Abstract: The present disclosure provides gene and gene sets, the expression of which is important in the classification and/or prognosis of cancer, in particular of renal cell carcinoma.

Abstract: The invention provides a method for determining the presence, species, and/or quantity of Leishmania in a sample.

Abstract: Biomarkers and methods using the biomarkers for classifying cancer in a patient (e.g., predicting the risk of cancer-specific death or cancer recurrence) are provided.

Abstract: ?-cell loss in In Type 1 diabetes is typically undetected until the development of hyperglycemia, at which point ?-cell mass is significantly reduced. Methylation sensitive quantitative real time PCR (qRTPCR) of demethylated circulating free ?-cell specific DNA can be used as a biomarker of ?-cell death. Such DNA includes insulin gene and amylin gene DNA. Detection may be by determination of a gene demethylation index. Methylated and demethylated DNA may be distinguished by bisulfite treatment and use of specific PCR primers or probes to detect the different bisulfite treatment products. Detection of demethylated circulating free amylin DNA is useful in identifying ?-cell death. The amylin DNA may be used in conjunction with other ?-cell specific genes, such as insulin, to provide a multi-gene approach towards the detection of ?-cell loss.

Abstract: The present disclosure describes a method of treating a sample comprising cells with a process of partial lysing. Cells are exposed to a process such as bead beating that lyses some cells in the mixture. The process generates a resultant sample mixture that is suitable for both cell morphology screening and genetic screening. A first portion of the partially lysed sample can be mounted on a slide and observed for atypical cells and cytologic abnormalities. A second portion of the partially lysed sample can be screened for genetic markers known to correlate with a risk of cervical cancer. The method is particularly useful for cervical screening, where a combination of cytology and genetic screening present a more complete picture of cervical health. The disclosed method streamlines the diagnostic process for protocols that require both types of assays, without compromising screening accuracy.

Abstract: Sepsis remains a leading cause of morbidity and mortality in neonates worldwide. There is also clinically a low threshold for suspicion of infection in neonates, in particular as presentation varies greatly from very subtle to catastrophic collapse. The lack of reliably sensitive tests and the potential life-threatening consequences of delayed treatment of infection results in the widespread use of empirical antibiotics exposing many infants without infection to broad-spectrum antibiotics. The present invention provides a series of patient-invariant biomarkers for screening neonates and other subjects for infection that predicts bacterial infection with high accuracy; and is further shown to have predictive value in identifying infection in suspected cases with blood-culture negative tests.

Abstract: This disclosure is in the field of molecular diagnostics and relates to a method for classifying samples obtained from patients diagnosed with multiple myeloma into three newly defined clusters. The disclosure also relates to a method for determining the prognosis of an individual diagnosed with multiple myeloma as well as a method for the prediction of the response to treatment of an individual diagnosed with multiple myeloma. More in particular, the disclosure provides a method for determining the disease outcome or the prognosis of a patient diagnosed with multiple myeloma by classifying said patient into a high risk or a low risk category, based on a 92-gene classifier.

Abstract: A system for the integrated and automated analysis of DNA or protein, including a single-use cartridge, with an analysis device having a control device, and devices for capturing and processing signals, the control device carrying out a completely automatic process and evaluation of molecular diagnostic analysis via single-use cartridges (Lab-on-a-Chip). Controlling of an analysis process, which occurs in the cartridge, involves the subsequent displacement and thermostatisation of liquids with a first device, and with a second device the signals which are obtained during the analysis are processed. The first and the second devices are synchronized in such a manner that the analysis process of the sample can be carried out in a totally integrated manner thus producing an immediate result.

Abstract: The present disclosure relates to methods involving HCR reactions that involve using trigger oligos to activate probes that initiate HCR.

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 provides methods for performing an imaging method to detect a moiety associated with labeled hydroxymethylated bases in nucleic acid sequences, such as detecting a moiety associated with glucosylated 5-hydroxmethylated cytosines.

Abstract: The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TET3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.

Abstract: Herein is provided a simple, reliable and accurate method for cellular analysis on hematology analyzers. In various aspects, the methods provide separation and/or differentiation between red blood cells (RBCs) and white blood cells (WBCs) by utilizing a fluorescent dye to selectively stain WBCs such that they emit stronger fluorescence signals. The method provides optimal detection limits on WBCs and RBCs, thereby allowing analysis of samples with sparse cellular concentrations. As few as one reagent may be used to prepare a single dilution for body fluid analysis, in order to simplify the body fluid analysis. Minimal damage to WBCs is attained using the lysis-free approach described in aspects of the disclosure.

