Abstract: Provided are methods for identifying antigens containing amino acid sequences for use in a cancer vaccine. The vaccines and methods of use for prophylaxis and/or therapy of cancer are included. The method involves: i) exposing cancer cells to a chemotherapeutic agent that damages DNA; ii) determining open reading frames encoded by mRNA transcribed from a gene in the cancer cells of i); iii) comparing the open reading frames of the mRNA of i) to open reading frames encoded by mRNA transcribed from the gene in the cancer cells that were not exposed to the chemotherapeutic agent, iv) determining a different open reading frame encoded by the mRNA of i) and an open reading frame of the mRNA of ii), wherein the different open reading frame encoded by the mRNA of i) encodes a contiguous amino acid sequence comprising the sequence of the antigen for use in the cancer vaccine.

Abstract: Described herein are methods of identifying tumor-specific epitopes from the cancer tissue DNA of cancer patients using both DNA sequencing and bioinformatics techniques. The identification of tumor-specific epitopes provides pharmaceutical compositions with a limited number of tumor-specific peptides suitable for personalized genomics-driven immunotherapy of human cancer. Specifically disclosed herein is a novel index called the Differential Agretopic Index (DAI) for the epitope which allows prediction of whether immunization with a particular epitope will be protective against the tumor. Pharmaceutical compositions and methods of administration are also included.

Abstract: Described herein are methods of identifying tumor-specific epitopes from the cancer tissue DNA of cancer patients using both DNA sequencing and bioinformatics techniques. The identification of tumor-specific epitopes provides pharmaceutical compositions with a limited number of tumor-specific peptides suitable for personalized genomics-driven immunotherapy of human cancer. Specifically disclosed herein is a novel index called the Differential Agretopic Index (DAI) for the epitope which allows prediction of whether immunization with a particular epitope will be protective against the tumor. Pharmaceutical compositions and methods of administration are also included.

Abstract: The invention provides methods of identifying the gene expression profile of a cell type present within a population of cells using single cell expression data by a residual minimization process. The methods of the invention can be used to infer the genes expressed by a rare cell type that can be difficult to measure experimentally due to its low abundance in an organism or sample of interest. The methods described herein can additionally be used to predicting the gene expression profile of a population of cells using single cell expression patterns as well as methods of quantitating the composition of a population.

Abstract: Described herein are methods of identifying tumor-specific epitopes from the cancer tissue DNA of cancer patients using both DNA sequencing and bioinformatics techniques. The identification of tumor-specific epitopes provides pharmaceutical compositions with a limited number of tumor-specific peptides suitable for personalized genomics-driven immunotherapy of human cancer. Specifically disclosed herein is a novel index called the Differential Agretopic Index (DAI) for the epitope which allows prediction of whether immunization with a particular epitope will be protective against the tumor. Pharmaceutical compositions and methods of administration are also included.

Abstract: A new pipeline for the rational design and interpretation of biomarker panels is provided. The pipeline includes: generating the maximally informative marker set from biomarker databases; selecting an optimal biomarker panel based on the desired accuracy, economic, and experimental constraints; and interpreting the assay results by a statistically robust matching to reference data. The pipeline can also be used to identify biological samples, including cell types and progenitor cells.