VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites

BMC Bioinformatics

Software

Stefano Beretta¹  Ivan Merelli²  Luciano Milanesi²  Eugenio Montini³  Andrea Calabria³  Stefano Brasca³  Giulio Spinozzi³ 

[1] Department of Computer Science, University of Milano Bicocca, Viale Sarca, 336, 20126, Milan, Italy;National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi, 93, 20090, Segrate, Italy;San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Via Olgettina, 58, 20132, Milan, Italy;

关键词: Open source software;    Bioinformatics pipeline;    Integration site analysis;    Gene therapy;    High-throughput sequencing;    Next-generation sequencing;    Workflow;   

DOI  :  10.1186/s12859-017-1937-9

 received in 2017-08-09, accepted in 2017-11-14,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundBioinformatics 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.ResultsHere 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).ConclusionsWe 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).

【 授权许可】

CC BY   
© The Author(s). 2017