Abstract: The present invention relates to the discovery that of a panel of serum or plasma markers may be used to diagnose Idiopathic Pulmonary Fibrosis (“IPF”) and distinguish this condition from other lung ailments. It further relates to the identification of markers associated with IPF disease progression.

Abstract: A relationship between cancer and ribonucleic acid (RNA) regulation is described by determining intracellular levels of niRN A regulators. Generally, mRNA levels are decreased in cancer cells that may be a reflection of either reduced mRNA expression and/or increased mRNA degradation. miRNAs are identified that hybridize to an mRNA that are suspected to mediate intracellular mRNA steady state levels. Alternatively, ribonucleic acid binding protein (RBP) levels may also mediate intracellular mRNA steady state levels. In particular, this invention demonstrates an effective clinical management strategy for uterine cell cancers may be implemented by taking advantage of an exemplary relationship between P2X7 mRNA and miRNAs including, but not limited to, miR-186 and/or miR-150.

Abstract: Methods and compositions are provided for diagnosing ovarian cancer in a mammalian subject, preferably in a serum or plasma sample of a human subject. The methods and compositions enable the detection or measurement in the sample or from a protein level profile generated from the sample, the protein level of one or more specified biomarkers. Comparing the protein level(s) of the biomarker(s) in the subject's sample or from protein abundance profile of multiple biomarkers, with the level of the same biomarker(s) or profile in a reference standard, permits the determination of a diagnosis of ovarian cancer, or the identification of a risk of developing ovarian cancer, or enables the monitoring of the status of progression or remission of ovarian cancer in the subject followed during a therapeutic protocol.

Abstract: The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provide methods for the sensitive and specific detection of target gene sequences and gene expression profiles.

Abstract: Provided are methods of treating breast cancer in a subject in need thereof comprising administering to the subject an effective amount of an inhibitor of miR-105 or an inhibitor of miR-122 are provided. Also provided herein are methods of determining a level of miR-105 or a level of miR-122 in a subject that has or is at risk for developing breast cancer. The method includes obtaining a biological sample from the subject and determining a level of miR-105 or a level of miR-122 or a combination thereof in the biological sample, wherein a higher level of miR-105 or miR-122 as compared to a control indicates that the subject has or is at risk of developing breast cancer.

Abstract: Agents that reduce the amount of IGFBP-2 and/or IGFBP-5 and that are known to be useful in the treatment of cancer result in increased expression of the protein clusterin. Since clusterin can provide protection against apoptosis, this secondary effect detracts from the efficacy of the therapeutic agent. In overcoming this, the present invention provides a combination of therapeutic agents that is useful in the treatment of cancer. The combination includes an agent that reduces the amount of IGFBP-2 and/or IGFBP-5 and that stimulates expression of clusterin as a secondary effect, and an oligonucleotide that is effective to reduce the amount of clusterin in cancer cells. In some embodiments of the invention, the agent that reduces IGFBP-2 and/or IGFBP-5 is a bispecific antisense species. The oligonucleotide may be an antisense oligonucleotide or an RNAi oligonucleotide.

Abstract: Methods and compositions are provided for diagnosing colorectal cancer in a mammalian subject, preferably in a serum or plasma sample of a human subject. The methods and compositions enable the detection or measurement in the sample or from a protein level profile generated from the sample, the protein level of one or more specified biomarkers. Comparing the protein level(s) of the biomarker(s) in the subject's sample or from protein abundance profile of multiple biomarkers, with the level of the same biomarker(s) or profile in a reference standard, permits the determination of a diagnosis of colorectal cancer, or the identification of a risk of developing colorectal cancer, or enables the monitoring of the status of progression or remission of colorectal cancer in the subject followed during a therapeutic protocol.

Abstract: An assay for mutations in JAK2 is described. The assay uses selective amplification of mutant alleles with a blocker probe which preferentially hybridises to wild type alleles. The same probe is then used to detect presence or absence of wild type sequences. It is not necessary to know the specific mutant sequence beforehand.

Abstract: This document provides methods and materials for detecting a nucleic acid expansion. For example, methods and materials for detecting the presence of an expanded number (e.g., greater than 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, or more copies) of a hexanucleotide repeat (e.g., GGGGCC) in the non-coding region of a C9ORF72 gene are provided.

Abstract: The invention provides methods and oligonucleotide primers for assaying Brassica napus plants for the presence or absence of mutations that confer resistance to imidazolinone herbicides. Specifically, the methods and primers of the invention are useful for detecting the PM1 mutation of the B. napus AHAS1 gene and the PM2 mutation of the B. napus AHAS3 gene.

Abstract: A method for detecting an abnormal cell based on gene expression analysis, which is useful for cancer diagnosis, is provided. A gene expression analysis method, comprising: measuring the expression level of a transcript of a human MLH1 gene containing the nucleotide sequence as shown in SEQ ID NO: 1 at the 5?-terminus thereof and the expression level of a transcript of a human MLH1 gene containing the nucleotide sequence as shown in SEQ ID NO: 2 at the 5?-terminus thereof, in a biological sample; and comparing the expression levels, thereby detecting a cell positive for microsatellite instability.

Abstract: Provided are novel methods and compositions for the diagnosis, prognosis and treatment of gynecological tumors, in particular uterine leiomyoma (UL). Furthermore, novel methods and compositions for the treatment of diseases characterized by an aberrant growth of mesenchymal stem cells and their descendants and for the treatment of pituitary and prostate tumors are described.

Abstract: An antibody against mutant ?-actinin-4 having an amino acid sequence with at least one amino acid residue substitution in the region between position 245 and 263 in the amino acid sequence of ?-actinin-4, wherein the antibody recognizes all or a part of the substituted amino acid residue(s) in the region.

Abstract: The present invention discloses a functional relationship between a recognized disease condition and a polymorphism in the nucleotide factor kappa B promoter (NFKB1). This relationship provides a platform for methods of altering promoter activity and for determining similar relationships between specific pathologies and identified polymorphisms. A statistically significant risk of developing ulcerative colitis was shown to be correlated with the presence of an ATTG insertion/deletion in the NFKB1 promoter and is likely to apply also to a variety of other inflammatory diseases.

Abstract: The present invention relates to methods, primers and probes useful for detecting the presence of mutant BRAF sequences in a sample, specifically for detecting the presence of the BRAF V600E, V600D, V600K, and V600M mutations.

Abstract: Provided are isolated genomic polynucleotide fragments that encode human SNARE YKT6, human glucokinase, human adipocyte enhancer binding protein (AEBP1) and DNA directed 50 kD regulatory subunit (POLD2), vectors and hosts containing these fragments and fragments hybridizing to noncoding regions as well as antisense oligonucleotides to these fragments. The invention is further directed to methods of using these fragments to obtain SNARE YKT6, human glucokinase, AEBP1 protein and POLD2 and to diagnose, treat, prevent and/or ameliorate a pathological disorder.

Abstract: The present invention provides serum paraoxonase 1 protein as a biomarker useful for early diagnosis of lung cancer.

Abstract: In one aspect, the present invention relates to methods for increasing, decreasing or maintaining the innate immune response in a mammalian subject comprising modulating the expression of DUX4-fl, or modulating the expression of beta-defensin 3 (DEFB103). In another aspect, the present invention relates to methods for increasing, decreasing or maintaining myogenesis or muscle differentiation in a mammalian subject comprising modulating the expression of beta-defensin 3 (DEFB103). In additional aspects, the present invention involves diagnostic methods based on assessment of identified biomarkers.

Abstract: The invention relates to isolated anti-microRNA molecules. In another embodiment, the invention relates to an isolated microRNA molecule. In yet another embodiment, the invention provides a method for inhibiting microRNP activity in a cell.

Abstract: Provided herein are compositions and methods for the modulation of ?miR-214 for the treatment and/of prevention of fibrosis and fibroproliferative conditions.

