Abstract: Apparatus, system and method for dispensing a particle-laden fluid from a fluid holding and dispensing micro-feature. In some implementations, the apparatus includes: a chamber having one or more surfaces that define a volume to receive fluid containing particulate matter, and an outlet port to dispense at least a portion of the fluid from the chamber. The outlet port may have a normal vector that, when the apparatus is positioned to dispense the fluid, is substantially perpendicular to gravity. The apparatus may be used to measure a number of individual particles from the fluid that flow through the outlet port over a period of them, measure a total volume of the fluid dispensed through the outlet port over the period of time, and calculate a concentration of the particulate matter within the chamber. In some implementations, the particle-laden fluid may be whole blood.

Abstract: The present invention discloses a method for detecting activities of a thioredoxin reductase, a detection device and an operation method therefor. The detection method comprises: solution preparation: preparing a working solution, an inhibitor solution, and a mixed agent; sample addition: adding the working solution into a control reaction cup, adding the inhibitor solution into an experimental reaction cup, and respectively adding a sample into the control reaction cup and the experimental reaction cup; incubation: putting the control reaction cup and the experimental reaction cup in a dark environment to perform incubation at a predetermined temperature for a first predetermined time; and measurement: adding the mixed agent into the control reaction cup and the experimental reaction cup and measuring the absorbance value at a predetermined wavelength for a second predetermined time.

Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules.

Abstract: The present invention discloses three molecular markers kits and applications for glaucoma diagnosis. The expressions of lncRNAs: T342877, lncRNAs: NR_026887, and lncRNAs: TCONS_00025577 are up-regulated in aqueous humors of patients with glaucoma compared with people in a control group. It indicates that lncRNAs: T342877, lncRNAs: NR_026887, and lncRNAs: TCONS_00025577 are highly expressed lncRNAs in glaucoma and are biomarkers that contribute to the diagnosis of glaucoma. The present invention provides a strong molecular biology basis for the diagnosis of glaucoma, and has far-reaching clinical significance and generalization performance.

Abstract: The subject matter of the present invention is a microfluidic process for treating and analysing a solution containing a biological material, comprising a step of introducing the solution into microchannels of a microfluidic circuit (1), a step of forming drops of this solution, under the effect of modifications of the surface tension of the solution, a step of moving the drops to one or more drop storage zones(s) (130), under the effect of modifications of the surface tension of the drops, a step of treating the drops and a step of analysing the drops.

Abstract: The present invention relates to the sample preparation of nucleic acids for diagnostic purposes. More precisely, the invention provides a process for simultaneously isolating at least a first and a second target nucleic acid from a plurality of different types of fluid samples and optionally amplifying said isolated nucleic acids in a simultaneous manner.

Abstract: A method for collecting microorganisms when contained in a fluid includes (i) introducing the fluid into a cavity of a collecting device via at least one admission duct, (ii) capturing the microorganisms when contained in the fluid with a set of beads retained in the cavity as the fluid passes through the set of beads, (iii) evacuating the fluid from the cavity via at least one evacuating duct, (iv) introducing a reaction liquid into the cavity via at least one admission channel, (v) collecting the microorganisms from the set of beads with the reaction liquid as the reaction liquid passes through the set of beads, and (vi) evacuating the reaction liquid from the cavity via at least one evacuating channel.

Abstract: Provided is a method for detecting CNV including: (A) providing at least three test samples; (B) purifying nucleic acid from each test sample; (C) dividing all the nucleic acid samples into groups; (D) conducting whole genome amplification for each nucleic acid sample in the nucleic acid sample groups; (E) labelling the amplified nucleic acid samples with two fluorescent dyes; (F) performing hybridization on a chip that contains a set of specific human genome probes; (G) analyzing the signal data sets via locally weighted scatterplot smoothing (Lowess); (H) calibrating the signal data in view of corresponding probe values in a probe values set for calibration; (I) analyzing the calibrated results to obtain the CNV result of the test sample of interest. The detection method saves the reference sample and is beneficial for high-throughput detection.

Abstract: Described herein, among other things, is a method of sequencing, comprising: concatenating a plurality of fragments of genomic DNA to produce concatenated DNA; sequencing the concatenated DNA to produce a plurality of sequence reads, wherein at least some of the sequence reads comprise: at least the sequence of the 3? and/or 5? ends of a fragment that corresponds to the locus of interest and sequence of one or both of the fragments that flank the fragment in the concatenated DNA; and grouping the sequence reads that corresponds to the locus of interest using, for each of the grouped sequence reads: the 3? and/or 5? end sequences; and/or the flanking sequence.

Abstract: Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

Abstract: The current teachings relate to methods for reducing adapter-dimer formation, particularly when preparing nucleic acids of interest for subsequent amplification and/or sequencing. Also described are kits for use in performing certain disclosed methods.

