Abstract: The present invention relates, inter alia, to methods for determining whether or not an animal and/or its offspring is more likely than not to have an increased tolerance to heat, an increased resistance to ticks, and/or a desirable coat texture. It also provides methods for selecting or rejecting animals, one or more cells or embryos, estimating the worth of an animal, generating animals having a desired genotype/phenotype, cloning and breeding animals and herd formation.

Abstract: High-throughput long read sequencing is used to perform immunogenomic characterization of expressed antibody repertoires in the context of vaccination. Informatic analysis allows global characterizations of isotype distributions, determination of the lineage structure of the repertoire and measure age and antigen related mutational activity. Global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.

Abstract: Provided herein are methods, compositions, and kits for assays, many of which involve amplification reactions such as digital PCR or droplet digital PCR. The assays may be used for such applications as sequencing, copy number variation analysis, and others. In some cases, the assays involve subdividing a sample into multiple partitions (e.g., droplets) and merging the partitions with other partitions that comprise adaptors with barcodes.

Abstract: Provided are methods and kits for classifying a subject as being more likely to have benign multiple sclerosis (BMS) or as being more likely to have typical relapsing remitting multiple sclerosis (RRMS). Classification of multiple sclerosis disease course is performed by comparing a level of expression of at least one gene involved in the RNA polymerase I pathway in a cell of the subject to a reference expression data of said at least one gene obtained from a cell of at least one subject pre-diagnosed as having BMS and/or from a cell of at least one subject pre-diagnosed as having typical RRMS, thereby classifying the subject as being more likely to have BMS or as being more likely to have typical RRMS. Also provided are methods of diagnosing and treating multiple sclerosis and methods of monitoring treatment efficiency.

Abstract: The present invention relates generally to compositions, methods and kits for detection of a molecule of interest. The present invention is based, at least in part, on the design of nucleic acid oligonucleotides such that they can be used as molecular building blocks which can be assembled (polymerized) to form a dsDNA polymerization product which can be detected and further, can be disassembled (depolymerized) such that the polymerization product is no longer detectable. The invention can be performed multiple times on the same cell population, and is therefore useful for highly sensitive in situ detection of multiple biomarkers.

Abstract: Compositions and methods for nucleic acid isolation from an environmental or biological sample comprising nucleic acid-analysis interferents, particularly from microbiome-containing samples, are provided.

Abstract: The present invention relates to self-contained integrated systems and methods for constructing nucleic acid profiles of human individuals and for identification of the human individuals.

Abstract: The disclosure provides method and kits for characterizing spliced m RNA isoforms. The disclosure also provides methods of screening for mutations and oligonucleotides that modulate splicing.

Abstract: Systems and methods for mitigating prostate cancer development are provided. Peripheral blood cells may be evaluated for the presence or quantity of gamma-H2AX foci, and/or for gene alterations encoding a protein with impaired or lack of function, for example, because the encoded protein is truncated, and correlating with prostate cancer development. Such nucleic acids may encode proteins from or peripheral to the DNA damage repair pathway and/or androgen receptor signaling pathway, or that are otherwise correlated with prostate cancer development. Such genes include one or more of AKR1C1, PALB2, APTX, BLM, BRCA1, CTBP1, DDB2, FANCA, FANCL, MBD5, MSH3, NEIL3, RAD51D, RAD54L2, SP1, TP53BP1, UBE2D3, UBE2V2, NRIP1, EFCAB6, CRISP3, PAPSS2, ATP6V0A2, ALG13, MGAT2, B3GAT3, DOLK, FLT3, ASXL1, KDR, or NOTCH2.

Abstract: The invention provides for methods for predicting age of a subject based on the epigenome of the subject.

