Tumor antigenicity processing and presentation

A method of treating a cancer in a patient in need thereof, the method comprising:

• obtaining omics data from a tumor tissue of the patient;
• identifying, using computational analysis of the omics data, a mutation in the omics data that gives rise to a tumor antigen, wherein the omics data is selected from genomics data, transcriptomics data, and/or proteomics data;
• determining, in silico, a HLA allele type of the patient in a process using HLA reference sequences in which a de Bruijn graph is constructed using a plurality of k-mers generated from the omics data, and in which a best fit between the de Bruijn graph and a HLA reference sequence determines the HLA allele type;
• matching, in silico, the HLA allele type of the patient and the tumor antigen with a majority allele type having a minimum predefined binding affinity to the same tumor antigen, wherein the majority allele type is one or more represented majority allele types among different ethnicities, different geographical locations, different gender, or family provenance;
• generating a cancer vaccine that comprises a recombinant nucleic acid encoding the tumor antigen, wherein the tumor antigen binds to both the patient specific HLA allele type and the majority allele type;
• and
• treating the cancer in the patient by administering the cancer vaccine.