Patent ID: 11965892
Assignee: BIONTECH US INC.
Field: Pharmaceuticals (Chemistry)
Classification: CPC G  A  C | IPC A  C  G

Claim 0:
1. A method of selecting a peptide sequence for producing a pharmaceutical composition, comprising:
(I) selecting one or more peptide sequences using a machine, wherein selecting one or more peptide sequences using the machine comprises:
(a) inputting into the machine amino acid sequence information of a set of candidate peptide sequences expressed by cancer cells of a single human subject,
wherein the machine comprises a trained machine learning immunoprecipitated HLA-peptide presentation prediction model, wherein the trained machine learning immunoprecipitated HLA-peptide presentation prediction model generates as an output a plurality of presentation predictions based on the amino acid sequence information of the set of candidate peptide sequences, wherein each presentation prediction of the plurality of presentation predictions is indicative of a presentation likelihood that a given peptide sequence of the set of candidate peptide sequences is presented by an MHC protein encoded by an HLA allele of the single human subject, wherein the trained machine learning immunoprecipitated HLA-peptide presentation prediction model has a presentation prediction value (PPV) of at least 0.35 according to a presentation PPV determination method,
wherein the trained machine learning immunoprecipitated HLA-peptide presentation prediction model comprises:
(i) a plurality of parameters
and
(ii) a function representing a relation between the amino acid sequence information received as input and the presentation likelihood generated as an output based on the amino acid sequence information and the plurality of parameters; and

(b) selecting at least one candidate peptide sequence based on the presentation likelihood; and

(II) producing a pharmaceutical composition comprising a recombinant polypeptide or a polynucleotide encoding the recombinant polypeptide, wherein the recombinant polypeptide comprises the at least one candidate peptide sequence selected from (I)(b) of the set of candidate peptide sequences that is expressed by a cancer cell of the single human subject and is presented by the MHC protein encoded by the HLA allele of the single human subject.