Abstract: This invention concerns the discovery of two distinct PCA3 mRNA sequences. One of these sequences corresponds to a short PCA3 mRNA molecule whereas the other PCA3 RNA molecule is longer as it comprises an additional sequence between exon 3 and exon 4a. The short RNA is associated with prostate cancer whereas the long RNA sequence is associated with a non-malignant state of the prostate. Based on the differential expression levels of these two PCA3 RNA sequences, protocols for the diagnosis of prostate disease are provided. The invention also relates to therapeutic approaches to prostate cancer.

Abstract: The present invention relates to HGyV, a human gyrovirus related to the chicken anemia virus (CAV). The present invention also relates to a new proteins encoded by HGyV, which proteins display some homology to CAV proteins. Among these new proteins, H-apoptin is of particular interest as it is herein found for the first time in a human virus and can be used for treating cancer. Also provided are methods for detecting the HGyV virus in a subject.

Abstract: A method for detecting the presence in a subject of a polymorphism linked to a gene associated with familial dysautonomia, said method comprising detecting a disruptive mutation in a gene of said subject encoding the I?B kinase-complex-associated protein, and, preferably, detecting a T?C change in position 6 of the donor splice site of intron 20 and/or a G?C transversion of nucleotide 2390 in exon 19 of the gene encoding the I?B kinase-complex-associated protein which is present on chromosome 9q31. Also disclosed are oligonucleotide primers useful in the detection method. This abstract is provided to comply with the rules requiring an abstract that will allow a searcher or other reader to ascertain quickly the subject matter of the technical disclosure. It is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the claims. 37 CFR §1.72(b).

Abstract: The present invention relates to a method for selecting a gene intended to predict the prognosis for a cancer, to the selected gene for predicting the prognosis of cancer and to a kit for predicting and a method for predicting metastasis in breast-cancer patients by using the same. In the present invention, a straight forward method is used to achieve high-reliability prediction of the patient's prognosis by analysing for the genetic characteristics of early stage breast cancer, and thus the present invention can be used to advantage in prognosis diagnosis which can reduce unnecessary anticancer therapy.

Abstract: Provided herein are sequences of the genomes and encoded proteins of new astrovirus species, and variants thereof. Also provided are methods of detecting the new astrovirus species and diagnosing astrovirus infection, methods of treating or preventing astrovirus infection, and methods for identifying anti-astrovirus compounds. Provided are two new astrovirus species named HMOAstV-A and HMOAstV-B, and both are distantly related to known astroviruses. Also provided is a new method of classifying astroviruses, where there are three groups of human astroviruses, including HAstV, AstV-MLB, and HMOAstV.

Abstract: The invention is directed towards methods and compositions for identifying the specific microorganisms present in a particular potion of a papermaking processes. The method involves obtaining a sample from the process which is such that little or no live examples of the microorganism remain. However because DNA from the organisms is still present, an analysis which identifies portions of DNA specific to the particular organism will correctly identify the microorganism present. This allows for analysis of infestations present on felts or paper sheets which typically no longer have many live microorganisms on them when samples are taken for analysis.

Abstract: The present invention discloses a series of genes and/or proteins associated with cutaneous squamous cell carcinoma (cSCC) and provides polynucleotides and/or polypeptides for use in the treatment and/or prevention of cSCC. The invention further relates to methods of diagnosing cSCC and provides oligonucleotides/polypeptide probes and primers.

Abstract: Provided are compositions comprising polyphosphate accumulating bacteria as well as a method for identifying said polyphosphate accumulating bacteria. Additionally provided is a method for treating various substances with said compositions.

Abstract: The subject invention pertains to an assay and a method for diagnosing, identifying and/or differentiating microorganisms, and in particular bacteria such as Mycobacterium spp. within biological samples. The present invention also relates to assays, gene arrays, probes and primers, nucleic acids and methods for detecting microorganisms in a sample.

Abstract: The invention provides corn event MON 87411, and plants, plant cells, seeds, plant parts, and commodity products comprising event MON 87411. The invention also provides polynucleotides specific for event MON 87411 and plants, plant cells, seeds, plant parts, and commodity products comprising polynucleotides specific for event MON 87411. The invention also provides methods related to event MON 87411.

