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Related Experiment Video

Updated: Jan 13, 2026

Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions
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PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites.

V K Pal1, M Canis1, E Stone2

  • 1Laboratory of Retrovirology, The Rockefeller University, New York.

Biorxiv : the Preprint Server for Biology
|January 9, 2026
PubMed
Summary
This summary is machine-generated.

We developed PRISM-seq, an ultra-sensitive method for mapping retroviral DNA insertions in genomes. This technique accurately identifies integration sites, even from a single molecule, improving gene therapy safety and HIV-1 research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Virology

Background:

  • Retroviral integration into host genomes is crucial for HIV-1 persistence and lentiviral vector applications in gene and cell therapies.
  • Current integration site assays face limitations in sensitivity, input needs, and analytical complexity, lacking single-molecule validation.
  • Accurate mapping of retroviral integration sites is essential for assessing gene therapy safety and understanding viral dynamics.

Purpose of the Study:

  • To introduce PRISM-seq, an ultra-sensitive workflow for genome-wide recovery of lentiviral-host junctions.
  • To develop BulkIntSiteR, an automated pipeline for integration site annotation.
  • To validate PRISM-seq's performance across diverse genomic regions and at single-molecule resolution.

Main Methods:

  • PRISM-seq workflow for genome-wide recovery of lentiviral-host junctions.
  • BulkIntSiteR open-source pipeline for automated integration site annotation.
  • Systematic characterization of assay- and amplification-associated noise.
  • Development of a five-step quality control framework to remove PCR and sequencing artifacts.

Main Results:

  • PRISM-seq accurately identifies proviral insertions in various genomic contexts, including euchromatin, heterochromatin, and centromeric regions.
  • High-confidence integration events were detected down to a single input template molecule.
  • The PRISM-seq workflow, coupled with BulkIntSiteR, demonstrated performance comparable to or exceeding high-input assays at a substantially reduced cost.
  • A robust quality control framework effectively removed PCR and sequencing artifacts.

Conclusions:

  • PRISM-seq offers an ultra-sensitive and accurate method for mapping retroviral integration sites genome-wide.
  • The workflow enables high-resolution analysis of integration events, crucial for gene and cell therapy development and HIV-1 research.
  • PRISM-seq facilitates quantitative clonal tracking and provides a cost-effective alternative to existing assays.