Revisiting neoantigen depletion signal in the untreated cancer genome

Steps for HLA-binding region checking

1. Download raw data from Van den Eynden J. et al. via zenodo https:// doi.org/10.5281/zenodo.2621365
2. Install and deploy antigen.garnish for IEDB score calculation
3. Identify neoantigens by the following approaches:
   • Neoantigens based only on MHC I binding (MHC affinity < 500 nM)
   • Differential agretopicity index(DAI, DAI > 5)
   • IEDB high neoantigens (IEDB score > 0.9)
4. Map the neoantigens to exome region
5. Calculate the overlap between neoantigen location and HLA binding/non-binding region from Van den Eynden J. et al.
6. Analyze and visualize the result

Reference

• Neoantigen dissimilarity to the self-proteome predicts immunogenicity and response to immune checkpoint blockade
• Luksza, M, Riaz, N, Makarov, V, Balachandran VP, et al. 2017. A neoepitope fitness model predicts tumour response to checkpoint blockade immunotherapy. Nature. 23;551(7681):512-516
• Van den Eynden, J., Jimenez-Sanchez, A., Miller, M.L. & Larsson, E. Lack of detectable neoantigen depletion signals in the untreated cancer genome. Nat Genet 51, 1741-1748 (2019).

LICENSE

MIT ©2020 Xuan Wang, Shixiang Wang, Tao Wu and Xue-Song Liu

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Cancer Biology Group @ShanghaiTech

Research group led by Xue-Song Liu in ShanghaiTech. University