Abstract: The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.

Abstract: Compositions are disclosed as nucleic acid sequences that may be used as amplification oligomers, including primers, capture probes for sample preparation, and detection probes specific for Legionella pneumophila 16S or 23S rRNA sequences or DNA encoding 16S or 23S rRNA. Methods are disclosed for detecting the presence of L. pneumophila in samples by using the disclosed compositions in methods that include in vitro nucleic acid amplification of a 16S rRNA sequence or DNA encoding the 16S rRNA sequence, or of a 23S rRNA sequence or DNA encoding the 23S rRNA sequence to produce a detectable amplification product.

Abstract: The present disclosure relates to methods for the diagnosis and evaluation of neoplastic disorders, particularly non-small cell lung cancer. Assays are described in which patient test samples are analyzed for the presence of one or more specific EML4-ALK fusion genes associated with neoplastic disorders.

Abstract: The invention relates to the treatment and the diagnosis of a group of patients bearing specific alleles of single nucleotide polymorphisms in the promoter region of the VEGFA gene. These patients are more responsive to Aflibercept and more likely to be efficiently treated by anti-VEGF therapy.

Abstract: Methods for detecting Legionella (such as Legionella spp., Legionella pneumophila, Legionella pneumophila serogroup 1, Legionella bozemanii, Legionella dumoffii, Legionella feeleii, Legionella longbeachae, and/or Legionella micdadei) are disclosed. A sample suspected of containing one or more Legionella nucleic acids is screened for the presence or absence of that nucleic acid. Determining whether Legionella nucleic acid is present in the sample can be accomplished by detecting hybridization between a Legionella probe and a nucleic acid in a sample. Also disclosed are probes and primers for the detection of Legionella, and kits that contain the disclosed probes and/or primers.

Abstract: Parkinson's disease is caused by the preferential loss of substantia nigra dopamine neurons. A Parkin Interacting Substrate, PARIS (ZNF746) is identified. The levels of PARIS are regulated by the ubiquitin proteasome system via binding to and ubiquitination by the E3 ubiquitin ligase, parkin. PARIS is a KRAB and zinc finger protein that accumulates in models of parkin inactivation and in human brain Parkinson's disease patients. PARIS represses the expression of the transcriptional co-activator, PGC-1? and the PGC-1? target gene, NRF-1 by binding to insulin response sequences in the PGC-1? promoter. Conditional knockout of parkin in adult animals leads to progressive loss of dopamine (DA) neurons that is PARIS dependent. Overexpression of PARIS causes selective loss of DA neurons in the substantia nigra, which is reversed by either parkin or PGC-1? co-expression. The identification of PARIS provides a molecular mechanism for neurodegeneration due to parkin inactivation.

Abstract: An object of the present invention is to provide a probe, a primer, a primer set and an antibody for use in the detection or selection of a dopaminergic neuron progenitor cell. The present invention provides a probe, a primer and a primer set for use in the detection or selection of a mesencephalon dopaminergic neuron progenitor cell, and preferably a dopaminergic neuron proliferative progenitor cell, which can hybridize with a nucleotide sequence of a 187A5 gene, or a complementary sequence thereto, and an antibody for use in the detection or selection of a mesencephalon dopaminergic neuron progenitor cell, and preferably a dopaminergic neuron progenitor cell, which is capable of binding to a 187A5 protein.

Abstract: The present invention relates to a biomarker for characterizing prostate cancer and method of using the same. More particularly, the invention relates to method of using a membrane-associated C family G protein-coupled receptor GPRC6A as biomarker of characterizing prostate cancer progression. The present invention also provides a kit for detecting prostate cancer in a subject.

Abstract: This invention includes a novel aad-12 transformation event for herbicide tolerance in soybean plants—referred to herein as pDAB4468-0416. This invention includes a heterologous polynucleotide inserted into a specific site within the genome of a soybean cell. In some embodiments, said event/polynucleotide can be “stacked” with other traits, including, for example, other herbicide tolerance gene(s) and/or insect-inhibitory proteins. Additionally, the subject invention provides assays for detecting the presence of the subject event in a sample (a soybean, for example). The assays can be based on the DNA sequence of the recombinant construct, inserted into the soybean genome, and on the genomic sequences flanking the insertion site. Kits and conditions useful in conducting the assays are also provided.

