Immune cell signatures

A method of priming a patient for immune therapy of a tumor, comprising:

• quantifying or obtaining expression levels for a plurality of somatic-specific single nucleotide variants (SNVs) from paired tumor and normal whole exome sequencing;
• predicting MHC1 binding affinity for neoepitope peptides resulting from said SNVs, wherein neoepitope binding to MHC1 results in silenced neoepitopes;
• identifying the patient for priming upon prediction of silenced neoepitopes;
• and
• administering the identified patient with epigenetic priming therapy prior to immune therapy.

A method of predicting an effective cancer therapy for a patient, comprising:

• sequencing whole genomic and transcriptomic data to obtain in silico expressed neoantigens and expressed checkpoint markers;
• predicting that a checkpoint therapy is an effective cancer therapy for the patient when the in silico sequencing data comprises (a) expressed neoantigens that are predicted to bind MEW, and (b) expressed checkpoint markers;
• predicting that a combination of a DNA hypomethylating agent and checkpoint therapy is an effective cancer therapy for the patient when the in silico sequencing data comprises neoantigens that are predicted to bind MEW, but binding is suppressed by methylation;
• and
• predicting that a combination of a HDAC inhibitor and checkpoint therapy is an effective cancer therapy for the patient when the in silico sequencing data comprises neoantigens that are predicted to bind MHC, but binding is suppressed by heterochromatin remodeling.