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A Comprehensive Survey of Mutations in Oesophageal Carcinoma Reveals Recurrent Neoantigens as Potential Immunotherapy Targets

Chen, C.; Liu, S.; Xiong, H.; Zhang, X.; Li, B.

2020-03-30 immunology
10.1101/2020.03.28.013201 bioRxiv
Show abstract

This study was aimed to investigate the mutations in Esophageal Carcinoma (EC) for recurrent neoantigen identification. A total of 733 samples with whole exome sequencing (WES) mutation data and 1153 samples with target region sequencing data were obtained from 7 published studies and GENIE database. Common HLA-I and HLA-II genotypes in both TCGA cohort and Chinese were used to predict the probability of public neoantigens in the dataset. Based on the integrated data, we not only obtained the most comprehensive EC mutation landscape so far, but also found 253 mutation sites which could be identified in at least 3 or more patients, including, TP53 p.R248Q, PIK3CA p.E545K, PIK3CA p.E542K, KRAS p.G12D, PIK3CA p.H1047R and TP53 p.C83F. These mutations can be recognized by multiple common HLA molecules (HLA-A11:01, HLA-B57:01, HLA-A03:01, DRB1-0301, DRB1-1202, et al.) in Chinese and TCGA cohort as potential public neoantigens. Overall, our analysis provides some potential targets for EC immunotherapy.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.