NeoPredPipe

NeoPredPipe predicts neoantigens from tumor-derived somatic variants using next-generation sequencing (NGS) data to assess neoantigen burden, tumor heterogeneity, and immune recognition potential.

Key Features:

• High-throughput processing: Processes single-region and multi-region tumor samples from next-generation sequencing (NGS) data to predict neoantigens derived from somatic mutations.
• Integration of established tools: Integrates widely adopted bioinformatics tools for neoantigen discovery and prediction to produce consolidated outputs.
• Neoantigen burden and heterogeneity metrics: Provides summary information on predicted neoantigen burden and delivers insights into tumor heterogeneity based on somatic mutation calls.
• HLA-aware prediction: Optionally incorporates patient-specific HLA haplotypes to refine prediction of immune recognition potential for candidate neoantigens.
• Rapid analysis capability: Enables high-throughput generation of neoantigen predictions and associated summaries to support timely downstream analyses.

Scientific Applications:

• Neoantigen prediction: Identification of putative neoantigens arising from somatic tumor variants for downstream immunological assessment.
• Tumor heterogeneity analysis: Characterization of intra-tumor heterogeneity through comparison of neoantigen and mutation distributions across regions.
• Immunotherapy research: Assessment of neoantigen recognition potential to support development and optimization of immunotherapeutic strategies.

Methodology:

Processes NGS data to identify somatic mutations and predict corresponding neoantigens; evaluates neoantigen immune recognition potential and incorporates tumor heterogeneity and patient-specific HLA haplotypes when provided.