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: A method of detecting a biological substance, including introducing a first substance dispersed in a solvent into a flow channel formed between a first substrate and a second substrate such that the first substance is placed in a first well formed in the first substrate, and detecting the first substance. The first well is formed such that the first well has an open side which faces downwards and is communicated with the flow channel, and the solvent has a specific gravity larger than a specific gravity of the first substance.

Abstract: Devices, systems, methods, and kits are disclosed for amplifying small quantities of nucleic acid and identifying the nucleic acid sequences of the amplified nucleic acid products.

Abstract: Provided herein is technology for gastrointestinal neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of gastrointestinal neoplasm, and classifying the site location of such a gastrointestinal neoplasm (e.g., a colorectal region, a pancreaticobiliary region, a gastroesophageal region).

Abstract: In one aspect, provided herein are methods for predicting the responsiveness of DLBCL patients to treatment with lenolidomide or Compound A; or a stereoisomer thereof; or a pharmaceutically acceptable salt, solvate, hydrate, co-crystal, clathrate thereof; or a polymorph thereof utilizing biomarkers or classifiers that correlate with responsiveness to one of these drugs. In another aspect, provided herein are methods for treating a DLBCL patient determined to be responsive to treatment with lenolidomide or Compound A; or a stereoisomer thereof; or a pharmaceutically acceptable salt, solvate, hydrate, co-crystal, clathrate thereof; or a polymorph thereof utilizing biomarkers or classifiers (or output thereof) that correlate with responsiveness to one of these drugs.

Abstract: A microfluidic sequencing device in which a stream of microdroplets at least some of which contain a single nucleotide base are made to undergo reaction with a capture system to capture and detect an ordered sequence of single nucleotide bases generated by progressive pyrophosphorolysis.

Abstract: This invention provides methods of using labeled nucleotide polyphosphate analogues to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, nucleotides and primer-conjugated nanopore proteins for use in such methods, and processes for producing such nucleotides and primer-conjugated nanopore proteins.

Abstract: Provided herein is an internal standard method for determining copy number of a pathogen DNA in an unpurified nucleic acid sample by using a known copy number of synthetic DNA that shares a consensus region sequence with the pathogen. The sample is subject to two amplification steps using locus-specific primers and fluorescent primers respectively to obtain fluorescent amplicons for the pathogen and synthetic DNA. These are hybridized with immobilized pathogen-specific and synthetic DNA-specific nucleic acid probes and imaged to obtain fluorescent signals for pathogen-specific and synthetic DNA-specific amplicons. Signal intensities are correlated with the known copy number of synthetic DNA to determine copy number of pathogen DNA in the plant. Also described herein is a method to simultaneously quantitate using the above method, copy numbers of both pathogen and plant DNA in a sample.

Abstract: Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Legionella pneumophila 16S or 23S rRNA sequences or DNA encoding 16S or 23S rRNA. Methods are disclosed for detecting the presence of L. pneumophila in samples by using the disclosed compositions in methods that include in vitro nucleic acid amplification of a 16S rRNA sequence or DNA encoding the 16S rRNA sequence, or of a 23S rRNA sequence or DNA encoding the 23S rRNA sequence to produce a detectable amplification product.

Abstract: Cloning vectors encoding endonuclease capable of removing false positives. Attempts to diagnose and/or select appropriate treatment methods via genetic screening can be rendered inaccurate do the presence of false positive. The error causing false positives may include double-stranded nucleic acids comprising a bulge and/or Y-junction. Expression vectors encoding an endonuclease capable of removing such error causing false positives are disclosed, along with methods of utilizing the encoded endonucleases to increase diagnostic accuracy and permit selection of more appropriate treatments.

Abstract: Provided herein is a dual amplification method for detecting plant pathogens by analysis of pathogen DNA in an unpurified nucleic acid sample from the plant. Pathogen-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 simultaneously detect both plant DNA and pathogen DNA in a single assay.

Abstract: Methods of distinguishing and identifying a patient with aggressive/indolent, prostatic adenocarcinoma comprising contacting a sample from the patient with a set of detectably labeled probes under hybridization conditions and determining the presence of chromosomal abnormalities in the sample; sets of probes for use in such methods; and kits comprising a set of probes and instructions for distinguishing or identifying a patient as having aggressive/indolent, prostatic adenocarcinoma.

