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Fig. 2 | Biomarker Research

Fig. 2

From: Advances of mRNA vaccine in tumor: a maze of opportunities and challenges

Fig. 2

The general process of neoantigen identification and the influence factors of each step. Firstly, tumor tissue and normal tissue (usually para-cancer tissue or peripheral blood mononuclear cells) were sampled, their DNA was extracted for whole exon sequencing, and tumor samples were conducted RNA sequencing. Then, mutations are identified by comparing tumor sequences with normal sequences. Combined with predicted HLA typing, there are two methods to obtain neoantigens: neoantigen prediction pipelines (1) are used to predict neoantigens or selection of peptides that specifically bind to MHC molecules by mass spectrometry analysis (2). Finally, T cell activation assays are conducted to verify whether the selected neoantigens can specifically activate T cells. FFPE: formalin fixed paraffin embedded; SNVs: single-nucleotide variants; LC–MS: liquid chromatography and mass spectrometry; TCR: T cell receptor; pMHC: peptide major histocompatibility complexs; LOH: loss of heterozygosity; TAP: transporter associated with antigen processing

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