Comprehensive genomic access to vector integration in clinical gene therapy. / Gabriel, Richard; Eckenberg, Ralph; Paruzynski, Anna; Bartholomae, Cynthia C.; Nowrouzi, Ali; Arens, Anne; Howe, Steven J.; Recchia, Alessandra; Cattoglio, Claudia; Wang, Wei; Faber, Katrin; Schwarzwaelder, Kerstin; Kirsten, Romy; Deichmann, Annette; Ball, Claudia R.; Balaggan, Kamaljit S.; Yáñez-Muñoz, R. J.; Ali, Robin R.; Gaspar, H. Bobby; Biasco, Luca; Aiuti, Alessandro; Cesana, Daniela; Montini, Eugenio; Naldini, Luigi; Cohen-Haguenauer, Odile; Mavilio, Fulvio; Thrasher, Adrian J.; Glimm, Hanno; von Kalle, Christof; Saurin, William; Schmidt, Manfred.

In: Nature Medicine, Vol. 15, No. 12, 2009, p. 1431-1436.

Research output: Contribution to journalArticle


  • Richard Gabriel
  • Ralph Eckenberg
  • Anna Paruzynski
  • Cynthia C. Bartholomae
  • Ali Nowrouzi
  • Anne Arens
  • Steven J. Howe
  • Alessandra Recchia
  • Claudia Cattoglio
  • Wei Wang
  • Katrin Faber
  • Kerstin Schwarzwaelder
  • Romy Kirsten
  • Annette Deichmann
  • Claudia R. Ball
  • Kamaljit S. Balaggan
  • Robin R. Ali
  • H. Bobby Gaspar
  • Luca Biasco
  • Alessandro Aiuti
  • Daniela Cesana
  • Eugenio Montini
  • Luigi Naldini
  • Odile Cohen-Haguenauer
  • Fulvio Mavilio
  • Adrian J. Thrasher
  • Hanno Glimm
  • Christof von Kalle
  • William Saurin
  • Manfred Schmidt


Retroviral vectors have induced subtle clonal skewing in many gene therapy patients and severe clonal proliferation and leukemia in some of them, emphasizing the need for comprehensive integration site analyses to assess the biosafety and genomic pharmacokinetics of vectors and clonal fate of gene-modified cells in vivo. Integration site analyses such as linear amplification-mediated PCR (LAM-PCR) require a restriction digest generating unevenly small fragments of the genome. Here we show that each restriction motif allows for identification of only a fraction of all genomic integrants, hampering the understanding and prediction of biological consequences after vector insertion. We developed a model to define genomic access to the viral integration site that provides optimal restriction motif combinations and minimizes the percentage of nonaccessible insertion loci. We introduce a new nonrestrictive LAM-PCR approach that has superior capabilities for comprehensive unbiased integration site retrieval in preclinical and clinical samples independent of restriction motifs and amplification inefficiency.
Original languageEnglish
Number of pages6
JournalNature Medicine
Journal publication date2009
Early online date22/11/09

ID: 1149354