Abstract: Disclosed herein are antisense compounds and methods for decreasing STAT3 mRNA and protein expression. Such methods, compounds, and compositions are useful to treat, prevent, or ameliorate hyperproliferative diseases.

Abstract: The invention provides a method of determining the prognosis of cancer in a subject. The method comprises (a) obtaining a sample from the subject, (b) analyzing the sample for the expression level of a carboxypeptidase E (CPE) splice variant, and (c) correlating the expression level in the sample with the prognosis of cancer in the subject. The invention further provides a method of diagnosing cancer, methods of treatment, kits for detecting mRNA expression of a CPE-?N, and inhibitors of CPE-?N and compositions thereof.

Abstract: The present invention provides compositions and methods based on genetic polymorphisms that are associated with response to statin treatment, particularly for reducing the risk of cardiovascular disease, especially coronary heart disease (such as myocardial infarction) and stroke. For example, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by these nucleic acid molecules, reagents and kits for detecting the polymorphic nucleic acid molecules and variant proteins, and methods of using the nucleic acid molecules and proteins as well as methods of using reagents and kits for their detection.

Abstract: The present invention provides novel mutations identified in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that can be used for a more accurate diagnosis of cystic fibrosis (CF) and CF related disorders. Methods for testing a sample obtained from a subject to determine the presence of one or more mutations in the CFTR gene are provided wherein the presence of one or more mutations indicates that the subject has CF or a CF related disorder, or is a carrier of a CFTR mutation.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with rheumatoid arthritis. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts.

Abstract: Method for the detection of a target sequence comprising ligating two probes when annealed adjacent to the target sequence, hybridization of a compound primer to the ligated probes and after elongation of the compound primer, amplifying the elongated compound primer from primers annealing to primer binding sites provided in the compound primer and one of the probes to produce detectably amplicons.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with cardiovascular disorders, particularly acute coronary events such as myocardial infarction and stroke, and genetic polymorphisms that are associated with responsiveness of an individual to treatment of cardiovascular disorders with statin. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: A method of determining the time of stroke symptom onset is provided including obtaining a biological sample from an individual; contacting the biological sample with a detection composition comprising at least one expression mediator of a LY96, ARG1, CA4, and a TLR expression mediators, or a combination of these expression mediators, wherein at least one of the expression mediators is associated with an acute phase response of ischemic stroke, for forming a detectable response; and correlating the detectable response with a time of onset of one or more stroke symptoms. A composition is provided having a nucleic acid probe, an antibody, or a purified biomarker that is specific for at least one of a LY96, ARG1, CA4, and TLR expression mediators, or a combination of these expression mediators.

Abstract: A nucleoside analog and a salt thereof represented by any of the general formulae (1) to (10) below: wherein R1, R2, and R3 are the same or different groups, and each of the R1, R2 and R3 is selected from a hydrogen atom, a protecting group for a functional group in nucleic acid synthesis, a phosphate group, a phosphate group protected by a protecting group in nucleic acid synthesis, and an activated phosphate group for solid phase synthesis; and Ar is one of an aromatic hydrocarbon group and a polyaromatic hydrocarbon group.

Abstract: The present invention provides a method for detecting the presence or absence of, or for discriminating between, blood type variants, including RHD*r?s, RHD*DIIIa, RHD*DIVa-2, RHCE*css and RHCE*ce733G. The method comprises genotyping a sample obtained from a human subject at one or more positions in intron 7 of the RHD gene and/or in intron 7 of the RHCE gene. The invention also provides products, in particular, probes, primers and kits for use in the method of the invention.

Abstract: Provided are isolated genomic polynucleotide fragments that encode human SNARE YKT6, human glucokinase, human adipocyte enhancer binding protein (AEBP1) and DNA directed 50 kD regulatory subunit (POLD2), vectors and hosts containing these fragments and fragments hybridizing to noncoding regions as well as antisense oligonucleotides to these fragments. The invention is further directed to methods of using these fragments to obtain SNARE YKT6, human glucokinase, AEBP1 protein and POLD2 and to diagnose, treat, prevent and/or ameliorate a pathological disorder.

