TY  - JOUR
AU  - Afzal, Saira
AU  - Wilkening, Stefan
AU  - von Kalle, Christof
AU  - Schmidt, Manfred
AU  - Fronza, Raffaele
TI  - GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data.
JO  - Molecular Therapy / Nucleic Acids
VL  - 6
SN  - 2162-2531
CY  - New York, NY
PB  - Nature Publ. Group
M1  - DKFZ-2017-01208
SP  - 133 - 139
PY  - 2017
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - pmid:28325279
C2  - pmc:PMC5363413
DO  - DOI:10.1016/j.omtn.2016.12.001
UR  - https://inrepo02.dkfz.de/record/124312
ER  -