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A multifunctional R package for identification of tumor-specific neoantigens

Hasegawa, T.; Hayashi, S.; Shimizu, E.; Mizuno, S.; Niida, A.; Yamaguchi, R.; Miyano, S.; Nakagawa, H.; Imoto, S.

2019-12-09 bioinformatics
10.1101/869388 bioRxiv
Show abstract

It is known that some mutated peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T-cells on the surface of a tumor cell. These peptides are termed neoantigen and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions, and structural variants. Beyond the existing applications, this package is capable of attaching and reflecting several additional information, e.g., wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information, and combinations of mutations to filter out infeasible peptides as neoantigen. AvailabilityThe R package is available at http://github/hase62/Neoantimon.

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