Neoantigens provide a promising source for targetting cancer cells through targeted re-activation of immune cells. However, identifying neoantigens is a challenges task due to their low abundance and cancer heterogeneity. In the previous project application, we successfully implemented a workflow to perform proteogenomics analysis for identifying neoantigens on several cancer cohorts. Results from those anlyses has been published and we are currently writing a main manuscript describing the workflow and its application to neantigen detection.
In order to leverage our ability in finding neoantgiens in a scalable manner, we have teamed up with coordinators at the proteomics division from European Bioinformatics Institute (EBI) to search beyond our local cohorts and utilize the large amounts of data stored there. This project has two sides, one is to investigate novel protein coding genes from non-coding RNAs and mutations, and the other is to search normal tissue proteomic datasets for previously identified neoantigens from our initial project. The second part of the project is rather important in detection of neoantigens since it enables us to avoid candidates that are expressed in normal tissues to ensure patient safety. It also enables us to cross check novel peptides and identify tissue-specific peptides that are also found in cancer samples.