Dataset Information

Potential genotoxicity from integration sites in CLAD dogs treated successfully with gammaretroviral vector-mediated gene therapy.

ABSTRACT: Integration site analysis was performed on six dogs with canine leukocyte adhesion deficiency (CLAD) that survived greater than 1 year after infusion of autologous CD34+ bone marrow cells transduced with a gammaretroviral vector expressing canine CD18. A total of 387 retroviral insertion sites (RIS) were identified in the peripheral blood leukocytes from the six dogs at 1 year postinfusion. A total of 129 RIS were identified in CD3+ T-lymphocytes and 102 RIS in neutrophils from two dogs at 3 years postinfusion. RIS occurred preferentially within 30 kb of transcription start sites, including 40 near oncogenes and 52 near genes active in hematopoietic stem cells. Integrations clustered around common insertion sites more frequently than random. Despite potential genotoxicity from RIS, to date there has been no progression to oligoclonal hematopoiesis and no evidence that vector integration sites influenced cell survival or proliferation. Continued follow-up in disease-specific animal models such as CLAD will be required to provide an accurate estimate of the genotoxicity using gammaretroviral vectors for hematopoietic stem cell gene therapy.

SUBMITTER: Hai M

PROVIDER: S-EPMC6291306 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Potential genotoxicity from integration sites in CLAD dogs treated successfully with gammaretroviral vector-mediated gene therapy.

Hai M M Adler R L RL Bauer T R TR Tuschong L M LM Gu Y-C YC Wu X X Hickstein D D DD

Gene therapy 20080327 14

Integration site analysis was performed on six dogs with canine leukocyte adhesion deficiency (CLAD) that survived greater than 1 year after infusion of autologous CD34+ bone marrow cells transduced with a gammaretroviral vector expressing canine CD18. A total of 387 retroviral insertion sites (RIS) were identified in the peripheral blood leukocytes from the six dogs at 1 year postinfusion. A total of 129 RIS were identified in CD3+ T-lymphocytes and 102 RIS in neutrophils from two dogs at 3 yea ...[more]

PMID: 18369320

Similar Datasets

Project description:BACKGROUND:Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution. The increasing number of gene therapy clinical trials combined with the increasing amount of Next Generation Sequencing data, aimed at identifying integration sites, require both highly accurate and efficient computational software able to correctly process "big data" in a reasonable computational time. RESULTS:Here we present VISPA2 (Vector Integration Site Parallel Analysis, version 2), the latest optimized computational pipeline for integration site identification and analysis with the following features: (1) the sequence analysis for the integration site processing is fully compliant with paired-end reads and includes a sequence quality filter before and after the alignment on the target genome; (2) an heuristic algorithm to reduce false positive integration sites at nucleotide level to reduce the impact of Polymerase Chain Reaction or trimming/alignment artifacts; (3) a classification and annotation module for integration sites; (4) a user friendly web interface as researcher front-end to perform integration site analyses without computational skills; (5) the time speedup of all steps through parallelization (Hadoop free). CONCLUSIONS:We tested VISPA2 performances using simulated and real datasets of lentiviral vector integration sites, previously obtained from patients enrolled in a hematopoietic stem cell gene therapy clinical trial and compared the results with other preexisting tools for integration site analysis. On the computational side, VISPA2 showed a?>?6-fold speedup and improved precision and recall metrics (1 and 0.97 respectively) compared to previously developed computational pipelines. These performances indicate that VISPA2 is a fast, reliable and user-friendly tool for integration site analysis, which allows gene therapy integration data to be handled in a cost and time effective fashion. Moreover, the web access of VISPA2 ( http://openserver.itb.cnr.it/vispa/ ) ensures accessibility and ease of usage to researches of a complex analytical tool. We released the source code of VISPA2 in a public repository ( https://bitbucket.org/andreacalabria/vispa2 ).

Dataset Information

Potential genotoxicity from integration sites in CLAD dogs treated successfully with gammaretroviral vector-mediated gene therapy.

Publications

Potential genotoxicity from integration sites in CLAD dogs treated successfully with gammaretroviral vector-mediated gene therapy.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets