Abstract: The invention provides a method for in-field detection of a distinctive marker. The method includes providing a sample from an article of interest and analyzing the sample to detect the presence of the distinctive marker. The analysis is performed using an in-field detection instrument. The in-field detection instrument includes a microsystem configured to perform sample in-answer out analysis and detect the presence of the distinctive marker in the sample.

Abstract: This invention provides methods of using circulating diseased cells in the diagnosis, prognosis, or monitoring of diseases or conditions. The invention also provides methods of using circulating diseased cells to identify markers of diseases or conditions. This invention also provides methods for assessing the risk of developing a disease or condition, prognosing said disease, monitoring said disease progression or regression, assessing the efficacy of a treatment, or identifying a compound capable of ameliorating or treating said disease or condition.

Abstract: The invention relates to methods and compositions that enable the rapid generation of high-order combinations of genetic elements, and that provide a barcoded basis for rapid characterization of the specific combination of genetic elements encoded within a single cell or in a pooled population.

Abstract: This invention relates generally to composition and methods for characterizing a methylome which comprises all or substantially all methylation states of a genome. In particular, a plurality of oligonucleotides, each representing nearly every possible methylation state of the cytosine position of each CG dinucleotide pair within a target nucleic acid of interest, and methods of using the plurality are provided herein.

Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well.

Abstract: Provided is a method for monitoring a gene mutation associated with a cancer in a patient over time. Also provided is a method of selecting and/or applying treatment or therapy for a subject.

Abstract: The present invention relates to compositions and methods useful for analyzing lariat RNA, which plays a role in the regulation of gene expression. A sample of RNA is specifically treated to remove linear mRNA and enrich for lariat RNA. The enriched lariat RNA sample may be analyzed further to identify introns, branch point sequences, alternative splicing patters, and gene transcription levels. The enriched lariat RNA sample may also be exploited as a detection or compound screening tool, as well as other uses.

Abstract: The present invention is a novel protocol for the massively parallel production of improved MIPs. The molecular improvements to the MIP cover the manufacturing of the probes, the workflow, the addition of unique sequence elements which connote sample specificity, and a sequence tag which uniquely identifies a specific molecule present in the initial sample population. Lastly, this invention also is combined with an empirical optimization strategy that overcomes issues of both locus representation and allelic bias. This improved technique is scalable and can be utilized to amplify targets comprised of a single locus' amplicon up to targeting more than 1 million loci.

Abstract: Different combinations of methylation status based biomarkers can be used to test for breast cancer with high sensitivity and high specificity.

Abstract: The present disclosure describes methods, devices, reagents, and kits for the detection of one or more target molecules that may be present in a test sample. The described methods, devices, kits, and reagents facilitate the detection and quantification of a non-nucleic acid target (e.g., a protein target) in a test sample by detecting and quantifying a nucleic acid (i.e., an aptamer) where the aptamer-aptamer interactions are significantly reduced or eliminated while maintaining the aptamer-target interaction.

Abstract: The invention relates to a method for enriching one or more target sequences of a deoxyribonucleic acid (DNA) in a composition, comprising the steps of providing a composition comprising one or more deoxyribonucleic acid (DNA) molecules, hybridizing to said one or more DNA molecules, one or more target specific ribonucleic acid (RNA) hybridization probes, thereby forming one or more RNA/DNA hybrids, capturing the RNA/DNA hybrids with one or more antibodies being specific for such RNA/DNA hybrids, thereby forming one or more RNA/DNA/antibody hybrids, isolating the one or more RNA/DNA/antibody hybrids, amplifying the one or more DNA molecules of the one or more RNA/DNA/antibody hybrids if necessary, and, optionally, sequencing the one or more DNA molecules of the one or more RNA/DNA/antibody hybrids or the amplification product, wherein the sequencing is preferably done by means of next generation sequencing.

Abstract: The present disclosure relates to methods of determining a treatment course of action. In particular, the present disclosure relates to mutations in the gene encoding estrogen receptor and their association with responsiveness to estrogen therapies for cancer.

Abstract: An active-source-pixel, integrated device capable of performing biomolecule detection and/or analysis, such as single-molecule nucleic acid sequencing, is described. An active pixel of the integrated device includes a sample well into which a sample to be analyzed may diffuse, an excitation source for providing excitation energy to the sample well, and a sensor configured to detect emission from the sample. The sensor may comprise two or more segments that produce a set of signals that are analyzed to differentiate between and identify tags that are attached to, or associated with, the sample. Tag differentiation may be spectral and/or temporal based. Identification of the tags may be used to detect, analyze, and/or sequence the biomolecule.

