[Problem] Provided is a method for detecting of an autofluorescence Liquid Biopsy of Methylated Fragmented DNA (fragmented nucleosome) released into the blood by cell apoptosis as a disease-related substance

[Solution] The inventive method comprises a) a step of capturing the fragmented DNA (fragmented nucleosome) in the analyte as a disease-related substance onto the plasmonic metal meso-crystals; b) a step of irradiating the captured fragmented DNA (fragmented nucleosome) on the plasmonic metal meso-crystal with excitation light to enhance the autofluorescence by the surface plasmon enhancing effect, and acquiring a fluorescent colony image via a filter in a longer wavelength range than the excitation light filter; c) a step of adopting a pixel that exhibits a brightness greater than or equal to a predetermined threshold value of said fluorescent colony image; d) calculating a ratio of a total area value of pixels greater than or equal to a predetermined threshold value of a different two-wavelength region of the adopted measurement region.

Methods and arrays for identifying the cell or tissue origin of DNA are provided. Accordingly there is provided a method of identifying DNA having a methylation pattern distinctive of a cell or tissue type or state comprising: labeling an epigenetic modification of interest in a DNA sample with a label; contacting said sample on an array comprising a plurality of probes for said DNA under conditions which allow specific hybridization between said plurality of probes and said DNA; and detecting said hybridization, wherein an amount of said label is indicative of the cell or tissue type or state, wherein the method is effected in the absence of amplification of said DNA.

Methods and arrays for identifying the cell or tissue origin of DNA are provided. Accordingly there is provided a method of identifying DNA having a methylation pattern distinctive of a cell or tissue type or state comprising: labeling an epigenetic modification of interest in a DNA sample with a label; contacting said sample on an array comprising a plurality of probes for said DNA under conditions which allow specific hybridization between said plurality of probes and said DNA; and detecting said hybridization, wherein an amount of said label is indicative of the cell or tissue type or state, wherein the method is effected in the absence of amplification of said DNA.

Provided herein are methods and kits for detecting the presence of DNA and/or RNA mutations associated with cancer (e.g., lung cancer). The methods and kits employ microcarriers, each with a probe specific for a DNA or RNA mutation and an identifier unique to the probe sequence. Upon isolation and amplification of nucleic acids from a sample, hybridization of amplified DNA with a probe, specific for a DNA or RNA mutation, that is coupled to a microcarrier indicates the presence of the mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays are provided. Representative genes that can be screened for mutations include, e.g., KRAS, NRAS, PIK3CA, BRAF, EGFR, AKT1, MEK1, and HER2 for DNA mutations and/or ALK, ROS, RET, NTRK1, and cMET for RNA mutations.

Provided herein are methods and kits for detecting the presence of DNA and/or RNA mutations associated with cancer (e.g., lung cancer). The methods and kits employ microcarriers, each with a probe specific for a DNA or RNA mutation and an identifier unique to the probe sequence. Upon isolation and amplification of nucleic acids from a sample, hybridization of amplified DNA with a probe, specific for a DNA or RNA mutation, that is coupled to a microcarrier indicates the presence of the mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays are provided. Representative genes that can be screened for mutations include, e.g., KRAS, NRAS, PIK3CA, BRAF, EGFR, AKT1, MEK1, and HER2 for DNA mutations and/or ALK, ROS, RET, NTRK1, and cMET for RNA mutations.

Provided are a method and system for screening neoantigen and uses of neoantigens. Specifically, provided are a method and system for screening neoantigens derived from a gene of which expression is essential for survival of a cancer cell and/or a is homogeneously expressed in all cells in cancer tissue as a diagnostic and/or therapeutic target, and uses of neoantigens.

Provided are a method and system for screening neoantigen and uses of neoantigens. Specifically, provided are a method and system for screening neoantigens derived from a gene of which expression is essential for survival of a cancer cell and/or a is homogeneously expressed in all cells in cancer tissue as a diagnostic and/or therapeutic target, and uses of neoantigens.

Methods for generating a composite biomarker that identifies a predicted level of responsiveness of a subject to a particular type of an immunotherapy treatment is provided. The method can include generating genomic metrics that represent one or more characteristics corresponding to one or more DNA sequences. The method can also include generating transcriptomic metrics represent one or more characteristics corresponding to a set of peptides that are translated from a corresponding RNA sequence of the one or more RNA sequences. The method can also include generating a composite biomarker score derived from the set of genomic metrics and the set of transcriptomic metrics. The method can also include determining, based on the composite biomarker score, a predicted level of responsiveness of the subject to a particular type of an immunotherapy treatment.

Novel NTRK1 fusion molecules, detection reagents, and uses and kits for evaluating, identifying, assessing and/or treating a subject having a cancer are disclosed.

Novel NTRK1 fusion molecules, detection reagents, and uses and kits for evaluating, identifying, assessing and/or treating a subject having a cancer are disclosed.