Abstract: Disclosed is a method of amplifying a nucleic acid sequence, wherein the method comprises subjecting a reaction mixture to at least one amplification cycle, wherein the reaction mixture comprises a double-stranded nucleic acid and at least two primers capable of annealing to complementary strands of the double-stranded nucleic acid and amplifying at least one short tandem repeat (STR) using a Family A DNA polymerase in a Fast PCR protocol having a two-step amplification cycle in 25 seconds or less. Also disclosed are real-time PCR methods using the two-step protocol and kits for STR profiling using the Fast PCR protocol.

Abstract: The present invention relates to the technical field of genetics and provides a method for detecting activity change of a transposon in a plant before and after stress treatment. The method includes the following steps: 1) respectively extracting total RNAs of samples before and after stress treatment; 2) respectively constructing cDNA libraries of the samples before and after stress treatment by using the total RNAs; 3) sequencing the cDNA libraries; 4) respectively screening siRNAs from raw sequencing data, and combining the screened siRNAs to obtain a total siRNA, and performing cluster clustering on the total siRNA; 5) extracting repeat in whole genome data by using repeatmasker software to obtain positional information of the plant whole genome transposon; and 6) obtaining activity change in the transposon of the plant before and after treatment by means of change in siRNA cluster expression quantity. The method fills the technical gap in the field of plant transposon activity detections.

Abstract: The disclosure relates to systems, software and methods for gerontological classification of subjects based on a detection of a plurality of epigenetic markers such as methylation status of nucleotides (e.g., CpG) in the genomic DNA.

Abstract: A polynucleotide sequencing method comprises (i) removing a label and a blocking moiety from a blocked, labeled nucleotide incorporated into a copy polynucleotide strand that is complementary to at least a portion of a template polynucleotide strand; and (ii) washing the removed label and blocking moiety away from the copy strand with a wash solution comprising a first buffer comprising a scavenger compound. Removing the label and blocking moieties may comprise chemically removing the moieties. The first buffer may also comprise an antioxidant and may be used in a scanning buffer used during a nucleotide detection step.

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

Abstract: A system for nucleic acid sequencing includes a machine-readable memory and a processor configured to execute machine-readable instructions. The instructions, when executed by the processor, cause the system to expose template polynucleotide strands in a plurality of defined spaces of a sensor array to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtain, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.

Abstract: The present disclosure provides variant Pol6 polymerase polypeptides, compositions comprising the Pol6 variant polypeptides, and methods for using the variant Pol6 polypeptides for determining the sequencing of nucleic acids, for example, by nanopore sequencing. The variant Pol6 polymerases possess decreased rates of dissociation of template from the polymerase-template complex, which result in increased processivity relative to the parental Pol6 polypeptides from which they are derived.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Abstract: Methods and compositions for generating chimeric RNAs comprising RNAs which interact with one another in a cell are provided. In some embodiments, the chimeric RNAs can be used to identify at least 100, at least 500, at least 1000 or more than 1000 RNA-RNA interactions in the cell.

Abstract: An example of an array includes a support including a plurality of discrete wells, a gel material positioned in each of the discrete wells, a sequencing primer grafted to the gel material, and a non-sequencing entity grafted to the gel material. Each of the sequencing primer and the non-sequencing entity is in its as-grafted form.

Abstract: Polynucleotide sequencing methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected. The detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated. Thus, at the end of the detection step, all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.

Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.

Abstract: The present disclosure is concerned with compositions and methods for the paired-end sequencing of target nucleic acids, and more particularly to obtaining nucleotide sequence information from two separate regions of target nucleic acids using amplification sites having a single type of surface primer.

Abstract: Provided herein are compositions and methods for generating phase-shift barcode oligonucleotides for library construction for next-generation sequencing. In some cases, barcode oligonucleotides are attached to particles or beads. Also provided are methods and kits for using the phase-shift barcode oligonucleotides in sequencing assays.

Abstract: The present invention relates to a composition for DNA sequence analysis and a method for DNA sequence analysis, the method comprising treating a sample with the composition. The composition of the present invention can attain efficient optical identification at a single-DNA molecule level by linking both an A/T-specific DNA-binder agent and an A/T-non-specific complementary DNA-binder agent to DNA, and thus can be helpfully used in studying chromosomal organization of genomes, protein immunolocalization, and the like.

