%0 Journal Article
%A Afzal, Saira
%A Wilkening, Stefan
%A von Kalle, Christof
%A Schmidt, Manfred
%A Fronza, Raffaele
%T GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.
%J Molecular Therapy / Nucleic Acids
%V 6
%@ 2162-2531
%C New York, NY
%I Nature Publ. Group
%M DKFZ-2017-01208
%P 133 - 139
%D 2017
%X Integration site profiling and clonality analysis of viral vector distribution in gene therapy is a key factor to monitor the fate of gene-corrected cells, assess the risk of malignant transformation, and establish vector biosafety. We developed the Genome Integration Site Analysis Pipeline (GENE-IS) for highly time-efficient and accurate detection of next-generation sequencing (NGS)-based viral vector integration sites (ISs) in gene therapy data. It is the first available tool with dual analysis mode that allows IS analysis both in data generated by PCR-based methods, such as linear amplification method PCR (LAM-PCR), and by rapidly evolving targeted sequencing (e.g., Agilent SureSelect) technologies. GENE-IS makes use of trimming strategies, customized reference genome, and soft-clipped information with sequential filtering steps to provide annotated IS with clonality information. It is a scalable, robust, precise, and reliable tool for large-scale pre-clinical and clinical data analysis that provides users complete flexibility and control over analysis with a broad range of configurable parameters. GENE-IS is available at https://github.com/G100DKFZ/gene-is.
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:28325279
%2 pmc:PMC5363413
%R 10.1016/j.omtn.2016.12.001
%U https://inrepo02.dkfz.de/record/124312