Abstract: A polynucleotide primer comprising at least the final six nucleotides of one of the following primer sequences, or a sequence complementary thereto: SEQ. ID NOS. 1 to 18, 21 to 45 or 74 to 77.

Abstract: A method of designing a primer for detecting a single nucleotide polymorphism (SNP), a method of detecting an SNP, a method of distinguishing SNPs, primers, detectable oligonucleotides, and kits.

Abstract: The present invention relates to methods and apparatus for conducting nucleic acid sequencing by pyrosequencing. The method comprises the steps of providing a platform having at least one well for containing at least one support surface, and providing at least one support surface within each well, wherein the support surface is adapted to immobilize a first binding partner or selectively immobilize a second binding partner. The method further comprises the steps of binding or immobilizing the first or second binding partner to the support surface and dispensing into each well from a point external of said platform a reagent, wherein after the dispensing step the platform is rotated sufficiently such that any residual or unreacted said reagent is substantially centrifugally removed from each well and/or each support surface, wherein during rotation each support surface is held within each well.

Abstract: A method of diagnosing a disease in a subject in need thereof is disclosed. The method comprises: (a) linking a plurality of non-contiguous DNA fragments from a sample of the subject to generate a polynucleotide product, the linking being effected by contacting the plurality of non-contiguous DNA fragments with a multiplex overlap-extension primer mix under conditions that allow simultaneous linkage of the DNA fragments and amplification of the polynucleotide product, wherein the primer mix comprises two flanking primers and at least one linker primer; and (b) determining a sequence of the polynucleotide product, wherein the sequence is indicative of the disease.

Abstract: The invention relates to methods based on the quantification of a set of biomarkers, preferably in biological samples isolated from skeletal muscle, for performing the diagnosis, prognosis and/or monitoring of muscular degeneration, preferably muscular degeneration caused by motor neuron diseases, more preferably amyotrophic lateral sclerosis (ALS); and to a kit for the diagnosis, prognosis and monitoring of said type of diseases. The method in the invention for the prognosis and/or monitoring of muscular degeneration makes it possible to determine the rate of progression of said degeneration (fast or slow rate of progression in relation to the normal rate of progression).

Abstract: The invention relates to a novel polypeptide vitamin K epoxide recycling polypeptide (VKORC1) as a target for coumarin and its derivatives. The invention further provides methods for identifying coumarin derivatives, and also claims VKORC1 polypeptides and VKORC1 nucleic acids containing a sequence abnormality associated with a VKORC1 associated deficiency such as warfarin resistance, wherein the VKORC1 polypeptides and VKORC1 nucleic acids can be used for diagnosing these deficiencies. Moreover, the invention relates to methods for identifying coumarin derivatives usable in pest control of rodents.

Abstract: Methods and compositions for detecting, identifying, and quantifying Brassica A genomic DNA are described. The methods are specific to the Brassica A genome and do not cross-react with other Brassica species, crops or weedy relatives that could contribute to contamination of a canola field.

Abstract: The present invention relates to the fields of biotechnology and molecular biology. In particular, the present invention relates to the construction and use of nucleic acid molecules comprising cloning sites which differ in nucleotide sequence. In particular embodiments, the present invention relates to nucleic acid molecules which contain recombination sites with different primer binding sites. These different primer binding sites may be used to sequence different ends of nucleic acid segments located between the two recombination sites.

Abstract: Disclosed are compositions including primers and probes, which are capable of interacting with the disclosed nucleic acids, such as the nucleic acids encoding the reverse transcriptase or protease of HIV as disclosed herein. Thus, provided is an oligonucleotide comprising any one of the nucleotide sequences set for in SEQ ID NOS:1-89, and 96-104. Also provided are the oligonucleotides consisting of the nucleotides as set forth in SEQ ID NOS:1-89, and 96-104. Each of the disclosed oligonucleotides is a probe or a primer. Also provided are mixtures of primers and probes and for use in RT-PCR and primary PCR reactions disclosed herein. Provided are methods for the specific detection of several mutations in HIV. Mutations in both the reverse transcriptase and the protease of HIV can be detected using the methods described herein.