Abstract: The invention is directed to compositions and methods for selectively reducing the expression of a gene product from a desired target gene in a cell, as well as for treating diseases caused by the expression of the gene. More particularly, the invention is directed to compositions that contain double stranded RNA (“dsRNA”), and methods for preparing them, that are capable of reducing the expression of target genes in eukaryotic cells. The dsRNA has a first oligonucleotide sequence that is between 25 and about 30 nucleotides in length and a second oligonucleotide sequence that anneals to the first sequence under biological conditions. In addition, a region of one of the sequences of the dsRNA having a sequence length of at least 19 nucleotides is sufficiently complementary to a nucleotide sequence of the RNA produced from the target gene to trigger the destruction of the target RNA by the RNAi machinery.

Abstract: RBC and platelet (Plt) alloimmunization requires antigen-matched blood to avoid adverse transfusion reactions. Some blood collection facilities use unregulated Abs to reduce the cost of mass screening, and later confirm the phenotype with government approved reagents. Alternatively, RBC and Plt antigens can be screened by virtue of their associated single nucleotide polymorphisms (SNPs). We developed a multiplex PCR-oligonucleotide extension assay using the GenomeLab SNPStream platform to genotype blood for a plurality of blood group antigen-associated SNPs, including but not limited to: RhD (2), RhC/c, RhE/e, S/s, K/k, Kpa/b, Fya/b, FY0, Jka/b, Dia/b, and HPA-1a/b.

Abstract: RBC and platelet (Plt) alloimmunization requires antigen-matched blood to avoid adverse transfusion reactions. Some blood collection facilities use unregulated Abs to reduce the cost of mass screening, and later confirm the phenotype with government approved reagents. Alternatively, RBC and Plt antigens can be screened by virtue of their associated single nucleotide polymorphisms (SNPs). We developed a multiplex PCR-oligonucleotide extension assay using the GenomeLab SNPStream platform to genotype blood for a plurality of blood group antigen-associated SNPs, including but not limited to: RhD (2), RhC/c, RhE/e, S/s, K/k, Kpa/b, Fya/b, FY0, Jka/b, Dia/b, and HPA-1a/b.

Abstract: The present invention provides compositions and methods for the optimization of cleavage of RNA species by RNase H. In some embodiments, the invention provides oligonucleotides that possess two or more regions of differing conformation, and at least one transitional nucleobase positioned between the regions that is capable of modulating transfer of the helical conformation characteristic of the region bound to the 3?hydroxy thereof, to the region bound to the 5? hydroxyl thereof.

Abstract: The present invention relates to PRAME specific primers and probes, diagnostic kits and methods. The invention further relates to treatment of specific populations of cancer patients suffering from PRAME expressing tumours.

Abstract: The invention provides a method of diagnosing Alzheimer's disease (AD) in a subject by determining the level of expression of one or more miRNAs molecules associated with AD, as well as various nucleic acid molecules relating thereto or derived thereof.

Abstract: The various embodiments of the present disclosure relate generally to single molecule sensitive probes for detecting RNA, and more particularly to multivalent fluorescent probes for detecting a single molecule of RNA in a cell. The present invention includes a RNA imaging probe comprising: a multivalent core comprising a plurality of attachment sites; a plurality of RNA/DNA chimeric oligonucleotides having a specificity for a target RNA, wherein a RNA/DNA chimeric oligonucleotide is bound to an attachment site of the multivalent core; and a plurality of fluorophores, wherein a fluorophore is bound to the RNA/DNA chimeric oligonucleotide.

