A process for analysing chromosome regions and interactions relating to prognosis of prostate cancer or DLBCL.

[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.

The invention provides a method of establishing a chicken methylation clock comprising: (a) determining the methylation ratio and the read coverage of the genomic CpG sites of an age-correlated training sample of a specific chicken tissue; (b) defining a set of CpG sites having reliable methylation ratios in all training samples of step (a) using a cutoff value; and (c) performing a penalized regression using the methylation ratios of step (b) as input and the age correlated to the training sample as dependent variable, by applying a penalized regression model; thereby obtaining a set of CpG sites with corresponding weighting factors and intercept of the linear model equation as parameters defining the chicken methylation clock.

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.

Described are methods of analyzing cell free DNA based on combining analysis of cfDNA methylation with analysis of the cfDNA nucleosome footprint and/or with analysis of cfDNA copy number alteration. The diagnostic performance of these methods, in particular relating to early or earlier stage diseases or disorders, is increased compared to the diagnostic performance of the individual cfDNA analysis methods.

Described herein are compositions, methods, and techniques to generate a cancer signature and uses thereof. The cancer signature can be used to determine a cancer progression risk of a subject based upon expression levels of genes of a progression gene signature in a sample. The methods can be used to predict a prognosis, to select an appropriate treatment regimen, to identify or screen for an agent effective against a cancer, or a combination thereof. Computer implemented methods and systems that implement those methods are also provided. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present disclosure.

The present invention provides methods for providing a prognosis for lung adenocarcinoma, using a panel of eight molecular markers that are differentially expressed in lung adenocarcinoma.

Disclosed herein are methods and kits for identifying a subject as having leukemia. Also provided herein are methods and kits for determining a leukemia subtype in subject. Further provided herein are methods and kits for determining the prognosis of a subject having leukemia and for determining the progression of leukemia in a subject.

The present invention relates to a method for providing information for colorectal cancer diagnosis, a composition for diagnosing colorectal cancer, and a kit comprising same, and, more particularly, to: a method for providing information for colorectal cancer diagnosis by using a primer for specifically amplifying plural methylated colorectal cancer marker genes; a composition for diagnosing colorectal cancer; and a kit comprising same.

Provided is a method for diagnosing upper urinary tract urothelial carcinoma with low invasiveness and high reliability. A method for identifying a cell or tissue having upper urinary tract urothelial carcinoma, comprising: detecting the DNA methylation level of at least one of specific CpG sites in genomic DNA derived from an upper urinary tract urothelial cell or a tissue containing the upper urinary tract urothelial cell; and determining whether the cell or tissue containing such a cell has upper urinary tract urothelial carcinoma on the basis of the detected DNA methylation level.