Ub-ISAP

Ub-ISAP automates identification and annotation of viral vector genomic integration sites from single- and paired-end sequencing reads to support gene therapy safety assessment.

Key Features:

• Automated integration site identification: Selects sequencing reads containing viral sequences and aligns them to the host genome from single- and paired-end datasets.
• Integration site annotation: Classifies unique integration sites as transcription start site-proximal, intragenic, or intergenic.
• UNIX-based workflow: Executes the processing pipeline within a UNIX environment.
• High-throughput processing: Automates selection and alignment steps to enable analysis of large-scale sequencing datasets.

Scientific Applications:

• Gene Therapy Safety Assessment: Analyzes integration site locations to detect potential disruption of host genes or regulatory regions.
• Efficiency Evaluation: Assesses the integration performance of viral vectors by quantifying integration events.
• Cancer Research: Generates integration-site datasets to study viral integration patterns relevant to oncogenesis and therapy.
• Genetic Mapping in Mutagenesis Screens: Maps viral elements in mutagenesis screens to assist in elucidating gene function and interactions.

Methodology:

Selection of sequencing reads containing viral sequences from single- and paired-end reads, alignment of those reads to the host genome, identification of unique integration sites, and classification into transcription start site-proximal, intragenic, or intergenic categories within a UNIX-based pipeline.