PGNneo

PGNneo identifies neoantigens derived from noncoding regions of the human genome using proteogenomics to enable discovery of peptide targets for cancer immunotherapy and personalized vaccine development.

Key Features:

• Comprehensive Modules: Four modules perform noncoding somatic variant calling and HLA typing; peptide extraction and customized database construction; variant peptide identification; and neoantigen prediction and selection.
• Validation Across Cancer Types: Demonstrated on two hepatocellular carcinoma (HCC) cohorts and applied to a colorectal cancer (CRC) cohort, identifying neoantigens from frequently mutated genes including TP53, WWP1, ATM, KMT2C, and NFE2L2.
• Utility in Low TMB Cancers: Focus on noncoding regions provides additional immune targets for tumors with low tumor mutational burden (TMB) in coding regions.

Scientific Applications:

• Neoantigen discovery: Identification of variant-derived peptides from noncoding genomic regions to expand the repertoire of candidate neoantigens for cancer immunotherapy.
• Vaccine target prioritization: Selection of predicted neoantigens to inform design of personalized cancer vaccines, including for tumors with low coding-region mutation burden.

Methodology:

Noncoding somatic variant calling, HLA typing, peptide extraction, customized database construction, variant peptide identification, and neoantigen prediction and selection.