EpiVIA

EpiVIA performs joint profiling of chromatin accessibility and lentiviral CAR-T cell integration sites to map chromatin state and vector insertion at population and single-cell resolution.

Key Features:

• Chimeric read parsing: Parses sequencing reads to identify chimeric fragments resulting from lentiviral vector integration into the host genome.
• Combined reference alignment: Classifies fragments based on alignment patterns to a combined host-plus-viral reference genome.
• Single-cell integration and accessibility mapping: Determines chromatin accessibility and precise CAR-T vector integration sites at single-cell and population levels.
• Host and viral genome mapping: Maps both host and viral genomic sequences to localize integration breakpoints and accessible chromatin regions.
• Validation on clonal cells: Validated using clonal cells with known integration sites to assess accuracy of lentiviral integration detection and chromatin accessibility measurement.

Scientific Applications:

• CAR-T integration site analysis: Identifies precise lentiviral insertion sites of CAR constructs within T cells to study insertional patterns.
• Chromatin accessibility profiling: Profiles accessible chromatin regions concomitant with integration to assess the regulatory context of insertions.
• Assessing effects on T cell regulation: Enables investigation of whether CAR construct integration alters regulatory landscapes that affect T cell proliferative competence.
• Mechanistic studies of CAR-T efficacy: Facilitates mapping of host gene regulation and cellular factors associated with durable responses following CAR-T therapy.

Methodology:

Parses sequencing reads to identify chimeric host–viral fragments, aligns fragments to a combined host-plus-viral reference genome, classifies alignment patterns to assign integration breakpoints, and maps chromatin accessibility and vector insertion sites at single-cell resolution.