ScanNeo2

ScanNeo2 predicts neoantigens and immunogenicity from diverse genomic and transcriptomic somatic variants to support cancer immunotherapy research.

Key Features:

• Automated end-to-end pipeline: Performs automated processing for neoantigen identification and immunogenicity prediction.
• Integration of genomic and transcriptomic alterations: Combines genomic and transcriptomic variant information for comprehensive neoantigen discovery.
• High-throughput processing from raw sequencing data: Processes raw sequencing data to enable large-scale neoantigen prediction.
• Multi-variant support: Detects and incorporates single-nucleotide variants (SNVs), insertions/deletions (indels), canonical splicing events, exitron-splicing anomalies, gene fusions, and other somatic variations.
• Immunogenicity prediction: Predicts the immunogenic potential of candidate neoantigens.
• Benchmark-validated performance: Benchmark results indicate accurate neoantigen identification across diverse variant sources.

Scientific Applications:

• Neoantigen discovery for cancer immunotherapy: Identifies tumor-specific neoantigens as targets for immune-based cancer treatments.
• Personalized therapeutic target identification: Supports the selection of individualized neoantigen targets for personalized therapy strategies.
• Comprehensive variant-driven profiling: Enables profiling of neoantigens arising from splicing events, exitrons, gene fusions, and other somatic alterations.
• Immunogenicity-informed therapy design: Provides immunogenicity predictions to inform design and prioritization of immune-based interventions.

Methodology:

Processes raw sequencing data, integrates genomic and transcriptomic alterations, detects somatic variant types (single-nucleotide variants, insertions/deletions, canonical splicing events, exitron-splicing anomalies, gene fusions, and other somatic variations), predicts resultant neoantigens and their immunogenicity, and evaluates prediction accuracy via benchmarking.