Abstract: Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided. For example, methods are presented for providing a surface comprising the plurality of array regions by exposing the surface to a solution comprising polymerase enzymes where each polymerase enzyme is bound to a binding structure having several functional moieties. The functional moieties of the binding structure react with the binding elements on the array regions such that the functional moieties on the binding structure react with other available binding sites in an array region, preventing other polymerase-binding structures from loading, and resulting in a single polymerase molecule bound to each of these regions.

Abstract: Provided is methods of detecting a mutation in a histiocytosis patient. Also provided is methods of selecting and/or applying treatment or therapy for a histiocytosis patient. Further provided is a method of treating a patient having a histiocytosis.

Abstract: The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same.

Abstract: The present invention provides a diagnostic agent for endometriosis for measuring the concentration of at least one miRNA selected from the group consisting of hsa-miR-708, hsa-miR-127-3p and hsa-miR-518d-3p in a sample derived from the blood of a subject, the agent containing an amplification primer for the miRNA as a main component. The present invention also provides a method of detecting endometriosis, including a step of measuring the concentration of at least one miRNA selected, from the group consisting of hsa-miR-708, hsa-miR-127-3p and hsa-miR-518d-3p in a sample derived from the blood of the subject. The diagnostic agent for endometriosis of the present invention and the diagnostic method using the agent are simple and low invasive and have high sensitivity and specificity.

Abstract: The present invention relates to systems and methods for performing isothermal amplification reactions. In particular, the present invention relates to denaturation methods for use in isothermal amplification reactions.

Abstract: The present invention provides methods to produce a reduced representation of a genome for sequencing and DNA polymorphism detection. In particular, the invention provides PCR-based methods, with normalization of the amplified products using a duplex-specific nuclease, in order to reduce over-representation of PCR products. Oligonucleotides for use in the disclosed method are also provided.

Abstract: The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom.

Abstract: The present invention relates to a cell based genomic Recorded Accumulative Memory (geRAM) system (also referred to herein as Genomically Encoded Memory (GEM)) for recoding data (i.e., changes in nucleic acid sequences in cellular DNA in response to physical and/or chemical signal(s)) from the cellular environment.

Abstract: The present invention relates to a method for identifying the variety of a hop by using an identification marker comprising at least one single nucleotide polymorphism that differs among varieties, and a method for preparing said identification marker. The present invention also provides a primer or a probe to be used in the method for identifying the variety of a hop, and a nucleic acid of a region including said identification marker. The present invention further provides a method for detecting the intrusion of different varieties in a hop sample.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with a therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: The present invention relates to mutations associated with neoplasia, such as meningioma. Thus, the invention relates to compositions and methods useful for the assessment, characterization, classification and treatment of neoplasia, including meningioma, based upon the presence or absence of mutations that are associated with neoplasia, including meningioma.

Abstract: The present disclosure relates to compositions and methods for detecting rare nucleic acid molecule mutations in a plurality of nucleic acid molecules. Also disclosed are methods for determining the size of a nucleic acid molecule using droplet digital PCR.

Abstract: Nucleic acids and proteins having a mutant C-RAF sequence, and methods of identifying patients having cancer who are likely to benefit from a combination therapy and methods of treatment are provided.

Abstract: The present disclosure provides methods for detecting mutations in a target nucleic acid molecule by rolling circle amplification of a library of double-stranded circular bar-coded template molecules. Also provided herein are methods for enriching a target nucleic acid molecule.

Abstract: The present invention relates generally to the fields of molecular biology and growth factor regulation. More specifically, the invention relates to therapies for the treatment of pathological conditions, such as cancer.

Abstract: Methods of selection of nucleic acids using solution hybridization, methods of sequencing nucleic acids including such selection methods, and products for use in the methods are disclosed.

Abstract: Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in the concentration of inorganic pyrophosphate (PPi), hydrogen ions, and nucleotide triphosphates.

Abstract: The present invention relates to a method and kit for the classification and prognosis of wounds of mammalian, in particular in human. The method defines a molecular signature that enables one to characterize a pathological wound healing such as chronic or non-healing wound.

Abstract: The present invention is directed to a method of detecting a genomic rearrangement in a nucleic acid sample with Long Insert Whole Genome Sequencing (LI-WGS). The method may include obtaining a nucleic acid sample and then fragmenting the nucleic acid sample (e.g., via sonication). In particular, the fragmenting may result in the production of a plurality of inserts. Thereafter, the method comprises purifying the plurality of inserts using magnetic beads and then amplifying the purified plurality of inserts. In addition, the method further comprises sequencing the purified and amplified plurality of inserts. In some aspects, the plurality of inserts have a length of between about 800 and about 1,100 base pairs.

