High-throughput mapping and clonal quantification of retroviral integration sites

Nicolas A. Gillet, Anat Melamed, Charles R.M. Bangham

Research output: Contribution in Book/Catalog/Report/Conference proceedingChapter (peer-reviewed)peer-review


We describe here a method to identify the position of retroviral insertion sites and simultaneously to quantify the absolute abundance of each clone, i.e., the number of cells having the provirus inserted at a given place in the host genome. The method is based on random shearing of the host cell DNA, followed by a linker-mediated PCR to amplify the genomic regions flanking the proviruses, and high-throughput sequencing of the amplicons. The quantification of the abundance of each infected clone allowed us to develop two new metrics: i. the oligoclonality index, which quantifies the nonuniformity of the distribution of clone abundance, and ii. an estimator of the total number of clones in the body of the host. These new tools are valuable for the study of retroviral infections and can also be adapted for the tracking of gene-edited cells.

Original languageEnglish
Title of host publicationHuman T-Lymphotropic Viruses
Subtitle of host publicationMethods and Protocols
EditorsClaudio Casoli
PublisherSpringer Verlag
Number of pages15
Publication statusPublished - 1 Jan 2017

Publication series

NameMethods in Molecular Biology
PublisherHumana Press Inc.
ISSN (Print)1064-3745


  • Clonal distribution
  • Clonal expansion
  • Clonality
  • Gene therapy
  • Gene-edited cells
  • Insertion sites
  • Number of clones
  • Off-target insertion
  • Oligoclonal
  • Retroviral integration sites


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