Bioinformatic Discovery of Tumor-Specific Neoantigens Arising from Chimeric RNAs

Cancer vaccines inducing immunogenic responses to tumor-specific neoantigens are rapidly emerging into a new frontier of cancer therapy. Chimeric RNAs encoding fusion proteins are a rich source of novel neoantigens. Here, we present a straightforward bioinformatic pipeline to identify immunogenic peptides produced from chimeric RNAs. We apply a bespoke script to identify fusion-specific peptide regions from chimeric transcript predictions and leverage the netMHCpan program to identify immunogenic peptides. In this paper, we provide a guide for installation and running of the program as well as discuss the rationale behind its design.