Abstract: In one aspect of the present disclosure is a targeted sequencing workflow where an input sample comprising a sufficient quantity of genomic material is provided such minimal or no amplification cycles are utilized prior to sequencing.

Abstract: In one aspect of the present disclosure is a targeted sequencing workflow where an input sample comprising a sufficient quantity of genomic material is provided such minimal or no amplification cycles are utilized prior to sequencing.

Abstract: The invention is a method of identifying a cognate antigen for a T-cell receptor using neoantigens from a patient's tumor cells combined with the patient's T-cells and using cell sorting, genome sequencing, expressing TCR genes, presenting tumor neoantigens on MHC complex and uniquely barcoding the T-cells where TCR recognition occurs to tag all components of the TCR recognition complex.

Abstract: Disclosed herein is a method of deriving a plurality of genetic variants from a homogenized input sample. Also disclosed herein are methods of identifying a plurality of genetic variants in a sample comprising: homogenizing one or more input samples to provide a homogenized sample; preparing genomic material isolated from the homogenized input sample for sequencing; and identifying the plurality of genetic variants within sequencing data derived after sequencing the prepared genomic material.

Abstract: The invention is a method of identifying a cognate antigen for a T-cell receptor using neoantigens from a patient's tumor cells combined with the patient's T-cells and using cell sorting, genome sequencing, expressing TCR genes, presenting tumor neoantigens on MHC complex and uniquely barcoding the T-cells where TCR recognition occurs to tag all components of the TCR recognition complex.

Abstract: Disclosed herein is a method of analyzing flow cytometry data for cells derived from homogenized whole tumor samples.

Abstract: In one aspect of the present disclosure is a targeted sequencing workflow where an input sample comprising a sufficient quantity of genomic material is provided such minimal or no amplification cycles are utilized prior to sequencing.

Abstract: Disclosed herein are multiplex methods for co-detecting a B cell marker, TP53 nucleic acid, and Chromosome 17 centromere DNA in a single sample. Samples stained for the B cell marker (e.g., CD79a protein), TP53 nucleic acid, and Chromosome 17 centromere DNA may allow for the identification of the subtype of chronic lymphocytic leukemia (CLL) with the 17p deletion. The methods feature staining the B cell marker (e.g., CD79a) a first distinct color, TP53 in a second distinct color, and chromosome 17 centromere DNA in a third distinct color. Further disclosed are nucleic acid probes specific for 19q12, INSR, ATM, DLEU2, TP53, and 13q12.