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Identification and ranking of recurrent neo-epitopes in cancer

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Item Type:Article
Title:Identification and ranking of recurrent neo-epitopes in cancer
Creators Name:Blanc, E. and Holtgrewe, M. and Dhamodaran, A. and Messerschmidt, C. and Willimsky, G. and Blankenstein, T. and Beule, D.
Abstract:BACKGROUND: Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognition process lies antigen presentation from somatic mutations. These neo-epitopes are emerging as attractive targets for cancer immunotherapy and new strategies for rapid identification of relevant candidates have become a priority. METHOS: We carefully screen TCGA data sets for recurrent somatic amino acid exchanges and apply MHC class I binding predictions. RESULTS: We propose a method for in silico selection and prioritization of candidates which have a high potential for neo-antigen generation and are likely to appear in multiple patients. While the percentage of patients carrying a specific neo-epitope and HLA-type combination is relatively small, the sheer number of new patients leads to surprisingly high reoccurence numbers. We identify 769 epitopes which are expected to occur in 77629 patients per year. CONCLUSION: While our candidate list will definitely contain false positives, the results provide an objective order for wet-lab testing of reusable neo-epitopes. Thus recurrent neo-epitopes may be suitable to supplement existing personalized T cell treatment approaches with precision treatment options.
Keywords:Cancer, Immunotherapy, Neo-Epitope, Neo-Antigen, Precision Treatment, Animals, Mice
Source:BMC Medical Genomics
Publisher:BioMed Central
Page Range:171
Date:27 November 2019
Official Publication:https://doi.org/10.1186/s12920-019-0611-7
PubMed:View item in PubMed
Related to:
https://edoc.mdc-berlin.de/17696/Preprint version

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