Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

BMC Bioinformatics

Software

Geoffrey B. McCowage¹  Atul Kamboj²  Belinda Kramer²  Claus V. Hallwirth³  Ian E. Alexander⁴ 

[1] Cancer Centre for Children, The Children’s Hospital, Westmead, NSW, Australia;Children’s Cancer Research Unit, Kids’ Research Institute, The Children’s Hospital at Westmead, Locked Bag 4001, 2145, Westmead, NSW, Australia;Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Westmead, NSW, Australia;Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Westmead, NSW, Australia;The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, NSW, Australia;

关键词: Gene therapy;    Integration site analysis;    Next-generation sequencing;    Viral vectors;   

DOI  :  10.1186/s12859-017-1719-4

 received in 2017-02-19, accepted in 2017-06-08,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function.ResultsWe have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic.ConclusionUb-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/.

【 授权许可】

CC BY   
© The Author(s). 2017