Gritstone Bio, Inc.

Gritstone Oncology, Inc.

Brendan Bulik-Sullivan

Roman Yelensky

Jennifer Busby

Adnan Derti

Thomas Francis Boucher

Given a set of therapeutic epitopes, a cassette sequence is designed to reduce the likelihood that junction epitopes are presented in the patient. The cassette sequence is designed by taking into account presentation of junction epitopes that span the junction between a pair of therapeutic epitopes in the cassette. The cassette sequence may be designed based on a set of distance metrics each associated with a junction of the cassette. The distance metric may specify a likelihood that one or more of the junction epitopes spanning between a pair of adjacent epitopes will be presented.

Reducing junction epitope presentation for neoantigens

A method for identifying neoantigens that are likely to be presented on a surface of tumor cells of a subject. Peptide sequences of tumor neoantigens are obtained by sequencing the tumor cells of the subject. The peptide sequence of each of the neoantigens is associated with one or more k-mer blocks of a plurality of k-mer blocks of the nucleotide sequencing data of the subject; The peptide sequences and the associated k-mer blocks 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 an MHC allele on the surfaces of the tumor cells of the subject. A subset of the neoantigens is selected based on the presentation likelihoods.

Neoantigen identification using hotspots

Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.

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Cambridge, MA, United States of America

Brendan Bulik-Sullivan