Abstract: The current disclosure provides a method that can specifically label and directly amplify 5hmC site on genomic DNA without pull-down or bisulfite treatment, which enables one to map the 5hmC site from a single DNA molecule. Aspects of the disclosure relate to a method for detecting 5-hydroxymethylcytosine (5hmC) nucleic acid bases in a nucleic acid molecule or a plurality of nucleic acid molecules, the method comprising: a. modifying the 5hmC nucleic acid base with a first functional group; b. covalently attaching a modified nucleic acid probe comprising a second functional group to the first functional group; wherein the nucleic acid probe and nucleic acid molecule are covalently linked through the first and second functional groups; c. annealing a primer to the nucleic acid probe; d. performing primer extension of the annealed primer to make a new strand; and e. detecting the new strand.

Abstract: The invention relates to methods of predicting resistance to Piscirickettsia salmonis infection in a salmonid, the method comprising determining in the salmonid the alleles present at one or more DNA polymorphism within a QTL, and predicting the ability of the salmonid to be resistant to Piscirickettsia salmonis infection based on the determination of the alleles, wherein the QTL is: (a) located in linkage group 21 (GenBank ID NC_034194.1) within the coho salmon genome, or in the chromosome of coho salmon that corresponds to that linkage group, when the salmonid is a coho salmon, or; (b) a QTL that is located in a linkage group that corresponds to linkage group 21 within the coho salmon genome, or in the chromosome of a salmonid that corresponds to that linkage group, when the salmonid is not a coho salmon. The invention further relates to probes and arrays useful in such method and related methods.

Abstract: Compositions, kits and methods for detecting a plurality of targets are provided herein. A probe-set composition is provided, including one or more first probes and one or more second probes. Each of the first probe includes a nucleic acid sequence complementary to a nucleic acid barcode of a corresponding target-specific binding partner, a first label, and a cleavage site for a first cleavage agent, wherein the first cleavage agent is capable of releasing the first label. Each of the second probes includes a nucleic acid sequence complementary to a nucleic acid barcode of a corresponding target-specific binding partner, a second label, a quench moiety that renders the second label undetectable, and a cleavage site for the first cleavage agent. The first cleavage agent is capable of releasing the quench moiety, whereby the second label is rendered detectable.

Abstract: The present invention relates to methods of predicting resistance to heart and skeletal muscle inflammation in salmonids, the method comprising determining the alleles present at a DNA polymorphism in the salmonid and predicting whether or not the salmonid is resistant to heart and skeletal muscle inflammation based on the determination of the alleles. The invention also relates to related methods of detecting, in a sample from a salmonid, the alleles present at a DNA polymorphism associated with resistance to heart and skeletal muscle inflammation, methods for obtaining an indication of risk of a salmonid developing heart and skeletal muscle inflammation, uses of such DNA polymorphisms, and methods of detecting, in a sample from a salmonid, one or more salmonid gene variants.

Abstract: The present disclosure relates to a computer-implemented method for processing data in one or more data processing devices to determine a likelihood score or the probability of immune-related adverse events associated with immunotherapy.

Abstract: The cMethDNA method of the present invention is a novel modification of the QM-MSP method (U.S. Pat. No. 8,062,849), specifically intended to quantitatively detect tumor DNA (or other circulating DNAs) in fluids such as serum or plasma at the lowest copy number yet reported. Unique compared to any other PCR-based assay, a small number of copies of a synthetic polynucleotide standard (STDgene) is added to an aliquot of patient serum. In a standard procedure, a cocktail of standards for a plurality of genes of interest (TARGETgene) is added to a sample of serum. Once total DNA is purified and processed, a PCR (multiplex step) is performed wherein the STDgene and the TARGETgene are co-amplified with the same external primer set. In the second nested PCR step, amplicons present in a dilution of the first PCR reaction are subjected to real time PCR, and quantified for each gene in one well by two-color real-time PCR.

Abstract: Systems and methods for detecting single nucleotide polymorphisms (SNPs) associated with keratoconus (KC) in a sample from a subject are described.

Abstract: Biomarkers and methods for identifying, verifying and confirming circulating serum-based microRNAs. The microRNAs (PARKmiRs) can be used to differentiate patient's suffering from Alzheimer's disease (AD) from non-AD patients.

Abstract: Methods for diagnosing the presence of Lupus, renal disease, and scleroderma in a subject are provided, such methods including the detection of levels of markers diagnostic of Lupus, renal disease, and scleroderma, including proteins, nucleic acids, and lipids. The invention also provides methods of treating Lupus, renal disease, and scleroderma by modulating the level or activity of the marker proteins, nucleic acids and lipids. Compositions in the form of kits and panels of reagents for detecting the markers of the invention are also provided.

Abstract: Provided is a method for predicting probability of ischemic stroke onset. A method for predicting a risk of ischemic stroke onset, the method comprising: a detection step of detecting presence or absence of a RNF213 p.R4810K gene variant in a sample derived from a test subject who does not develop ischemic stroke; and a determination step of determining whether a probability of ischemic stroke onset of the test subject is high or not, based on the presence or absence of the RNF213 p.R4810K gene variant in the detection step, and gender information of the test subject. A genetic marker for predicting a risk of ischemic stroke onset using gender information, comprising a RNF213 p.R4810K gene variant. A biomarker for predicting a risk of ischemic stroke onset using gender information, comprising a polypeptide encoded by a RNF213 p.R4810K gene variant.

Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

Abstract: Disclosed are methods of attenuating activity of the PME-1 gene. siRNAs or shRNAs are used to target against PME-1, thereby reducing the PME-1 mRNA. It is disclosed that the siRNAs or shRNAs targeted against PME-1 attenuate the epithelial to mesenchymal transition, thereby inhibit endometrial cancer development. A kit containing siRNA or shRNA reagents for attenuating the PME-1 gene expression is also disclosed.

Abstract: Spliceosome mutations are described herein, including mutations in the PHF5A and SF3B1 subunits. This application also describes detecting the presence and/or absence of mutations in the spliceosome, as well as methods of diagnosing responsiveness to splice modulator treatment, methods of treating neoplastic disorders, and methods of monitoring or altering the treatment based on mutation status.

Abstract: Molecular profiles of metastatic tumors can be more accurately determined using combination of DNA mutational profiles and RNA expression profiles of selected genes that show substantial changes upon anti-tumor treatment. Such combinatorial information can be used to determine differential pathway activity that may be related to the sensitivity or resistance to the anti-tumor treatment.

Abstract: The present invention easily identifies a genotype for gene mutations related to myeloproliferative neoplasms. The present invention comprises a mutant probe that specifically hybridizes with a gene mutation related to myeloproliferative neoplasms in JAK2, a mutant probe that specifically hybridizes with a gene mutation related to myeloproliferative neoplasms in CALR, and a mutant probe that specifically hybridizes with a gene mutation related to myeloproliferative neoplasms in MPL.

Abstract: The present invention provides diagnostic and therapeutic methods and compositions for cancer. The invention provides methods of determining whether an individual having a cancer is likely to respond to treatment comprising a pan-RAF dimer inhibitor and a MEK or PI3K inhibitor, methods of predicting responsiveness of an individual having a cancer to treatment comprising a pan-RAF dimer inhibitor and a MEK or PI3K inhibitor, methods of selecting a therapy for an individual having a cancer, and methods of treating an individual having cancer based on the presence of a biomarker of the invention (e.g., a KRAS activating mutation, e.g., a KRAS-G13D mutation, or an NRAS activating mutation).

Abstract: The invention provides methods for the use of gene expression measurements to classify or identify tumors in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

Abstract: The disclosure generally relates to methods for treating non-small cell lung cancer patients based on use of blood-based tumor mutation burden to predict overall survival in patients treated with durvalumab, tremelimumab, and/or a chemotherapy agent. The disclosure also relates to methods for treating non-small cell lung cancer patients based on identification of mutations in circulating tumor DNA associated with sensitivity or resistance to immunotherapy.

Abstract: The present invention provides methods for diagnosing whether a human subject has a prostate carcinoma, methods for differentiating a high grade prostate cancer from a low grade prostate cancer in a human subject having a prostate carcinoma, and kits for detecting prostate cancer cells in a sample from a human subject.

Abstract: It is intended to provide a kit or device for the detection of liver cancer and a method for detecting liver cancer. The present invention relates to a kit or device for the detection of liver cancer, comprising a nucleic acid capable of specifically binding to miRNA in a sample of a subject, and a method for detecting liver cancer, comprising measuring the miRNA in vitro.

Abstract: This invention relates to a kit or a device for the detection of stomach cancer and a method for detecting stomach cancer, and provides a kit or a device for the detection of stomach cancer, comprising a nucleic acid(s) capable of specifically binding to a miRNA(s) in a sample from a subject, and a method for detecting stomach cancer, comprising measuring the miRNA(s) in vitro.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: A method of distinguishing between urothelial carcinoma and squamous cell carcinoma of head and neck and lung primaries is presented. A 19-gene signature was developed which differentiates between metastatic urothelial carcinoma and squamous cell carcinoma in a metastatic site when the primary site is either known or unknown.

Abstract: The present invention relates to systems, devices and methods for diagnosing cancer. In various embodiments, the present invention provides a method for quantifying a 5?-htRNA; a method for quantifying a 3?-htRNA; a method for obtaining a DNA library of 5?-htRNAs and a DNA library of 5?-htRNAs obtained therefrom; and a method for obtaining a DNA library of 3?-htRNAs and a DNA library of 3?-htRNAs obtained therefrom. The invention also teaches a method for determining the presence or absence of a cancer cell in a biological sample; a method of diagnosing cancer in a subject; and a method of prognosing cancer in a subject.