Abstract: Disclosed is nucleic acid preserving compositions and methods of manufacturing and using the same. Compositions include a carrier, a chaotropic agent, a buffering agent, a chelating agent, a surfactant, an alcohol, an acid, and a mucolytic agent. Compositions as aqueous solutions can include water as a carrier. Preferred embodiments include water, guanidine thiocyanate, Tris, EDTA, SLS, SDA 3C, HCl, and N-acetyl-L-cysteine. Some embodiments include a colored dye as a visual indicator. Methods of manufacturing include combining the components into a mixture, such as an aqueous solution. Methods of use include providing a biological sample that includes nucleic acid and contacting the biological sample with the composition. Kits include the composition disposed in a portion of a biological sample collection apparatus.

Abstract: Provided herein is a dual amplification method for identifying plant pathogens by analysis of pathogen DNA in an unpurified nucleic acid sample from the plant. Pathogen-specific and/or plant-specific primers are used to generate a first set of amplicons that are further amplified in a second amplification step using fluorescent tagged pathogen-specific primers. Fluorescent amplicons thus generated are hybridized with pathogen-specific nucleic acid probes that are immobilized on a solid support using bifunctional polymer linkers. The hybridized microarray is imaged to obtain fluorescent images of the amplicons and the nucleic acid probes, which are superimposed to detect the pathogen present in the plant. Also described herein is a method to identify a plant by analysis of plant DNA and a method to simultaneously detect both plant DNA and pathogen DNA in a single assay.

Abstract: Provided herein are methods and kits for distinguishing 5-hydroxymethylcytosine from 5-methylcytosine.

Abstract: A DNA sequencing device, and related method, which include an electrode and a plurality of spaced apart alignment structures. The electrode defines an electrode gap, the electrode being operable to detect a change in tunneling current as a DNA strand passes through the electrode gap. The plurality of spaced apart alignment structures are arranged to position nucleotides of the DNA strand in a predetermined orientation as the DNA strand passes through the electrode gap.

Abstract: Disclosed are methods for polynucleotide sequencing that detect the location of selected nucleobases with greater precision. The methods can be used to determine the location and nature of modified bases in a polynucleotide, that is, non-canonical bases, or to improve accuracy of sequencing of “problem” regions of DNA sequencing such as homopolymers, GC rich areas, etc. The sequencing method exemplified is nanopore sequencing. Nanopore sequencing is used to generate a unique signal at a point in a polynucleotide sequence where an abasic site (AP site, or apurinic or apyrimidinic site) exists. As part of the method, an abasic site is specifically created enzymatically using a DNA glycosylase that recognizes a pre-determined nucleobase species and cleaves the N-glycosidic bond to release only that base, leaving an AP site in its place.

Abstract: A micro-fluidic chip and its modification method and application in detection of food bacteria quality, includes the following steps: changing a functional group —CH3 on the internal surface of micro-fluidic channel of micro-fluidic chip to a functional group —OH through modification; Supplying amino silane reagent to the micro-fluidic channel; supplying dendritic polymer as modified by —COOH to internal surface of the micro-fluidic channel after drying; grafting primer of aminated aptamer RCA on terminus 5? and hybrid from its padlock probe on dendrimer on internal surface of the micro-fluidic channel; wherein, the padlock probe is the complementary sequence of the aptamer of the target pathogenic bacteria to be tested; after that, supplying RCA reaction reagent to the micro-fluidic channel to make aptamer RCA generate long-chain aptamer in series. The present invention adopts two RCA reactions of varied functions in combination, and uses dendritic polymer to modify internal surface of the chip.

Abstract: The invention relates to the use of inductively coupled plasma mass spectroscopy for cellular sample analysis. In some embodiments a method of performing mass spectroscopy analysis using an inductively coupled plasma mass spectroscopy system is provided. The method may include introducing a cellular sample comprising one or more cells or cellular particles into an inductively coupled plasma of the inductively coupled plasma mass spectroscopy system. The method may further include using the inductively coupled plasma mass spectroscopy system to assess the cellular sample by detecting and measuring one or more element tags in the cellular sample based on the element or isotopic compositions of the one or more element tags.