Abstract: Oligonucleotides directed against the hypoxia-inducible factor-1? (HIF-1?) gene are provided for modulating the expression of HIF-1?. The compositions comprise oligonucleotides, particularly antisense oligonucleotides, targeted to nucleic acids encoding the HIF-1?. Methods of using these compounds for modulation of HIF-1? expression and for the treatment of diseases associated with the hypoxia-inducible factor-1? are provided. Examples of diseases are cancer and pre-eclampsia. The oligonucleotides may be composed of deoxyribonucleosides, a nucleic acid analog, or Locked Nucleic Acid (LNA) or a combination thereof.

Abstract: Methods of lung cancer in a sample from a patient are provided. Methods of detecting changes in expression of one or more target RNAs associated with lung cancer are also provided. Compositions and kits are also provided.

Abstract: The present invention embraces microRNA-antagonists and activators of homeobox D10 protein; Zinc finger, MYND domain containing 11 protein; or RB1-inducible coiled-coil 1 protein for use in decreasing glial tumor cell proliferation and treating glioma.

Abstract: The present invention is directed to small interfering RNA molecules (siRNA) targeted against an allele of interest, and methods of using these siRNA molecules.

Abstract: MicroRNA genes are highly associated with chromosomal features involved in the etiology of different cancers. The perturbations in the genomic structure or chromosomal architecture of a cell caused by these cancer-associated chromosomal features can affect the expression of the miR gene(s) located in close proximity to that chromosomal feature. Evaluation of miR gene expression can therefore be used to indicate the presence of a cancer-causing chromosomal lesion in a subject. As the change in miR gene expression level caused by a cancer-associated chromosomal feature may also contribute to cancerigenesis, a given cancer can be treated by restoring the level of miR gene expression to normal. microRNA expression profiling can be used to diagnose cancer and predict whether a particular cancer is associated with an adverse prognosis. The identification of specific mutations associated with genomic regions that harbor miR genes in CLL patients provides a means for diagnosing CLL and possibly other cancers.

Abstract: Methods and compositions for providing a prognosis or diagnosis for a human patient having renal cell cancer are provided. The method relates to the discovery of SNPs which are associated with a favorable prognosis and response to therapy in RCC.

Abstract: Disclosed are a composition for diagnosis of lung cancer including an antibody specific to GPI specific phospholipase D1 (GPLD1) protein, which is an effective biomarker for early diagnosis of lung cancer, and a composition for diagnosis of lung cancer including a primer or probe specific to a nucleic acid encoding the GPLD1 protein. The lung cancer diagnostic marker may be effectively used in early diagnosis of lung cancer and also, is very useful for evaluating progression of a disease and prognosis before and after treatment of the same.

Abstract: Expressed Sequence Tags (ESTs) isolated from the Western Corn Rootworm, Diabrotica virgifera virgifera LeConte, are disclosed. The invention encompasses nucleic acid molecules that encode D. v. virgifera protein homologs and fragments thereof. In addition, antibodies capable of binding the proteins are encompassed by the present invention. The disclosed ESTs have particular utility in isolating genes and promoters, identifying and mapping the genes involved in developmental and metabolic pathways, and determining gene function. The ESTs provide a unique molecular tool for the targeting and isolation of novel genes for plant protection and improvement. The invention also relates to methods of using the disclosed nucleic acid molecules, proteins, fragments of proteins, and antibodies, for example, for gene identification and analysis, and preparation of constructs.

Abstract: Therapeutic agents which target heat shock protein (hsp) 27 in vivo are used to provide treatment to individuals, particularly human individuals, suffering from prostate cancer and other cancers that overexpress hsp27. A therapeutic agent, for example an antisense oligonucleotide or RNAi nucleotide inhibitor with sequence specificity for hsp27 mRNA, for example human hsp27 mRNA, is administered to an individual suffering from prostate cancer or some other cancer expressing elevated levels of hsp 27 in a therapeutically effective amount. The therapeutic agent is suitably formulated into a pharmaceutical composition which includes a pharmaceutically acceptable carrier, and packaged in dosage unit form. A preferred dosage unit form is an injectable dosage unit form.

Abstract: Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.

Abstract: We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in glioblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.