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QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis

Abstract

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/− 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations (‘random set’). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with ‘safe’ insertion profiles.

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Acknowledgements

We thank Sigrid Heil, Hans-Jürgen Engel and Bernhard Berkus from the G402 lab of the German Cancer Research Center for their skillful technical assistance. We also thank Mohammed Abba for his critical discussions and editorial advice. This work was supported by grants FR1732/3–1 and RO3500/1–1 of the Priority Program SPP1230 of the German Research Foundation (Bonn, Germany), the HW & J Hector Foundation (Mannheim, Germany), the Alfried Krupp von Bohlen und Halbach Foundation (Essen, Germany), the Ingrid zu Solms Foundation (Frankfurt, Germany) and the Hella Bühler Foundation (Heidelberg, Germany).

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Correspondence to S Laufs.

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Appelt, JU., Giordano, F., Ecker, M. et al. QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis. Gene Ther 16, 885–893 (2009). https://doi.org/10.1038/gt.2009.37

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