Abstract: In some embodiments, the present invention concerns antisense oligonucleotides against targets of miR-21. In some embodiments, the invention is directed to a method for diagnosing fibrosis and/or fibrosis related diseases and to a method for screening a pharmaceutically active compound for the treatment of fibrosis and/or fibrosis related diseases. The present invention further relates to compositions for use in the treatment, amelioration, and/or prevention of fibrosis. In certain embodiments, the compositions modulate the activity of a miRNA for the treatment, amelioration, and/or prevention of fibrosis. In certain embodiments, the compositions inhibit the activity of miR-21 for the treatment, amelioration, and/or prevention of fibrosis.

Abstract: The present disclosure provides methods and compositions for performing nucleic acid reactions, such as hot-start digital polymerase chain reaction (dPCR).

Abstract: Primers having abasic regions or mismatches for amplifying sequences suspected of having methylation. Primers having abasic regions or mismatches for amplifying sequences adjacent to suspected or known methylated sequences. Methods of using primers having abasic regions or mismatches for identification of methylated sequences or sequences adjacent to suspected or known methylation sequences.

Abstract: Primers having abasic regions or mismatches for amplifying sequences suspected of having methylation. Primers having abasic regions or mismatches for amplifying sequences adjacent to suspected or known methylated sequences. Methods of using primers having abasic regions or mismatches for identification of methylated sequences or sequences adjacent to suspected or known methylation sequences.

Abstract: Primers having abasic regions or mismatches for amplifying sequences suspected of having methylation. Primers having abasic regions or mismatches for amplifying sequences adjacent to suspected or known methylated sequences. Methods of using primers having abasic regions or mismatches for identification of methylated sequences or sequences adjacent to suspected or known methylation sequences.

Abstract: The invention provides for isolated nucleic acid sequences of newly discovered micro RNAs that have been identified to exist in normal Human B cells and/or in tumor-related Human B cells, using an integrated bioinformatics method and pipeline described herein.

Abstract: MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the possibility that additional miRNAs are present in the human genome, we have developed an experimental approach called miRNA serial analysis of gene expression (miRAGE) and used it to perform the largest experimental analysis of human miRNAs to date. Sequence analysis of 273,966 small RNA tags from human colorectal cells allowed us to identify 200 known mature miRNAs, 133 novel miRNA candidates, and 112 previously uncharacterized miRNA* forms. To aid in the evaluation of candidate miRNAs, we disrupted the Dicer locus in three human colorectal cancer cell lines and examined known and novel miRNAs in these cells. The miRNAs are useful to diagnose and treat cancers.

Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provides methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.

Abstract: Amplification oligonucleotides for use in amplifying a sequence contained in nucleic acid derived from Chlamydophila pneumoniae.

Abstract: Described herein are primers and probes useful for the binding, detecting, differentiating, isolating, and sequencing of HSV-1 and/or HSV-2 viruses.

Abstract: An oligonucleotide, primer or probe comprises the nucleotide sequences of any of SEQ ID NO. 5, 6, 7, 2, 3, 4, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 25. The oligonucleotides are useful for the detection of the methylation status of a gene, in particular the MAGE-A3 gene. The oligonucleotides are useful in primer pairs, kits and methods for determining the methylation status of the MAGE-A3 gene and for diagnosing cancer, directing therapy and selecting subjects for treatment. The primer or probe can comprise a loop or hairpin structure and can be used in real-time methylation specific PCR.

Abstract: The invention pertains to certain genetic variants on Chr5p12 and Chr10q26 as susceptibility variants of breast cancer. Methods of disease management, including diagnosing increased and/or decreased susceptibility to breast cancer, methods of predicting response to therapy and methods of predicting prognosis using such variants are described. The invention further relates to kits useful in the methods of the invention.

Abstract: The developed oligonucleotide microchip for simultaneous, rapid identification of multiple crucial forest Phellinus pathogens was based on the DIG or biotin-labeled specific probes derived form ribosomal DNA genes (ITS1-5.8S-ITS2), by using reverse-dot hybridization. The chip can precisely and accurately identify and diagnose seventeen Phellinus species, including notorious hardwood and conifer tree killer, P. noxius and P. weirii, with a sensitivity of 1 pg DNA/?l on Nylon membrane, and 100 fg DNA/?l on plastic chip, respectively. Verification and identification of forest Phellinus pathogens infested authentic samples or voucher specimens can be accomplished within 7 hr.

