Abstract: The invention features methods for the identification of genomic aberrations in circulating tumor cells (CTCs) isolated from peripheral blood. In various embodiments of the disclosure, the methods involve isolation of a small number of purified circulating multiple myeloma cells, purification of genomic DNA from the cells, and sequencing of the genomic DNA.

Abstract: The subject matter disclosed herein is generally directed to CD8+ tumor infiltrating lymphocytes comprising gene signatures associated with response to immunotherapy treatment. Moreover, the subject matter disclosed herein is generally directed to methods and compositions for use of the gene signatures. Specifically, disclosed herein are gene signatures associated with response to checkpoint blockade therapy and immune cell subtypes characterized by said gene signatures. Further disclosed are methods of using said gene signatures and immune cell subtypes. Further disclosed are pharmaceutical compositions comprising populations of CD8+ TILs enriched for a specific subtype.

Abstract: The disclosure features compositions and methods that are useful for determining the fraction of tumor-derived DNA (tumor fraction; TF) in cell free DNA (cfDNA). The methods involve calculating the fraction of tumor-derived DNA in the cfDNA using a combination of copy number alteration data and fragment length distribution data.

Abstract: The disclosure provides molecular classifiers for use in the characterization and diagnosis of lung cancer and methods of selecting and treating subjects with appropriate personalized cancer treatments, including but not limited to CDK4/6 inhibitors, c-Met inhibitors, PD-1/PD-L1 inhibitors and combinations thereof.

Abstract: The present invention features methods for characterizing mutational profiles in patients with bladder cancer.

Abstract: The invention provides a molecular classifier and a targeted sequencing assay for use in characterization and treatment of diffuse large B-cell lymphoma.

Abstract: The invention provides compositions and methods useful in characterizing and/or treating classical Hodgkin's Lymphoma and/or primary mediastinal B-cell lymphoma (PMBL). In embodiments, the characterization is carried out using a biological sample comprising circulating tumor DNA (ctDNA) from a subject.

Abstract: The invention provides methods for characterizing microsatellite instability in biological samples and for selecting a treatment for a subject having a neoplasia.

Abstract: The present invention relates to methods of determining a cancer treatment prognosis for a subject in need thereof by evaluating epigenetic and genetic changes within a tumor sample from the subject. The present invention further provides methods of treating cancer in a subject by evaluating epigenetic and genetic changes within a tumor sample from the subject. In addition, the present invention provides methods of screening test agents to identify agents that decrease tumor cell plasticity.

Abstract: The present invention features methods for characterizing mutational profiles in patients with bladder cancer.

Abstract: The disclosure features in some aspects methods for identifying subjects with constitutional mismatch repair deficiency (CMMRD), a mismatch repair deficiency (MMD) cancer, a polymerase proofreading deficiency (PPD) cancer, and/or a MMD&PPD cancer. The disclosure also features in some aspects methods for predicting response of a subject to immunotherapy.

Abstract: As described below, the present invention features compositions, panels of biomarkers, and methods for characterizing chronic lymphocytic leukemia (CLL) for prognosis and selection of a subject for a treatment and/or inclusion in a clinical trial.

Abstract: A system and method for determining the exact pair of alleles corresponding to polymorphic genes from sequencing data and for using the polymorphic gene information in formulating an immunogenic composition. Reads from a sequencing data set mapping to the target polymorphic genes in a canonical reference genome sequence, and reads mapping within a defined threshold of the target gene sequence locations are extracted from the sequencing data set. Additionally, all reads from the set data set are matched against a probe reference set, and those reads that match with a high degree of similarity are extracted. Either one, or a union of both these sets of extracted reads are included in a final extracted set for further analysis. Ethnicity of the individual may be inferred based on the available sequencing data which may then serve as a basis for assigning prior probabilities to the allele variants. The extracted reads are aligned to a gene reference set of all known allele variants.

Abstract: The present disclosure relates to detecting microsatellite indels in cancer patients and those at high risk for cancer, and is useful for early detection of specific types of cancer and early onset of relapse. More particularly, the present disclosure relates to compositions, methods, and kits for classifying and treating neoplasia and tumors with microsatellite instability. The instant classifier identifies preferred therapeutic options, including combination therapies, for MSI tumor or cancer, and is particularly useful for patient stratification so that patients who would be treatable by immunotherapy drugs may be identified at a very low cost.

Abstract: The present invention provides methods of predicting a patient's response to immunotherapy, in particular checkpoint blockade therapy, and provides for treatments. Disclosed herein are novel combinations of factors identified in tumors used to predict response and provide for treatments. Also, disclosed are methods of treatment that can shift a tumor to a responder phenotype.

Abstract: The disclosure relates to methods for increasing the speed and efficiency of computational genomics. In particular, the disclosure relates to methods of scaling computational genomics by using one or more specialized architectures for highly parallelized computations, such as graphics processing units (GPUs), tensor processing units (TPUs), and field programmable gate arrays (FPGAs), and the like, to compute the computational genomics calculations.

Abstract: Method, system and an article of manufacture for clustering and thereby identifying predefined antigens reactive with undetermined immunoglobulins of sera derived from patient subjects in need of diagnosis of disease or monitoring of treatment.

Abstract: The present invention relates to methods of determining a cancer treatment prognosis for a subject in need thereof by evaluating epigenetic and genetic changes within a tumor sample from the subject. The present invention further provides methods of treating cancer in a subject by evaluating epigenetic and genetic changes within a tumor sample from the subject. In addition, the present invention provides methods of screening test agents to identify agents that decrease tumor cell plasticity.

Abstract: The present invention features methods for characterizing mutational profiles in patients with bladder cancer.

Abstract: The present invention relates to methods of determining a cancer treatment prognosis for a subject in need thereof by evaluating epigenetic and genetic changes within a tumor sample from the subject. The present invention further provides methods of treating cancer in a subject by evaluating epigenetic and genetic changes within a tumor sample from the subject. In addition, the present invention provides methods of screening test agents to identify agents that decrease tumor cell plasticity.