Abstract: The present disclosure relates to a system, method, and kit for particle detection and analysis. Devices disclosed herein may include at least an optical source, a fluidic chip containing a multiplex bead array, and a detection module, wherein the sample flows within the fluidic chip past a detection window, where the cells or particles are imaged by an image acquisition and analysis module that may include an optical detector. The image acquisition and analysis module counts the labeled particles and software allows for analysis of bead population.

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: Methods, compositions, and kits for stabilizing both human and microbial deoxyribonucleic acid (DNA) present in complex biological samples, such as feces, are disclosed. In particular, aqueous compositions for stabilizing DNA contained in biological samples at ambient temperature are disclosed, together with associated methods and kits using same. In one aspect, the compositions comprise a chelating agent present at a concentration of at least about 150 mM, and the composition has a pH of at least about 9.5.

Abstract: Provided are polynucleotide constructs useful in a nanopore analysis using enzyme activity. The polynucleotide constructs include a strand portion of interest to be analyzed in the nanopore analysis and having a 5? end and a 3? end, and a folded sequence located 3? or 5? of and adjacent to an end of the strand portion of interest, where the folded sequence can block the activity of a processive enzyme. In some embodiments, the polynucleotide constructs further include an enzyme binding sequence located 3? of and adjacent to an end of the folded sequence, and an enzyme displacement sequence located 5? of the strand portion of interest. Such polynucleotide constructs further include a threading sequence located 5? of the enzyme displacement sequence and at a 5? terminal end of the polynucleotide construct, where the processive enzyme has a processive activity in a direction from 3? to 5? on the polynucleotide construct.

Abstract: The present invention relates to nucleic acids and methods for detecting pathogens and beneficial microorganisms.

Abstract: The present invention is directed to methods for improving assay specificity and performance in binding assays.

Abstract: Methods are provided for diagnosing, detecting, or prognosticating a GEP-NEN based on the expression level score of biomarkers exhibiting differential expression in subjects having a GEP-NEN relative to a reference or control sample. The invention also provides compositions and kits comprising these biomarkers and methods of using these biomarkers in subsets or panels thereof to diagnose, classify, and monitor GEP-NEN and types of GEP-NEN. The methods and compositions provided herein may be used to diagnose or classify a subject as having a GEP-NEN, to distinguish between different stages of GEP-NENs, e.g., stable or progressive, to provide a measure of risk of developing a progressive GEP-NEN, and to gauge the completeness of treatments for GEP-NEN including, but not limited to surgery and somatostatin therapy.

Abstract: Provided herein is a method for detecting at least two distinct oligonucleotides of equal length in parallel from one biological sample, comprising the steps of providing a biological sample containing or suspected of containing oligonucleotides of interest; forming a hybridization mixture using at least two fluorescently labelled detection molecules with different surface charges; separating the detection molecules hybridized to the oligonucleotides by anion exchange HPLC; and detecting the hybridized detection molecule-oligonucleotide moieties by quantitative fluorescence readout. In a further aspect, a kit comprising at least two detection molecules is provided. In another aspect, provided herein is the use of at least two detection molecules with different surface charges for quantitatively detecting at least two distinct oligonucleotides of equal length in parallel from one biological sample.

Abstract: Provided herein are methods of adjusting or selecting a gluten peptide therapy based on the human leukocyte antigen (HLA) genotype, in particular HLA-DQ2.5 homozygosity, of a subject having or suspected of having Celiac disease. Also provided herein are methods of identifying (e.g., diagnosing) a subject, such as a subject having or suspected of having Celiac disease and/or assessing the efficacy of treatment of Celiac disease, e.g. by determining responsiveness to a therapeutic gluten peptide composition or cytokine response, and kits relating thereto.

