| CPC G16B 20/30 (2019.02) [A61K 39/0011 (2013.01); G16B 20/20 (2019.02)] | 20 Claims |
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1. A method for producing a cancer vaccine composition comprising one or more nucleic acid sequences encoding a number A of neoepitopes, wherein A is an integer from 3 to 100, said method comprising:
A) Producing A nucleic acid sequences encoding said A neoepitopes selected by a method comprising the steps of:
a) Obtaining one or more nucleic acid sequence encoding one or more neoepitopes from an individual having or suspected of having cancer comprising a tumor, each neoepitope comprising at least one minimal epitope, wherein each neoepitope comprises at least one mutation compared to a reference sequence, wherein the at least one minimal epitope consists of a number of amino acids equal to or smaller than the number of amino acids of the neoepitope and comprises said at least one mutation; wherein the one or more nucleic acid sequences encoding the neoepitopes comprise at least one mutation which is specific for the tumor;
b) Measuring a MHC I and/or MHC II binding affinity for the at least one minimal epitope and a corresponding reference peptide, wherein the binding affinity is determined by in silico prediction by calculating a % Rank score, wherein a low % Rank score indicates a strong binding affinity and a high % Rank score indicates a weak binding affinity, and wherein the corresponding reference peptide is obtained from body fluid or healthy tissue of the same individual or in a normal, healthy population;
c) Producing said A nucleic acid sequences,
wherein said A neoepitopes comprise at least three of the top ten highest ranking MHC binding neoepitopes comprising at least one minimal epitope predicted to bind to MHC I and/or to MHC II, when ranked with respect to their likelihood of clinical utility by:
i) determining the number of minimal epitopes comprised in the MHC binding neoepitopes, wherein neoepitopes comprising a high number of minimal epitopes are ranked higher than neoepitopes comprising a lower number of minimal epitopes;
ii) determining a MHC I binding differential of the MHC I binding neoepitopes, wherein the MHC I binding differential is given by the formula (% Rank score (MHC I) for reference)/(% Rank score (MHC I) for neoepitope) wherein neoepitopes with a high MHC I binding differential are ranked higher than neoepitopes with a lower MHC I binding differential;
iii) determining whether the at least one mutation is in an anchoring position or a non-anchoring position of the minimal neoepitope for each minimal epitope comprised within the neoepitopes, wherein minimal neoepitopes with the mutation in an anchoring position are prioritized;
iv) prioritizing the MHC I binding neoepitopes with respect to their MHC I rank, wherein neoepitopes with a low % Rank score (MHC I) are ranked higher than neoepitopes with a higher % Rank score (MHC I), wherein the % Rank score (MHC I) of a neoepitope comprising one or more minimal epitopes predicted to bind to MHC I is equal to the lowest % Rank score (MHC I) of said one or more minimal epitopes; and
v) determining a BLOSUM score, wherein the MHC I binding neoepitopes are prioritized with respect to their BLOSUM score in a descending order, wherein the BLOSUM score of a neoepitope is equal to the BLOSUM score of the best ranking minimal epitope it comprises, wherein a minimal epitope with a BLOSUM score <2 is prioritized; and
B) Producing the cancer vaccine composition comprising said A nucleic acid sequences encoding said A neoepitopes produced in step (A).
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