Abstract: The present disclosure is directed methods and products for synthesizing and using targeted templated assembly reactants comprising at least one nucleic acid recognition moiety, at least one selectively-reactive moiety, and at least one effector partial moiety. The nucleic acid recognition moiety can bind a target nucleic acid sequence within a sample. The nucleic acid recognition moiety also can bind the selectively-reactive moiety. Additionally, the effector partial moiety can bind the selectively-reactive moiety to produce an active effector structure. Also disclosed are methods of delivering the targeted templated assembly reactants and active effector structures formed from the targeted templated assembly reactants.

Abstract: The present invention relates to a method, in particular an in vitro method, for identifying certain immune cells of a mammal, comprising analysing the methylation status of at least one CpG position in the gene CCR6 and/or BLR1 or an orthologous or paralogous gene thereof, and the use of DNA-methylation analysis of the genes of the proteins CCR6 and/or BLR1 for a detection and quality assurance and control of certain immune cells. In particular, the present invention relates to analysing the methylation status of at least one CpG position in the gene CCR6 in T cells. Furthermore, the present invention relates to a kit for performing the above methods, as well as to respective uses.

Abstract: The disclosed subject matter relates to brush polymer-oligonucleotide conjugates comprising oligonucleotides covalently attached to the backbone of a non-cationic, sterically congested brush polymer and the use of such polymer-oligonucleotide conjugates in antisense gene regulation and as diagnostic agents.

Abstract: Embodiments of the invention include methods and compositions for producing standards for noninvasive prenatal genetic diagnostics and for the detection and monitoring of cancer. The compositions can include a plurality of different nucleosomal DNA fragments derived from either primary cells or cell lines and can include one or more synthetic oligonucleotides. The amount of the different nucleosomal DNA fragments can be varied so as to simulate naturally occurring cell free DNA samples obtained from the blood of the pregnant woman or naturally occurring cell free DNA samples obtained from the blood of cancer patients.

Abstract: A method for the prediction, prognosis and/or diagnosis of bladder cancer or bladder cancer recurrence in a subject, the method includes: providing a test sample from the subject; measuring DNA methylation levels of at least a portion of two or more polynucleotides selected from the group consisting of HOXA9, SOXI, NPY, IRAK3, L1-MET, and Z02 in the test sample; calculating a risk score based on the measured DNA methylation levels, comparing the calculated risk score to a cut-off value derived from a reference DNA methylation profile based on DNA methylation levels of the one or more biomarkers derived from a control group, members of which had bladder cancer; and based on the comparison calculated risk score to the cut-off value, determining at least one of: (1) whether bladder cancer has recurred; (2) whether there is likelihood that the bladder cancer will recur; and (3) whether the patient has bladder cancer.

Abstract: This invention relates to the use of metal (VI) oxo complexes to catalyse the selective oxidation of 5hmC residues in polynucleotides to 5fC residues. This may be useful in the identification of modified cytosine residues in a population of polynucleotides comprising a sample nucleotide sequence. A first portion of the population is oxidised with a metal (VI) oxo complex and then the first portion and a second portion of said population are both treated with bisulfite. The residues in the first and second portions that correspond to a cytosine residue in the sample nucleotide sequence are identified following treatment and the identities of these residues are used to determine the modification of the cytosine residue in the sample nucleotide sequence. Methods, reagents and kits are provided.

Abstract: A method for determining the sequence of nucleotide bases in a polynucleotide analyte is provided. It is characterised by the steps of (1) generating a stream of single nucleotide bases from the analyte by pyrophosphorolysis; (2) producing captured molecules by reacting each single nucleotide base with a capture system labelled with detectable elements in an undetectable state; (3) releasing the detectable elements from each captured molecule in a detectable state and (4) detecting the detectable elements so released and determining the sequence of nucleotide bases therefrom. The method can be used advantageously in sequencers involving the use of microdroplets.

Abstract: Analyte filter arrays and methods for making an analyte filter array are provided. The arrays are formed using a dispersion of filter particles having selected moieties attached to the surface of the particles and a microarray having complementary moieties formed in an array on a substrate, such that each filter particle is attached to a selected region of the microarray. The moiety on the substrate may be RNA or DNA or other molecule. The substrate may be a surface of a detector array, a membrane that may be placed in registration with the detector array or a stamp used to transfer the filter array to a detector array.