Abstract: An assembly and a method are disclosed for analyzing nucleic acid sequences by way of so-called sequencing-by-synthesis. According to an embodiment of the invention, a chemical substance group that is released when a nucleotide bonds to a nucleic acid sequence to be sequenced is detected. The reagents are applied by way of a spraying device to a sensor that detects the released substance group. This has the advantage that no lateral flow occurs. The rate of false-negative and false-positive results is significantly reduced. Furthermore, a small amount of the reagent is sufficient to completely wet the sensor. Filling of the supply and discharge lines as for a flow cell is not necessary.

Abstract: The present invention provides a method for detecting transplantation failure of a transplanted organ or cells which comprises detecting a donor-positive but recipient-negative DNA marker in the recipient's plasma using pyrophosphorolysis activated polymerization. Because of the high sensitivity, specificity and selectivity of pyrophosphorolysis activated polymerization, transplantation failure can be detected at early stages and treatment can be initiate earlier.

Abstract: Methods and kits for diagnosing or predicting head and neck squamous cell carcinoma (HNSCC) and for predicting responsivity to therapeutic regimens for treating HNSCC are disclosed.

Abstract: Disclosed herein are markers whose mutational status is associated with sensitivity to treatment with NAE inhibitors. Mutational status is determined by measurement of characteristics of markers associated with the marker genes. Compositions and methods are provided to assess markers of marker genes to predict response to NAE inhibition treatment.

Abstract: The current disclosure describes materials and methods for identifying subjects that would benefit from treatment with a DNA topoisomerase 1 inhibitor, based on the levels of cullin 4B gene, RNA and protein levels in the subject. The disclosure identifies CUL4B as a predictive biomarker for cancer diagnosis and the subsequent treatment with directed therapeutic agents. The current disclosure also identifies novel therapeutic agents that modulate the level of CUL4B expression, and sensitize a subject to treatment with a second therapeutic agent.

Abstract: Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes: combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe comprises an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; removing non-target sequences from the 3? end of the target sequence by means of one or more 3? exonucleases thereby generating a blunt ended duplex or a staggered end at the 3? end of the target sequence; optionally ligating a 3? duplex adaptor or a duplex end of a hairpin adaptor to the 3? end of the target sequence and the 5? end of the target isolation probe; extending the 3? end o

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: The present invention relates to small RNAs, inhibitors thereof, inhibitors of enzymes producing thereof, and their use to modulate the response of a cell to a DNA damaging event. The invention concerns also a method to detect the presence or quantify DNA damage.

Abstract: The present invention provides a chimera nucleic acid obtained from circulatory system for monitoring tumor status. The nucleic acid comprises partial sequence derived from host genome and partial sequence derived from non-host genome. The partial sequence derived from host genome and the partial sequence derived from non-host genome form a chimera junction. The chimera junction is obtained from cell-free nucleic acids and is indicative of disease status.

Abstract: This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule.

Abstract: An object of the present invention is to develop and provide a method for efficiently producing a nucleic acid aptamer, particularly, a DNA aptamer, having higher specificity and binding activity against a target substance than those of nucleic acid aptamers obtained by conventional methods. The present invention provides a transcribable or replicable nucleic acid aptamer comprising a natural nucleotide and a non-natural nucleotide having an artificial base-pairable artificial base. The present invention also provides a method for sequencing a non-natural nucleotide-containing single-stranded nucleic acid molecule selected from a single-stranded nucleic acid library.

Abstract: The present invention relates to diagnostic and prognostic methods and kits for determining genetic predisposition for at least one AChE-associated disorder, as well for diagnosing, prognosing and monitoring said disorders. The methods of the invention are based on detection of specific SNPs that modulate the interaction of different miRNAs to AChE 3?-UTR.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: A method and a composition for improving gut micro biota structure, selectively increase a first gut microbiota population while simultaneously decrease a second gut micro biota population in a subject. The first gut micro biota population includes a short-chain fatty acid (SCFA)-producing bacterium and the second gut microbiota population includes an endotoxin-producing bacterium.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: Provided herein are methods for accurately determining the alleles present at a locus that is broadly applicable to any locus, including highly polymorphic loci such as HLA loci, BGA loci and HV loci. Embodiments of the disclosed methods are useful in a wide range of applications, including, for example, organ transplantation, personalized medicine, diagnostics, forensics and anthropology.

Abstract: Provided herein are compositions and methods for the detection of Streptococcus agalacticae.