Abstract: Described is a multi-regional, multi-omics approach to uncovering the mechanisms of immune escape in carcinoma. Immunotherapy with ant-PD1 and anti-CTLA4 elicits a heterogeneous immunological response across different regions of the tumor. Several genetic alterations associated with high intra-tumoral heterogeneity (ITH) shape tumor microenvironment (TME).

Abstract: Methods, systems, and apparatus, including computer programs encoded on computer-storage media, for classification of a single cell from a biological sample of an entity. In one aspect, the method can include obtaining data indicating a plurality of reference positions where a known variant sequence exists for the entity in respective reference positions of the plurality of reference positions, obtaining a plurality of reads for the single cell from the biological sample of the entity, determining, for respective reads of the obtained plurality of reads, a score indicating whether a variant sequence in the respective reads of the biological sample of the entity matches the plurality of reference positions where the known variant sequence exists, and classifying the single cell as a tumor cell or normal cell based on an aggregation of the score determined for the respective reads of the obtained plurality of reads.

Abstract: A potential prognostic biomarker is based on a combination of a composite score generated by sequence analysis of global human endogenous retrovirus (hERV)/retro-transposon transactivation and a cell signature generated using deconvolution of immune cells within a tumor sample for predicting the efficacy of chemotherapeutic agents and immune checkpoint inhibitors. Correlation analysis of the composite score with cell signature within a tumor sample enables survival analysis in individuals receiving chemotherapeutic agents and immune checkpoint inhibitors.

Abstract: Presented herein are methods and compositions for determining MSI status and LS screening in a single test of colorectal cancer tissue. Also presented herein are methods for determining MSI status in a sample of cell-free DNA obtained from blood obtained from a cancer patient.