Abstract: Disclosed is a gene expression panel that can be used to predict prostate cancer (PCa) progression. Some embodiments provide methods for predicting clinical recurrence of PCa. Some embodiments provide a method for predicting progression of prostate cancer in an individual, the method comprising: (a) receiving expression levels of a collection of signature genes from a biological sample taken from said individual, wherein said collection of signature genes comprises at least two genes selected from the group consisting of: NKX2-1, UPK1A, ADRA2C, ABCC11, MMP11, CPVL, ZYG11A, CLEC4F, OAS2, PGC, UPK3B, PCBP3, ABLIM1, EDARADD, GPR81, MYBPC1, F10, KCNA3, GLDC, KCNQ2, RAPGEF1, TUBB2B, MB, DUOXA1, C2orf43, DUOX1, PCA3 and NPR3; (b) applying the expression levels to a predictive model relating expression levels of said collection of signature genes with prostate cancer progression; and (c) evaluating an output of said predictive model to predict progression of prostate cancer in said individual.

Abstract: The present invention provides a method for diagnosing and determining prognosis of gastric cancer in a subject by detecting suppressed expression of the REC8 gene, which in some cases is due to elevated methylation level in the genomic sequence of this gene. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for treating gastric cancer by increasing REC8 gene expression or activity. Lastly, a highly sensitive and accurate detection method is provided for rapid determination of REC8 gene methylation status.

Abstract: Seven protective alleles for IgA nephropathy have been discovered that can be identified by analyzing a DNA sample for seven respective SNPs. A method is provided for identifying and treating subjects at risk of developing IgA neuropathy based on a new seven-SNP genetic risk score. Also provided are screening methods to identify compounds that bind to and reduce the expression or biological activity of a either CFHR1 or CFHR3.

Abstract: Methodologies for labeling the epigenetic modification 5-hydroxymethyl-cytosine (5hmC) along a DNA molecule, and for imaging this epigenetic modification along a DNA molecule are disclosed. Related compositions and reagents, and methods of preparing same are also disclosed.

Abstract: The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.

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: Disclosed herein are biomarkers of platelet function and methods for assessing platelet function in response to anti-platelet therapy and for determining a prognosis, diagnosis, or risk identification in a patient by detecting at least one biomarker of platelet function in the patient as well as determining amounts thereof. The biomarkers may be used to identify a patient as a candidate for treatment with an antiplatelet agent and to monitor and adjust antiplatelet therapy in a patient.

Abstract: The disclosed embodiments include methods to form STC and STMC for use in determining presence of cancer, and methods to detect presence of cancer. In one embodiment, A portion of a STC is stained. The STC includes normal cells and cancer cells of a type of cancer co-cultured based on at least one cell culturing factors. The at least one co-culture factors includes a type of the cancer cells being cultured, a ratio of the cancer cells to the normal cells being co-cultured, seeding density of the normal cells and the cancer cells being co-cultured, a type of cell growth supplement used to facilitate culturing the cells, and a concentration of the cell growth supplement used to facilitate co-culturing the cells. The stained portion is observed to determine presence of one or more biomarker types that indicate presence of cancer.

Abstract: The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.

Abstract: A method to detect prostate cancer comprising contacting a sample of prostate cells from the patient with a set of detectably labeled probes under hybridization conditions and determining the presence of chromosomal abnormalities in prostate tumor tissue, PIN (intra-epithelial neoplasia), histologically benign tissue and benign prostatic hyperplasia (BPH); a method to combine immunofluorescence and FISH (IF-FISH) to facilitate the assessment of chromosomal abnormalities; a set of probes; and a kit comprising the set of probes and instructions for diagnosing prostate cancer in a patient.

Abstract: Described herein are fluid-manipulation-based devices. Fluid manipulations as described herein can be configured to perform assays on biological samples. In an embodiment, the device includes a reaction chamber, which can includes an integrated sample isolation module, a cell lysis module, a biological target purification module, and an assay mixing module, which can include a microbead with a capture molecule coupled thereto and a nanoparticle having a probe molecule coupled thereto via a label, which can be a spectroscopic label. In an embodiment, the capture and probe molecules can be configured to be coupled together via a biological target to form a biological molecule bead complex. Devices and methods as described herein can manipulate and analyze nanoliter volumes of fluid, microliter volumes of fluid, milliliter volumes of fluid, or greater. Embodiments of the present disclosure can enable random biological assays and rapid, simultaneous analysis of multiple biological samples.