Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.09.375204v1?rss=1 Authors: Kosaloglu-Yalcin, Z., Lee, J., Nielsen, M., Greenbaum, J., Schoenberger, S. P., Miller, A., Kim, Y. J., Sette, A., Peters, B. Abstract: MHC class I antigen processing consists of multiple steps that result in the presentation of MHC bound peptides that can be recognized as T cell epitopes. Many of the pathway steps can be predicted using computational methods, but one is often neglected: mRNA expression of the epitope source proteins. In this study, we improve epitope prediction by taking into account both peptide-MHC binding affinities and expression levels of the peptide's source protein. Specifically, we utilized biophysical principles and existing MHC binding prediction tools in concert with RNA expression to derive a function that estimates the likelihood of a peptide being presented on a given MHC class I molecule. Our combined model of Antigen eXpression based Epitope Likelihood-Function (AXEL-F) outperformed predictions based only on binding or based only on antigen expression for discriminating eluted ligands from random background peptides as well as in predicting neoantigens that are recognized by T cells. We also showed that in cases where cancer patient-specific RNA-Seq data is not available, cancer-type matched expression data from TCGA can be used to accurately estimate patient-specific gene expression. Using AXEL-F together with TGCA expression data we were able to more accurately predict neoantigens that are recognized by T cells. The method is available in the IEDB Analysis Resource and free to use for the academic community. Copy rights belong to original authors. Visit the link for more info