Abstract: Methods and kits are provided for screening a patient for bladder cancer. Embodiments include those involving centromeric probes to chromosomes 3, 7, and 10 and a locus-specific probe to 5p15.

Abstract: Disclosed herein are methods and kits for identifying a subject as having breast cancer. Also provided herein are methods and kits for determining the prognosis of a subject having breast cancer and for determining the progression of breast cancer in a subject.

Abstract: This invention intends to develop many DNA markers for a plant of the genus Fragaria and detect powdery mildew resistance with high precision by using the many DNA markers. The marker associated with powdery mildew resistance in a plant of the genus Fragaria comprises a continuous nucleic acid region sandwiched between the nucleotide sequence as shown in SEQ ID NO: 1 and the nucleotide sequence as shown in SEQ ID NO: 19 in the chromosome of the plant of the genus Fragaria.

Abstract: Provided herein is technology relating compositions and methods for analysis of methylated DNA from a subject. The technology also relates to use of endogenous methylated DNAs as internal controls for marker gene methylation assays.

Abstract: The invention pertains to analyzing the levels of DNA methylation at specific genetic loci to detect specific body fluids, for example, vaginal secretions or vaginal epithelial cells, semen or sperms, saliva or buccal epithelial cells, or blood or blood cells. Particularly, the levels of methylation of DNA at the genetic loci corresponding to SEQ ID NOs: 1, 6, 11, and 16, more particularly, SEQ ID NOs: 25, 26, 27, and 28, are used to detect vaginal secretions or vaginal epithelial cells, semen or sperms, saliva or buccal epithelial cells, and blood or blood cells, respectively. The level of methylation at the specific loci can be determined by sequencing of the amplicons produced using specific primers designed to amplify the specific loci. Kits containing the primers and reagents for carrying out the methods disclosed herein are also provided.

Abstract: The invention provides methods and compositions for the detection of Chlamydia trachomatis in a test sample. Its presence or absence in the sample is determined by nucleic acid based testing methods using primers and/or probes and or molecular beacons that bind to the 23S ribosomal genes or gene transcripts.

Abstract: A probe combination for detecting cancer includes one or more sets of partial hepatitis B virus (HBV) targeting probes. When sequences of each of the sets of partial HBV targeting probes are aligned, an overall sequence of the aligned set of probes matches a reference sequence of a genome of a HBV genotype or a direct repeat (DR) region on the genome. In the aligned set of probes, each of the probes overlap with one or two adjacent probes by a portion of a length of the probe. The probe combination may further includes one or more sets of hotspot gene targeting probes targeting cancer hotspot genes such as CTNNB1, TERT, and TP53 genes, one or more sets of exogenous gene targeting probes targeting portions of a lambda phage genome, and endogenous gene targeting probes targeting endogenous genes such as GAPDH and GdX genes.

Abstract: The present invention relates to a method for predicting the degree of weight loss attainable by applying one or more dietary interventions to a subject and/or the degree of maintenance of weight loss following one or more dietary interventions; which method comprises determining the level of microRNA-486 (miR-486) in one or more samples obtained from the subject; and/or determining the nucleotide of the subject at one or more polymorphic positions genetically linked to miR-486.

Abstract: The present invention relates to methods for detecting a genetic deletion at the SHOX locus of a horse, where the presence of such a genetic deletion indicates that the horse is a carrier of disease-causing mutation that can lead to skeletal atavism. The invention further provides nucleic acid primers and probes for use in methods for detecting the presence or absence of disease-causing genetic deletion at the SHOX locus of a horse.

Abstract: Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Abstract: Disclosed herein are methods for determining inflammation in subjects. Also disclosed are methods for determining whether a subject has sepsis. The methods include determining methylation of preproinsulin DNA and chromatin target of PRMT1 (CHTOP).

Abstract: The invention provides PRKC gene fusions, PRKC fusion proteins, and fragments of those genes and polypeptides. The invention further provides methods of diagnosing and treating diseases or disorders associated with PRKC fusions, such as conditions mediated by aberrant PRKC expression or activity, or overexpression of PRKC.

Abstract: The present invention relates to a composition for detecting an epidermal cell growth factor receptor gene mutation and to a kit comprising the composition and, more specifically, to a primer and probe set composition for detecting an epidermal cell growth factor gene mutation, and to a kit for detecting an EGFR gene mutation, comprising the composition. A method according to the present invention can not only predict and diagnose responsiveness to a therapeutic agent for the prognosis of a cancer patient, but also predict a cancer metastasis or relapse Thus, the method can be useful for the purposes of determining the need to administer an anticancer therapeutic agent and guiding the direction of future treatment, and for monitoring a cancer metastasis or relapse.

Abstract: The present invention relates to the identification of a novel allele of the RHD gene associated with a weak D phenotype and the kits and methods for detecting this allele.

Abstract: Efficient harvesting of cells, cell fragments, free nuclei, and DNA material from female reproductive system is made possible by processing gelatinous part of cervical mucus. Rinsing may be used to separate the gelatinous part of cervical mucus from the remainder of the cervical mucus sample.

Abstract: Described herein various PCR based assays that can detect H. penaei and/or V. parahaemolyticus that causes AHPND in a nucleic acid sample obtained from one or more shrimp. In some aspects, the PCR based assays can detect one or more of the following genes: the flgE gene from H. penaei, the shrimp 18s rRNA gene, the shrimp beta actin gene from shrimp, a bacterial 16S rRNA gene from bacteria (any type of bacteria) the Vibrio pirA gene, and the Vibrio pirB gene. The assays described herein can be single assays or can be multiplexed such that more than one gene and/or more than one bacterial species can be detected in a single reaction. Other compositions, compounds, methods, features, and advantages of the present disclosure will be or become apparent to one having ordinary skill in the art upon examination of the following drawings, detailed description, and examples.

Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.

Abstract: A method of detecting death of a cell type or tissue in a subject is disclosed. The method comprises determining whether cell-free DNA comprised in a fluid sample of the subject is derived from the cell type or tissue, wherein the determining is effected by ascertaining the methylation status of at least four methylation sites on a continuous sequence of the cell-free DNA, the sequence comprising no more than 300 nucleotides, wherein a methylation status of each of the at least four methylation sites on the continuous sequence of the DNA characteristic of the cell type or tissue is indicative of death of the cell type or tissue. Kits for detecting cell death are also disclosed.

Abstract: A method for detecting a bacterium of the genus Novosphingobium, includes a first step of amplifying nucleotides using a test DNA as a template and primers capable of amplifying a nucleotide sequence of consecutive 94 or more nucleotides and 136 or less nucleotides in the nucleotide sequence of SEQ ID NO: 1 to obtain an amplified product; and a second step of detecting the amplified product.

Abstract: A method for analyzing cell free DNA (cfDNA) from the bloodstream of a cancer patient is provided. In some embodiments, the method may comprise sequencing at least part of the coding sequences of TP53 and KRAS in a sample of the cfDNA, analyzing the sequences to identify nucleotide transversions in the coding sequences of the genes, relative to reference sequences of the genes. In some embodiments, the method may comprise counting the total number of identified nucleotide transversions. The presence of nucleotide transversions indicates that the patient will be more responsive to the immune checkpoint inhibitor, whereas a decreased number of transversions or no transversios indicates that the patient will be less responsive to the immune checkpoint inhibitor.