Abstract: Novel time and temperature integrator (TTI) assays, kits containing the components of the assays, and the novel components for those assays are provided herein. These novel TTI assays evaluate and/or determine the inactivation of biological material in/on a sample by quantifying the degradation of DNA using qPCR. The sample can be a food product (e.g., fruits, vegetables, meat from animals, or eggs) while the item can be any object (e.g., medical equipment, especially reusable medical equipment) for which one needs to determine that the amount of inactivation of specific hazardous biological material on the object or in a sample is at or below a pre-determined amount.

Abstract: The present disclosure is directed to methods and kits for identifying, enriching, and evaluating templated assembly reactants. Some embodiments disclose methods for identifying templated assembly targets by synthesizing templated assembly reactants, hybridizing the templated assembly reactants to target nucleic acids, performing a templated assembly reaction, and identifying the target nucleic acids that hybridized to the templated assembly reactants. Libraries of templated assembly reactants, a kit for identifying templated assembly targets, and a pair of templated assembly targets enriched from a library of chemically-ligated oligonucleotides spatially elicited (CLOSE) products are also disclosed.

Abstract: Provided herein, in some embodiments, are methods and compositions for protein identification.

Abstract: The methods and apparatus of the present invention allow the evaluation of inflammation of the esophagus. Measurements may be utilized, for example, to diagnose a disease of the esophagus, to monitor inflammation of the esophagus, or to access the treatment of a disease of the esophagus. In one embodiment, the invention comprises a method for measuring esophageal inflammation comprising deploying a device into the esophagus of a subject, removing the device after a predetermined period of time, analyzing the device for a diagnostic indicator of esophageal inflammation and evaluating the diagnostic indicator to diagnose esophageal inflammation.

Abstract: The invention relates to a method for confirming an amplified nucleic acid target sequence (target sequence), preferably from human samples, during a multiplication reaction in a collective and continuous reaction batch as a one-pot process, wherein the confirmation of the target sequence amplification product is obtained by means of a hapten-pair-marked artificial template amplification product. The artificial template sequence is amplified and optionally marked by means of the 5?-cleavage products of the at least one target-sequence-specific FEN probe. The 5?-cleavage product of the at least one target-sequence-specific FEN probe is obtained only if the FEN probe hybridizes, by means of the target-sequence-specific 3? sequence thereof, to a complementary sequence segment of the at least one target sequence. The detection of the obtained plurality of template amplification products occurs distinctly and preferably by means of immunochromatographic methods.

Abstract: The present invention relates to a composition for detecting microbial contamination comprising a preparation for detecting nucleases, and a use thereof. A probe for measuring nucleic acid double-stranded nucleases, according to the present invention, may detect the comprehensive nucleic acid degradation capability of nucleases, whereby it is possible to quickly and precisely detect and quantify live microorganisms in a sample in a simple manner. Moreover, since the probe of the present invention is characterized in that signals of fluorescence consistently increase; is capable of measuring live microorganisms; and consists of a double-stranded nucleic acid, the probe is excellent for storage in a kit or a cartridge. As such, it is expected that the probe of the present invention may be used to easily and simply measure and compare the degree of contamination of microorganisms in an environment.

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: 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: Biomarkers and methods of using them for aiding diagnosis, prognosis, and treatment of critically ill patients are disclosed. In particular, the invention relates to the use of biomarkers for prognosis of mortality in critically ill patients with sepsis, severe trauma, or burns.

Abstract: Disclosed is a high-throughput sequencing method for methylated CpG island in trace DNA, comprising the steps of: 1) treating a DNA sample with bisulfite; 2) adding the treated sample obtained in step 1) to a PCR system containing a primer A for linear amplification; 3) adding an exonuclease having single-stranded DNA cleaving activity to the PCR product in step 2) and inactivating the exonuclease after the reaction; 4) adding the product in step 3) to a PCR system containing a primer B for linear amplification; 5) adding the product in step 4) to a PCR system containing the corresponding adapter primer C and adapter primer D for amplification; and 6) purifying the PCR product in step 5) to obtain a DNA library with a specific length and carrying out the sequencing.