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Nucleic Acids Research Advance Access published online on October 5, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl716
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A high throughput method for genome-wide analysis of retroviral integration

Julie Mantovani, Nathalie Holic, Kelly Martinez, Olivier Danos and Javier Perea*

Genethon–CNRS–Université d'Evry Val d'Essonne UMR 8115 Evry, France

*To whom correspondence should be addressed. Tel: +33 169472833; Fax: +33 169472838; Email: javier.perea{at}genethon.fr

Received July 3, 2006. Revised September 7, 2006. Accepted September 15, 2006.

Retroviral and lentiviral vectors integrate their DNA into the host cell genome leading to stable transgene expression. Integration preferentially occurs in the proximity of active genes, and may in some case disturb their activity, with adverse toxic consequences. To efficiently analyze high numbers of lentiviral insertion sites in the DNA of transduced cells, we developed an improved high-throughput method called vector integration tag analysis (VITA). VITA is based on the identification of Genomic Tags associated to the insertion sites, which are used as signatures of the integration events. We use the capacity of MmeI to cleave DNA at a defined distance of its recognition site, in order to generate 21 bp long tags from libraries of junction fragments between vector and cellular DNA. The length of the tags is sufficient in most cases, to identify without ambiguity an unique position in the human genome. Concatenation, cloning and sequencing of the tags allow to obtain information about 20–25 insertion sites in a single sequencing reaction. As a validation of this method, we have characterized 1349 different lentiviral vector insertion sites in transduced HeLa cells, from only 487 sequencing reactions, with a background of <2% false positive tags.


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