Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.

Abstract: Various flowcell configurations and systems are provided as are methods of making and using same. The flowcells, systems, and methods of use can be useful in carrying out sequencing reactions and next generation sequencing methods.

Abstract: The present disclosure relates generally to compositions and methods for the reuse of arrays, including microarrays. Specifically, the present disclosure discloses polynucleotide targets comprising nucleotide analogs that are not present within the probe polynucleotides immobilized on the array. The nucleotide-analog containing targets can be chemically modified to reduce their thermal stability and thus easier to remove from the array. In preferred embodiments, the disclosure relates to DNA probes hybridized to single-stranded deoxyribouridine-containing targets, the targets subsequently being chemically modified using a uracil DNA glycosylase and/or nuclease. Accordingly, the disclosure allows for the glycosylase treated, deoxyuridine-containing targets to be removed from the array by exposure to less stringent denaturing conditions than otherwise would have been required.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis.

Abstract: The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes.

Abstract: The present teachings provide methods, compositions, and kits for detecting target analytes, including proteins. In some embodiments, cleavage reactions are performed in the context of proximity probe reactions that query target proteins, wherein the presence and/or quantity of cleavage products is indicative of the presence and/or quantity of a target protein. In some embodiments, the cleavage fragments are quantitated using a real time PCR assay comprising a stem-loop primer, wherein the stem-loop primer comprises a self-complementary hairpin structure and a free 3? end end complementary to the cleavage product. In some embodiments, polymerase extension approaches are employed in the context of proximity probe reactions.

Abstract: Methods for determining the methylation state of at least one target nucleotide that employ a reaction catalyzed by a structure-specific nuclease, typically coupled with a ligation reaction are disclosed. By detecting the cleaved flap, a ligation product, a ligation product surrogate, a hybridization complex, or combinations thereof, one can infer the degree to which the corresponding target nucleotide is methylated. Certain of the disclosed methods are particularly useful for evaluating bisulfite-treated target sequences and determining the degree of target nucleotide methylation. The disclosed methods are well suited for rapidly analyzing a large number of target sequences, typically in one or more multiplex reactions. Kits for performing coupled nuclease and ligase methylation detection assays are also disclosed.

Abstract: The present teachings provide novel methods, compositions, and kits for forming multi-labeled polynucleotides. In some embodiments of the present teachings, multiplexed amplification reactions are performed with a plurality of primer pairs, wherein one primer in a given primer pair comprises a distinct label. Additional labeling of the resulting amplicons can be accomplished by using at least one bridge oligonucleotide to ligate a labeled tag oligonucleotide to each labeled extension product, thereby forming a plurality of multi-labeled polynucleotides. Detection of labels such as florophores and mobility modifiers in the plurality of multi-labeled polynucleotides can identify a sample. Such sample identification can be performed using a mobility dependent analysis technique such as capillary electrophoresis, and can applicable in the field of forensics.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis.

Abstract: The present teachings pertain to methods, reaction mixtures, and kits for ligating polynucleotides. In some embodiments, a heat-activatable ligation agent, a phosphorylation agent, and a decontamination agent are included in the same ligation reaction mixture with at least one probe set, at least one linker set, and at least one target polynucleotide. A reaction at a first temperature results in hybridization of the probes to the target, phosphorylation of the probes, and decontamination of unwanted reaction components. A reaction at a second temperature results in the ligation of the probes together. In some embodiments, the present teachings are applied in highly multi-plexed ligation reactions in which a plurality of single nucleotide polymorphisms in a plurality of target polynucleotides are queried, and eventually detected using a mobility dependent analysis technique.

Abstract: Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.

Abstract: The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.

Abstract: Compositions comprising at least two polymerases, including a lesion repair polymerase, are provided. Methods for producing primer extension products using at least two polymerases, including a lesion repair polymerase, are also provided. Kits for producing primer extension products comprising at least two polymerases, including a lesion repair polymerase, are also provided.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or a process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, oxidation reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis. The method further comprises a mechanism for storing data, evaluating data, graphing data, and determining conformance to established criteria.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or a process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, oxidation reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis. The method further comprises a mechanism for storing data, evaluating data, graphing data, and determining conformance to established criteria.

Abstract: Methods and apparatus for evaluating the quality of a sample of a product, an ingredient, an environment or a process by measuring multiple parameters thereof, including light emitted from a reacting sample containing ATP, ADP, alkaline phosphatase or other parameters such as pH, temperature, conductivity, oxidation reduction potential, dissolved gases, specific ions, and microbiological count. The apparatus comprises an integrated sample testing device used to collect a sample, mix reagents, react the sample, and collect it in a measurement chamber. The apparatus also comprises an instrument having a photon detection assembly for use with the sample testing device. The instrument can also comprise one or more sensing probes and a communication port to facilitate data collection, transfer and analysis. The method further comprises a mechanism for storing data, evaluating data, graphing data, and determining conformance to established criteria.

Abstract: A deck post (or brace) having a non-circular cross-section is secured to a roof deck. A lead pipe jack (sleeve) is slid over the post. A waterproofing assembly having a collar and a skirt is provided; the collar has an opening with generally the same non-circular cross-section as that of the post. The collar opening is positioned on the deck post, and the unit is slid down the post until the collar is at the top of the sleeve, the skirt extending down over the sleeve. A clamp is then positioned and tightened around the collar to provide a watertight seal on the deck post. When the post is already installed on a roof deck and the sleeve and the waterproofing assembly cannot be slid into place on the post, a modified retrofit waterproofing assembly and sleeve are used to provide the waterproofing. The modified sleeve is a split lead flashing jack with an open seam on one side. The sleeve is opened up, wrapped around the post and soldered closed.