ISAnalytics

ISAnalytics enables comprehensive and high-throughput clonal tracking studies using vector integration sites as markers of cellular identity in gene therapy applications.

Key Features:

• Workflow Automation: Supports automation of insertion site workflow within laboratory workflows and standard procedures.
• Clonal Tracking Analysis: Performs base and advanced analysis for insertion site tracking including clonal abundance, clonal expansions, and statistics for insertional mutagenesis.
• Longitudinal Analysis: Supports longitudinal analysis of clones over time, proliferation and differentiation for hematopoietic stem cell biology in vivo.
• Metadata-Driven Framework: Enables users to focus on biological questions and hypotheses rather than on computational aspects.
• Efficient Data Structures: Implements efficient and scalable data structures benchmarked with previous methods.
• Reproducibility and Reporting: Grants reproducibility and full analytical control through interactive web-reports.
• Flexible Applications: Applicable for all viral vector-based clonal tracking applications as well as genetic barcoding or cancer immunotherapies.

Scientific Applications:

• Gene Therapy Safety Assessment: Assesses the safety and long-term efficacy of hematopoietic stem cell gene therapy treatments in clinical trials.
• Hurler Disease Clinical Trials: Supports clinical trial use cases for Hurler disease through comprehensive clonal tracking and analysis.
• Hematopoietic Reconstitution Studies: Unravels hematopoietic reconstitution in gene therapy applications with unprecedented resolution.
• Insertional Mutagenesis Monitoring: Provides statistics and analysis for monitoring insertional mutagenesis events in transduced stem cells.
• In Vivo Stem Cell Biology: Provides basic biology insights of transduced stem cells in vivo through longitudinal clonal analysis.

Methodology:

ISAnalytics imports clones identified externally and processes them using efficient and scalable data structures. The package is implemented as an R package with a module with Shiny interface for interactive analysis.