomatous disease gene therapy.Cell reports. Medicine · 2023Trial
- Successful engraftment of gene-corrected hematopoietic stem cells in non-conditioned patients with Fanconi anemia.Nature medicine · 2019Trial
- Extended follow-up of in vivo BCMA CAR-T therapy in relapsed/refractory multiple myeloma.Nature medicine · 2026Article
- intmap: fast and flexible mapping of mobile DNA integration for basic and translational research.Bioinformatics (Oxford, England) · 2026Article
- Article
- Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming.Cell reports · 2025Article
- Comparing acute versus AIDS ART initiation on HIV-1 integration sites and clonal expansion.Signal transduction and targeted therapy · 2025Article
- Comprehensive analysis of off-target and on-target effects resulting from liver-directed CRISPR-Cas9-mediated gene targeting with AAV vectors.Molecular therapy. Methods & clinical development · 2024Article
- The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice.Molecular therapy. Methods & clinical development · 2024Article
- A Naturally Active Spy Transposon Discovered from the Insect Genome of Colletes gigas as a Promising Novel Gene Transfer Tool.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Restoration of T and B Cell Differentiation after RAG1 Gene Transfer in Human RAG1 Defective Hematopoietic Stem Cells.Biomedicines · 2024Article
- Prenatal AAV9-GFP administration in fetal lambs results in transduction of female germ cells and maternal exposure to virus.Molecular therapy. Methods & clinical development · 2024Article
- A novel preclinical model of mucopolysaccharidosis type II for developing human hematopoietic stem cell gene therapy.Gene therapy · 2023Article
- Article
- ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications.Briefings in bioinformatics · 2023Article
- Partial correction of immunodeficiency by lentiviral vector gene therapy in mouse models carryingFrontiers in immunology · 2023Article
- Vector genome loss and epigenetic modifications mediate decline in transgene expression of AAV5 vectors produced in mammalian and insect cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data.The Journal of molecular diagnostics : JMD · 2022Article
- Comprehensive transcriptome-wide analysis of spliceopathy correction of myotonic dystrophy using CRISPR-Cas9 in iPSCs-derived cardiomyocytes.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- 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
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integration site profiling and clonality analysis of viral vector distribution in gene therapy is a key factor to monitor the fate of gene-corrected cells, assess the risk of malignant transformation, and establish vector biosafety. We developed the Genome Integration Site Analysis Pipeline (GENE-IS) for highly time-efficient and accurate detection of next-generation sequencing (NGS)-based viral vector integration sites (ISs) in gene therapy data. It is the first available tool with dual analysis mode that allows IS analysis both in data generated by PCR-based methods, such as linear amplification method PCR (LAM-PCR), and by rapidly evolving targeted sequencing (e.g., Agilent SureSelect) technologies. GENE-IS makes use of trimming strategies, customized reference genome, and soft-clipped information with sequential filtering steps to provide annotated IS with clonality information. It is a scalable, robust, precise, and reliable tool for large-scale pre-clinical and clinical data analysis that provides users complete flexibility and control over analysis with a broad range of configurable parameters. GENE-IS is available at https://github.com/G100DKFZ/gene-is.
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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.