Abstract: This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.

Abstract: The present invention relates to oligonucleotides complementary to a target polynucleotide, wherein the oligonucleotide comprises an LNA unit, a mismatch nucleobase, and an allele-specific nucleobase corresponding to an allele of the target polynucleotide. The invention further includes methods of using such oligonucleotides to detect and quantitate the frequency of particular alleles of a target polynucleotide.

Abstract: The present invention relates to a method for efficiently producing homozygous organisms from a heterozygous non-human starting organism, comprising providing of a heterozygous starting organism; allowing the starting organism to produce haploid cells; creating homozygous organisms from the haploid cells thus obtained; and selecting the organisms having the desired set of chromosomes; wherein during production of the haploid cells no recombination occurs in order to obtain a limited number of genetically different haploid cells. Recombination can also be prevented or suppressed.

Abstract: The invention provides methods and compositions relating to identification and use of genetic information from the FOXO3A gene that can be used for determining and increasing an individual's likelihood of longevity and of retaining physical and cognitive function during aging, and for determining and decreasing an individual's likelihood of developing a cardiovascular-, metabolic- or age-related disease, including coronary artery (heart) disease, stroke, cancer, chronic pulmonary disease, diabetes, Parkinson's disease and dementia.

Abstract: The present invention features compositions and methods for introducing, into cells, nucleic acids whose expression results in chromosomal silencing. The nucleic acids are targeted to specific chromosomal regions where they subsequently reduce the expression of deleterious genes, or cause the death of deleterious cells. Where the nucleic acid sequence is a silencing sequence, it may encode an Xist RNA or other non-coding, silencing RNA. Accordingly, the present invention features, inter alia, nucleic acid constructs that include a transgene (e.g., a silencing sequence encoding an Xist RNA or other non-coding RNA that silences a segment of a chromosome); first and second sequences that direct insertion of the silencing sequence into a targeted chromosome; and, optionally, a selectable marker.

Abstract: The present invention is a kit and method for isolating and quantitating miRNA and to the use of such methods in the diagnosis and prognosis of disease.

Abstract: The present invention provides a portable system for real-time population-scale HLA genotyping and/or allelotyping in a field environment and methods of such population-scale HLA genotyping. The individual components of the system are portable to and operable within a field environment thereby providing high throughput with real-time geno- or allelotyping. Also provided are HLA gene-specific primers and HLA allele-specific or single nucleotide polymorphism-specific hybridization probes. In addition the present invention provides a microarray comprising the hybridization probes. Further provided is a kit comprising the HLA gene-specific primers and the microarray.

Abstract: Methods and materials for detection of aneuploidy and other chromosomal abnormalities using fetal tissue are disclosed. Results can be obtained rapidly, without cell culture. The method uses digital PCR for amplification and detection of single target sequences, allowing an accurate count of a specific chromosome or chromosomal region. Specific polynucleic acid primers and probes are disclosed for chromosomes 1, 13, 18, 21, X and Y. These polynucleic acid sequences are chosen to be essentially invariant between individuals, so the test is not dependent on sequence differences between fetus and mother.

Abstract: The methods and apparatus 100 disclosed herein concern DNA sequencing. In some embodiments of the invention, the methods comprise measuring the distance between labeled nucleotides 220, such as nucleotides labeled with bulky groups. The methods may further comprise placing identical template DNA 200 into four reaction chambers 110, 120, 130, 140, each containing a different labeled nucleotide precursor, synthesizing complementary strands 230, 240, 250 and detecting labeled nucleotides 220. The distances between labeled nucleotides 220 may be used to construct 450 distance maps 310, 320, 330, 340 for each type of labeled nucleotide 220. The distance maps 310, 320, 330, 340 may be aligned 520 to obtain a nucleic acid sequence 210. Overlapping data analysis and frequency analysis may be used to construct 450 the distance maps 310, 320, 330, 340 and non-overlapping data analysis may be used to align 520 the distance maps into a sequence 210.