pTuneos

pTuneos identifies and prioritizes tumor neoantigens using next-generation sequencing (NGS) data, focusing on whole-exome sequencing and RNA-seq.

Key Features:

• Neoantigen identification and prioritization: Identifies candidate tumor neoantigens from NGS-derived variant and expression evidence and ranks them for downstream analysis.
• RefinedNeo Scoring Scheme: Evaluates the probability that a predicted neoepitope is processed by MHC class I proteins and recognized by T cells.

Scientific Applications:

• Melanoma Cancer Vaccine Cohort: Demonstrates superior performance in predicting MHC presentation and T cell recognition of candidate neoantigens.
• TIL-Recognized Neopeptide Data: Demonstrates superior performance in predicting MHC presentation and T cell recognition of candidate neoantigens.
• TCGA Cohorts: Demonstrates superior performance in predicting MHC presentation and T cell recognition of candidate neoantigens.
• Melanoma and NSCLC checkpoint blockade immunotherapy: Demonstrates superior performance in predicting MHC presentation and T cell recognition of candidate neoantigens.

Methodology:

Processes whole-exome sequencing and RNA-seq NGS data and applies the RefinedNeo scoring scheme to evaluate the probability that predicted neoepitopes are processed by MHC class I proteins and recognized by T cells.