Abstract: A method for diagnosing an active Mycobacterium tuberculosis infection by detecting certain RNA biomarkers present in secreted extracellular vesicles isolated from a bodily fluid. The RNA biomarkers in the secreted extracellular vesicles may include a certain Mycobacterium RNAs as well as certain host cell RNAs. Also provided is an RNA signature of certain Mycobacterium and host cell RNA present in secreted extracellular vesicles indicative of an active tuberculosis infection.

Abstract: Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.

Abstract: The present invention provides methods for detecting a target nucleic acid in a sample by, for example, incubating the target nucleic acid with a detection probe containing a nucleic acid sequence complementary to at least a portion of the target nucleic acid and a nuclease enzyme that specifically cleaves double-stranded nucleic acids. Hybridization between the detection probe and the target nucleic acid thereby leads to cleavage of the detection probe, releasing a portion of the probe attached to a detectable agent. The portions of the digested probes attached to the detectable agent can be separated from unbound probe and detected in order to determine the presence of the target nucleic acid in the sample. Thus, the invention enables rapid and accurate analysis of a sample for the presence of desired nucleic acid biomarkers.

Abstract: A method of determining of the presence or absence of a target RNA component in a sample, the method comprising steps of: (a) contacting the sample with a composition comprising (i) a quaternary ammonium compound or a precursor thereof, which should extract/release the nucleic acid from the sample; (b) optionally storing and/or transporting the composition obtained in step (a); (c) contacting the composition obtained in step (a) with a composition comprising a proteinaceous washing agent, e.g. BSA or casein for stabilizing the RNA for transport and/or storage; and (d) using the composition obtained in step (c) in an amplification method, e.g. RT-PCR.

Abstract: This invention relates generally to compositions and methods for identifying the regulatory network that modulates, controls or otherwise influences dendritic cell (DC) response(s), for example, dendritic cell maturation, dendritic cell antiviral response(s) and/or dendritic cell inflammatory response(s), as well compositions and methods for exploiting the regulatory network that modulates, controls or otherwise influences dendritic cell response(s) in a variety of therapeutic and/or diagnostic indications.

Abstract: Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

Abstract: LncRNAs are emerging as important oncogenic drivers in many cancers, but comprehensive, agnostic studies to identify key lncRNAs involved in GBM are lacking. Described herein are new lncRNA involved in gliomagenesis and prognosis, elucidating the biological functions of these relatively unknown biological actors and opening new therapeutic avenues for therapeutic development.

Abstract: The present invention relates to methods of determining the sequence of nucleotides in target nucleic acid molecules. Thus, the invention relates to methods of sub-unit sequencing. The methods comprise the use of identification nucleic acid detection entities which specifically hybridize to the target nucleic acid, bind identification tags and have localization tags transiently bind thereto.

Abstract: Disclosed are methods for diagnosing Parkinson's disease, or identifying a risk of developing Parkinson's disease, comprising measuring the amount of a biomolecule in a blood sample, liver sample, or hepatocyte. Also disclosed are methods for preventing or treating Parkinson's disease, comprising administering a therapeutically effective plurality of hepatocytes to a subject in need thereof.

Abstract: 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.

Abstract: The present invention is directed methods for identifying, in a sample, one or more target nucleotide sequences differing from other nucleotide sequences in the sample by one or more nucleotides, one or more copy numbers, one or more transcript sequences, and/or one or more methylated residues, using ligation detection reactions, polymerase mediated extension reactions, and/or cleavage reactions. The present invention is also directed to methods for identifying, in a sample, one or more nucleotides in a target nucleotide sequence.

Abstract: A system and method for isolating and analyzing single cells, wherein the system includes: an array of wells defined at a substrate, each well including an open surface and a well cavity configured to capture cells in one of a single-cell format and single-cluster format, and a fluid delivery module including a fluid reservoir superior to the array of wells through which fluid flow is controlled along a fluid path in a direction parallel to the broad face of the substrate; and wherein the method includes: capturing a population of non-cell particles into the array of wells in single-particle format; releasing, from the non-cell particles, a set of probes into the array of wells; capturing a population of cells into the array of wells in single-cell format; releasing biomolecules from each captured cell into the array of wells; and generating a set of genetic complexes comprising the biomolecules associated with a single captured cell and a subset of probes within individual wells of the array of wells.

Abstract: The present invention relates to an in vitro method of identifying a molecular subtype of a tumor in a cancer patient and to a method of stratifying a cancer patient for tumor treatment. The present invention further relates to kits that are useful for identifying a molecular subtype of a tumor in a cancer patient.

Abstract: The present disclosure relates to normalization of biological samples, particularly samples comprising nucleic acids to be sequenced. The normalization protocols described herein may be utilized across multiple samples to cap total stoichiometric input and minimize variations in transcript abundance on a per-sample basis in a multiplexed fashion to dramatically increase the accuracy, capacity and efficiency of nucleic acid sequencing.

Abstract: The present invention relates to methods to detect an amount of DNA that originates from cells of a given type, where the sample comprising such DNA in admixture with DNA that does not originate from such cells. Such methods are based on differential methylation, at certain regions, of the DNA that originates from the given type of cells compared to the admixed DNA. Such methods have particular application in the detection, from a biological fluid from a pregnant female, of cell free DNA that originates from a foetus or the placenta of a foetus, or the detection, from a biological fluid from an individual, of cell free DNA that originates from cells of a tumour.

Abstract: The invention relates to methods of analysing a sample from a subject having or suspected of having Crohn's disease for the abundance of the subject's nucleic acid (e.g., DNA) in the sample. The invention also relates to methods for measuring abundance of nucleic acid (e.g., DNA) in stool from a human subject having or suspected of having Crohn's Disease (CD). In various embodiments, an in vitro method includes analysing the relative abundance of the host (human) DNA in said sample of stool or nucleic acid extracted or isolated from a stool sample from the host (human); determining the relative abundance of the host (human's) DNA in the sample; and associating the abundance of the host (human) DNA with the host (human) providing the stool sample, or the host (human) providing the stool sample from which the nucleic acid was extracted.

Abstract: Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of ˜90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention and monitoring.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: Systems and methods to diagnose sarcoidosis are described. In addition to diagnosing sarcoidosis, the systems and methods can distinguish sarcoidosis from tuberculosis. Further disclosed is a cDNA library and methods of its use for reliably identifying sarcoidosis markers.

Abstract: The present invention provides a plurality of pairs of proximity probes, each pair being capable of binding to a different target analyte, wherein the first and second proximity probes of each pair of probes comprise universal oligonucleotides conjugated to their analyte binding moieties, and hybridised to the universal oligonucleotides are different tag oligonucleotides comprising universal complement domains common to all tag oligonucleotides and unique domains unique to each tag oligonucleotide, as well as methods for their production.