Patent ID: 11920202
Assignee: UNIVERSITY OF CONNECTICUT
Field: Measurement (Instruments)
Classification: CPC C  G | IPC C  G

Claim 12:
13. A method of treating a cancer patient comprising identifying an unbiased population of tumor rejection mediating neoepitopes (TRMNs) by;
comparing a cancer cell exome sequence from the cancer patient to a reference exome sequence and identifying single nucleotide variants (SNVs) in the cancer cell exome sequence compared to the reference exome sequence;
validating the SNVs using nucleic acid sequencing;
identifying 8-14 amino acid putative neoepitopes including the validated SNVs, wherein the putative neoepitopes are unbiased by MHC binding and/or CD8T* reactivity;
calculating an IC50 for an MHC allele for each 8-14 amino acid putative neoepitope including the SNVs and calculating an IC50 for the MHC allele for a corresponding non-mutated amino acid sequence for each validated SNV;
plotting the putative neoepitope IC50s on the x-axis, and the non-mutated amino acid sequence IC50s on the y-axis to provide a bivariate scatter plot;
clustering the putative neoepitopes in the bivariate scatter plot using model-based clustering based on parameterized finite Gaussian mixture models using the IC50s
selecting as TRMNs the neoepitopes in the bivariate scatter plot which are clustered putative neoepitopes in the space greater than 501 nM on the x-axis and greater than 501 nM on the y-axis
wherein the TRMNs are in an elliptical cluster encompassed by a circle having a center at 27,176.9 nM for the x-axis and 33,556.51 nM for the y-axis, and a radius of 33,195 nM from the center, and/or
wherein the TRMNs are in an elliptical cluster encompassed by a circle having a center at 27,176.9 nM for the x-axis and 33,556.51 nM for the y-axis and a radius of 22,430 nM from the center;

producing a peptide population or a nucleic acid population for expressing the peptide population, the peptide population comprising 15-100 different amino acid peptides, the peptides including one or more of the TRMNs;
producing a pharmaceutical composition comprising a pharmaceutically acceptable carrier and the peptide population or nucleic acid population; and
administering the pharmaceutical composition to the cancer patient.