IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods.

ABSTRACT:

Background

Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed standardized bioinformatics pipelines to process IS sequencing data, to generate reports, and/or to perform comparative studies across different GT trials. Keeping up with the technological advances in the field of IS analysis, different computational pipelines have been published over the past decade. These pipelines focus on identifying IS from single-read sequencing or paired-end sequencing data either using read-based or using sonication fragment-based methods, but there is a lack of a bioinformatics tool that automatically includes unique molecular identifiers (

SUBMITTER: Yan A 

PROVIDER: S-EPMC10354991 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature