Identification of tumor-protective epitopes for the treatment of cancers

A method of identifying tumor epitopes in a cancer patient, comprising

• sequencing at least a portion of the cancer patient's RNA or DNA in both a healthy tissue and a cancer tissue, to produce a healthy tissue RNA or DNA sequence and a cancer tissue RNA or DNA sequence,
• comparing the healthy tissue RNA or DNA sequence and the cancer tissue RNA or DNA sequence and identifying differences between the healthy tissue RNA or DNA sequence and the cancer tissue RNA or DNA sequence to produce a difference DNA marker set,
• analyzing the difference DNA marker set to produce a tumor-specific epitope set, wherein the tumor-specific epitope set comprises one or more tumor-specific epitopes, and wherein analyzing the difference DNA marker set to produce a tumor-specific epitope set is independent of whether one or more tumor-specific epitopes are related to cancer-causing pathways,
• calculating a numerical value called the Differential Agretopic Index for each tumor-specific epitope in the tumor-specific epitope set by subtracting a numerical score for a non-mutated amino acid sequence of the healthy tissue corresponding to the mutated amino acid sequence of the tumor-specific epitope from a numerical score for the tumor-specific epitope, wherein the numerical scores are calculated using an epitope predictive algorithm that predicts the binding of epitope peptides to MHC molecules,
• ranking the tumor-specific epitope set by the Differential Agretopic Index for each epitope in the set to identify a subset of 10 to 50 top-ranked tumor-specific epitopes,
• producing a pharmaceutical composition comprising a pharmaceutically acceptable carrier and one or more peptides comprising one or more tumor-specific epitopes selected from the subset of 10 to 50 top-ranked tumor-specific epitopes, or one or more polypeptides containing one or more tumor-specific epitopes selected from the subset 10 to 50 top-ranked tumor-specific epitopes, or one or more polynucleotides encoding one or more peptides comprising one or more tumor-specific epitopes selected from the subset of 10 to 50 top-ranked tumor specific epitopes, and wherein a non-mutated amino acid sequence of the healthy tissue corresponding to at least one of the one or more tumor-specific epitopes selected from the subset of 10 to 50 top-ranked tumor-specific epitopes has a negative numerical score, and
• optionally administering the pharmaceutical composition to the cancer patient.