PGNneo: A Proteogenomics-Based Neoantigen Prediction Pipeline in Noncoding Regions.

ABSTRACT: The development of a neoantigen-based personalized vaccine has promise in the hunt for cancer immunotherapy. The challenge in neoantigen vaccine design is the need to rapidly and accurately identify, in patients, those neoantigens with vaccine potential. Evidence shows that neoantigens can be derived from noncoding sequences, but there are few specific tools for identifying neoantigens in noncoding regions. In this work, we describe a proteogenomics-based pipeline, namely PGNneo, for use in discovering neoantigens derived from the noncoding region of the human genome with reliability. In PGNneo, four modules are included: (1) noncoding somatic variant calling and HLA typing; (2) peptide extraction and customized database construction; (3) variant peptide identification; (4) neoantigen pred

SUBMITTER: Tan X 

PROVIDER: S-EPMC10000440 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature