ArticleGene therapy2009
QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.
Article in Gene therapy, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 50 citations in OpenAlex.
- PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites.bioRxiv : the preprint server for biology · 2026Article
- IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods.BMC bioinformatics · 2023Article
- Effective, safe, and sustained correction of murine XLA using a UCOE-BTK promoter-based lentiviral vector.Molecular therapy. Methods & clinical development · 2021Article
- Shifting Retroviral Vector Integrations Away from Transcriptional Start Sites via DNA-Binding Protein Domain Insertion into Integrase.Molecular therapy. Methods & clinical development · 2019Article
- UM171 Enhances Lentiviral Gene Transfer and Recovery of Primitive Human Hematopoietic Cells.Molecular therapy. Methods & clinical development · 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
- Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.BMC bioinformatics · 2017Article
- GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.Molecular therapy. Nucleic acids · 2017Article
- INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.Molecular therapy. Methods & clinical development · 2017Article
- Prolonged Integration Site Selection of a Lentiviral Vector in the Genome of Human Keratinocytes.Medical science monitor : international medical journal of experimental and clinical research · 2017Article
- High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies.Molecular therapy. Methods & clinical development · 2015Article
- Rapamycin relieves lentiviral vector transduction resistance in human and mouse hematopoietic stem cells.Blood · 2014Article
- Vector integration and tumorigenesis.Human gene therapy · 2014Article
- Development and Evaluation of Quality Metrics for Bioinformatics Analysis of Viral Insertion Site Data Generated Using High Throughput Sequencing.Biomedicines · 2014Article
- Long-term episomal transgene expression from mitotically stable integration-deficient lentiviral vectors.Human gene therapy · 2014Article
- VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites.Genome medicine · 2014Article
- Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies.Journal of stem cell research & therapy · 2013Article
- Patterns of scAAV vector insertion associated with oncogenic events in a mouse model for genotoxicity.Molecular therapy : the journal of the American Society of Gene Therapy · 2012Article
- Retroviral infection of hES cells produces random-like integration patterns.Molecules and cells · 2012Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.
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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.