Identification of neoantigens with MHC class II model

A method for identifying T-cells that are antigen-specific for at least one neoantigen that is likely to be presented by class II MHC alleles on surfaces of tumor cells of a subject. Peptide sequences of tumor neoantigens are obtained by sequencing the tumor cells of the subject. The peptide sequenc...

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Bibliographische Detailangaben
Hauptverfasser:	YELENSKY, Roman, PALMER, Christine, BULIK-SULLIVAN, Brendan, SKOBERNE, Mojca, YOUNG, Lauren Elizabeth, FRANCIS, Joshua Michael, BUSBY, Jennifer, CAO, Minh Duc, DAVIS, Matthew Joseph, BOUCHER, Thomas Francis
Format:	Patent
Sprache:	eng
Schlagworte:	BEER BIOCHEMISTRY CALCULATING CHEMISTRY COMPOSITIONS THEREOF COMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS COMPUTING COUNTING CULTURE MEDIA ELECTRIC DIGITAL DATA PROCESSING ENZYMOLOGY HUMAN NECESSITIES HYGIENE MEDICAL OR VETERINARY SCIENCE METALLURGY MICROBIOLOGY MICROORGANISMS OR ENZYMES MUTATION OR GENETIC ENGINEERING ORGANIC CHEMISTRY PEPTIDES PHYSICS PREPARATIONS FOR MEDICAL, DENTAL, OR TOILET PURPOSES PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS SPIRITS VINEGAR WINE
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Beschreibung
Zusammenfassung:	A method for identifying T-cells that are antigen-specific for at least one neoantigen that is likely to be presented by class II MHC alleles on surfaces of tumor cells of a subject. Peptide sequences of tumor neoantigens are obtained by sequencing the tumor cells of the subject. The peptide sequences are input into a machine-learned presentation model to generate presentation likelihoods for the tumor neoantigens, each presentation likelihood representing the likelihood that a neoantigen is presented by the class II MHC alleles on the surfaces of the tumor cells of the subject. A subset of the neoantigens is selected based on the presentation likelihoods. T-cells that are antigen-specific for at least one of the neoantigens in the subset are identified. These T-cells can be expanded for use in T-cell therapy. TCRs of these identified T-cells can also be sequenced and cloned into new T-cells for use in T-cell therapy.