Abstract: 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.

Abstract: Disclosed herein are compositions that include antigen-encoding nucleic acid sequences having multiple iterations of KRAS neoepitope-encoding sequences and/or lacking immunodominant epitopes. Also disclosed are nucleotides, cells, and methods associated with the compositions including their use as vaccines.

Abstract: Methods and compositions for monitoring mutation burden, cancer status, vaccine efficacy using cell-free DNA sequencing are disclosed.

Abstract: Compositions include modified adenoviruses. Nucleotides, cells, and methods associated with the compositions, including their use as vaccines. Viral vectors using a TET promoter system and methods of producing viruses having the same.

Abstract: Disclosed herein are alphavirus vectors that include neoantigen-encoding nucleic acid sequences derived from a tumor of a subject. Also disclosed are nucleotides, cells, and methods associated with the vectors including their use as vaccines.

Abstract: Disclosed herein are alphavirus vectors that include neoantigen-encoding nucleic acid sequences derived from a tumor of a subject. Also disclosed are nucleotides, cells, and methods associated with the vectors including their use as vaccines.

Abstract: Disclosed herein are alphavirus vectors that include neoantigen-encoding nucleic acid sequences derived from a tumor of a subject. Also disclosed are nucleotides, cells, and methods associated with the vectors including their use as vaccines.

Abstract: Methods are provided to separately isolate antigen-binding T cells and antigen-activated T cells derived from a starting population of peripheral blood mononuclear cells, and to identify overlapping T cell receptor clonotypes. Antigens include personal and shared neoantigens as well as cancer-testis antigens. The T cell receptor clonotypes can be further used to develop cancer treatment therapies.

Abstract: 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.

Abstract: 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.