ArticleMolecular therapy. Methods & clinical development2017
INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.
Article in Molecular therapy. Methods & clinical development, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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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
98 citing papers in PubMed.
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- Long-term outcomes after gene therapy for adenosine deaminase severe combined immune deficiency.Blood · 2021Trial
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- CD19-targeting CAR T cell immunotherapy outcomes correlate with genomic modification by vector integration.The Journal of clinical investigation · 2020Trial
- Quantification and localization of integrated HIV-1 in memory and naïve CD4+ T cells from adolescents and young adults with perinatally-acquired HIV-1.PLoS pathogens · 2026Article
- The LEDGIN GS-9822 inhibits HIV-2 infection and enhances HIV-2 latency.Microbiology spectrum · 2026Article
- intmap: fast and flexible mapping of mobile DNA integration for basic and translational research.Bioinformatics (Oxford, England) · 2026Article
- Is the molecular microenvironment of the latent HIV reservoir predictable using deep learning approaches?Journal of virology · 2026Review
- Implications of the FDA's new plausible mechanism framework for the development of a personalized in vivo prime editing platform.American journal of human genetics · 2026Review
- Positioning HIV SMRTcap within the HIV reservoir toolbox.PLoS pathogens · 2026Article
- DNA-PKcs inhibitor AZD7648 reveals sgRNA cross-contaminants and enhanced sensitivity of genome engineering off-target activity in HSPCs.Nucleic acids research · 2026Article
- Clonal dynamics of HIV-infected and uninfected T cells.EBioMedicine · 2026Article
- RAAVioli: A comprehensive approach to characterizing AAV vector integrations and rearrangements.Molecular therapy. Advances · 2026Article
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- Ex vivo long-term expansion of human hematopoietic stem and progenitor cells as a tool for modeling vector integration sites and clonality.Journal of translational medicine · 2026Article
- PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites.bioRxiv : the preprint server for biology · 2026Article
- Dynamics of natural and pharmacologic control of an SIV variant with an envelope trafficking defect.The Journal of experimental medicine · 2026Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences. During library preparation, DNAs are broken by sonication, so that after ligation-mediated PCR the number of ligation junction sites can be used to infer abundance of gene-modified cells. We generated integration sites of known positions in silico, and we describe optimization of sample processing parameters refined by comparison to truth. We also present a novel graph-theory-based method for quantifying integration sites in repeated sequences, and we characterize the consequences using synthetic and experimental data. In an accompanying paper, we describe an additional set of statistical tools for data analysis and visualization. Software is available at https://github.com/BushmanLab/INSPIIRED.
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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.