Abstract: Methods and apparatus are described for detecting specific binding between first and second chemical entities. The first chemical entity in association with a first fluorophore is immobilized. The second chemical entity is allowed to bind with the immobilized first chemical entity. The second chemical entity is or becomes coupled to a second fluorophore, which forms a FRET pair with the first fluorophore. The bound chemical entities are exposed to radiation at an excitation frequency for either the first or the second fluorophore, and polarization anisotropy of a FRET fluorescent signal from the bound chemical entities is measured to detect specific binding between the first and second chemical entities.

Abstract: Methods of identifying malignant thyroid tissue comprising testing a thyroid tissue sample for the expression of at least two genes chosen from CCND2, PCSK2, and PLAB. Kits for use in the disclosed methods are also provided.

Abstract: The invention relates to copy number profile analysis. Specifically, copy number profile analysis is used to determine whether two or more separate tumors in a single individual are derived from a common source.

Abstract: The present invention is directed to kits and compositions for generating a signal indicative of the presence of a target nucleic acid sequence in a sample, comprising a nucleic acid polymerase lacking 5? to 3? exonuclease activity and a thermostable FEN nuclease consisting of a 5? to 3? exonuclease and/or endonuclease activity.

Abstract: The invention provides allelic ladder mixtures and individual alleles suitable for use in such mixtures. The allelic ladder mixtures give improved identification and distinguishing capabilities, particularly suitable in forensic investigations.

Abstract: This invention provides compositions and methods for genetic testing of an organism and for correlating the results of the genetic testing with a unique marker that unambiguously identifies the organism. The markers may be internal markers, such as for example single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), or other sites within a genomic locus. Alternatively, the markers may be external, such that they are separately added to the genetic sample before testing.

Abstract: The invention is drawn to isolating sequence variants of a genetic locus of interest using a modified iterative primer extension method. The nucleic acids analyzed are generally single stranded and have a reference sequence which is used as a basis for performing iterative single nucleotide extension reactions from a hybridized polymerization primer. The iterative polymerization reactions are configured such that polymerization of the strand will continue if the sequence of the nucleic acid being analyzed matches the reference sequence, whereas polymerization will be terminated if the nucleic acid being analyzed does not match the reference sequence. Nucleic acid strands that have mutations can be isolated using a variety of methods and sequenced to determine the precise identity of the mutation/polymorphism. By performing the method on both strands of the nucleic acid being analyzed, virtually all possible mutations can be identified.

Abstract: Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.

Abstract: The invention provides compositions, kits and methods of generating a signal indicative of the presence of a target nucleic acid sequence in a sample by forming a cleavage structure. The cleavage structure is formed by incubating a sample containing a target nucleic acid with a downstream probe that forms a 3? flap when hybridized to the target. The cleavage structure is cleaved with a 3? nuclease and a detectable signal is produced.

Abstract: The invention relates to the use of mass labelled probes to characterize nucleic acids by mass spectrometry. Thus the invention provides methods of detecting the presence of a target nucleic acid in a sample, using a circularizing probe in which a mass tag is present in the probe. Further methods of detecting the presence of a target nucleic acid are provided, which in contrast use a probe detection sequence in the circularizing probe, wherein the probe detection sequence is detected with a probe attached to a mass tag. Methods for determining a genetic profile from the genome of an organism also form part of the invention.

Abstract: The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e.g., oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb).

Abstract: The invention relates to the identification of biologically-active DNA-binding sites to which a protein of interest binds in a cell. The invention also relates to the identification of agents and conditions which alter the biologically-active DNA-binding sites to which a protein binds. One aspect of the invention also provides methods for identifying pathways that are regulated by transcriptional regulators and for modulating the activity of the pathways.

Abstract: The invention is a method for detecting a change in the conformational or energetic state of a molecular species, comprising the steps of: (i) immobilizing the molecular species, under conditions suitable for the reaction to occur; (ii) contacting at least part of the molecular species with a localized electromagnetic field; and (iii) detecting a change in dielectric constant during or after the reaction, to thereby detect a change in the conformational or energetic state of the molecular species.

Abstract: Compositions and methods of use are disclosed for the analysis of polynucleotides isolated in individual reaction compartments.

Abstract: Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

Abstract: The present teachings generally relate to methods, kits, and compositions for detecting target polynucleotide sequences. The teachings also relate to ligation and amplification reactions that generate self-complementary polynucleotide products. In some embodiments, ligation reactions are performed with probes that result in the formation a self-complementary ligation product. Ligation of a hairpin linker to the self-complementary ligation product can form a loop ligation product. In some embodiments, the loop ligation product can be amplified with rolling circle amplification. Detection of a loop ligation product can serve to determine the identity of a target polynucleotide.

Abstract: Methods for diagnosis and treatment of cancer using ID4 are disclosed. Specifically, epigenetic inactivation of ID4 in colorectal carcinomas and breast correlates with poor differentiation and unfavorable prognosis. Further, aberrant hypermethylation of ID4 gene promoter region increases risk of metastasis in colorectal and breast cancer.

Abstract: The present invention describes novel oligonucleotides targeted to nucleic acid sequences derived from Crytosporidium organisms, and Crytosporidium parvum organisms in particular, which are useful for determining the presence of Cryptosporidium organisms in a test sample. The oligonucleotides of the present invention include hybridization assay probes, helper probes and amplification primers. The present invention further describes a novel method for obtaining purified ribonucleic acid from viable oocysts.

Abstract: The invention relates to compositions and methods for generating a signal indicative of the presence of a target nucleic acid in a sample utilizing a primer-probe duplex.

Abstract: The invention relates to methods for identifying the sequence of one or more variant nucleotides in nucleic acid molecules. The method involves cleaving a double-stranded nucleic acid molecule containing a mismatch with a mismatch-specific endonuclease which cleaves on the 3? side of the mismatch, and preserving the integrity of the variant nucleotide by ligating a Double-Stranded Linker with a degenerate 3?-overhang to said variant nucleotide. Because the variant nucleotide is immediately adjacent to the linker, PCR and/or sequence-by-synthesis analysis can be readily carried out.