Abstract: A method of preparing cells from a patient specimen comprising a tissue or a clump of cells; a method of in situ hybridization (ISH) or immunohistochemistry (IHC); a method of theranosing a patient's response to an active agent that targets the tyrosine kinase pathway; an improvement of a method of theranosis comprising the method of ISH or IHC; a cell support on the surface of which are cells, which have been contacted with detectably labeled probes with the method of ISH or IHC; and a kit comprising (a) a cell support and/or at least one probe for ISH or IHC, and (b) instructions for carrying out the method of ISH or IHC on a cell support.

Abstract: Provided herein is technology relating to enzymatic modification of nucleic acids and particularly, but not exclusively, to methods and compositions relating to using uracil-DNA-N-glycosylase for minimizing or eliminating errors in a DNA sequence due to deamination of cytosine residues.

Abstract: The present invention relates to systems and methods for performing multiplex amplification reactions. In particular, the present invention relates to multiplex methylation-specific amplification systems and methods.

Abstract: Method for amplification, alone or in further combination with detection or detection and quantitation, of RNA from fusion gene variants, method of distinguishing same, and oligonucleotide primers and probes and kits for use in the methods.

Abstract: A method of preparing cells from a patient specimen comprising a tissue or a clump of cells; a method of in situ hybridization (ISH) or immunohistochemistry (IHC); a method of theranosing a patient's response to an active agent that targets the tyrosine kinase pathway; an improvement of a method of theranosis comprising the method of ISH or IHC; a cell support on the surface of which are cells, which have been contacted with detectably labeled probes with the method of ISH or IHC; and a kit comprising (a) a cell support and/or at least one probe for ISH or IHC, and (b) instructions for carrying out the method of ISH or IHC on a cell support.

Abstract: Compositions and methods for the efficient extraction, enrichment and isolation of nucleic acids from fresh, fixed or fixed and embedded cells, tissues, biological materials and cellular source material.

Abstract: Methods for detecting cancer that include hybridizing a set of chromosomal probes to a biological sample obtained from a patient, and identifying if aneusomic cells are present in a selected subset of cells obtained from the biological sample are described. A set of chromosomal probes and kits for detecting cancer that include sets of chromosomal probes, are also described.

Abstract: Methods, systems, apparatus and machine readable media are disclosed to sequence nucleic acid. An example method includes subjecting a sequence of target nucleotide bases captured on a microtransponder to a plurality of sequencing reactions to build a sequence of labeled nucleotide bases that are complementary to and bound to the sequence of target nucleotide bases. The example method also includes identifying each labeled nucleotide base of the sequence of labeled nucleotide bases and each respective complementary target nucleotide base of the sequence of target nucleotide bases to which the labeled nucleotide base is bound after each sequencing reaction. In addition, each labeled nucleotide base of the sequence of labeled nucleotide bases and each respective complementary target nucleotide base of the sequence of target nucleotide bases to which the labeled nucleotide base is bound is associated with a microtransponder identification number.

Abstract: The present invention provides methods, kits, and oligonucleotides for detecting and analyzing the nucleotide sequence of a reverse transcriptase (RT) region of the polymerase (Pol) gene of Hepatitis B Virus (HBV). In certain embodiments, a target RT region is amplified and subjected to DNA sequencing. The sequence obtained is compared to one or more DNA sequences characteristic of an HBV genotype or serotype, and/or one or more DNA sequences characteristic of an HBV mutation that confers resistance to a drug or vaccine, to determine the HBV genotype or serotype of the amplified product and/or the presence or absence of one or more DNA sequences characteristic of an HBV mutation that confers resistance to a drug or vaccine.

Abstract: Compositions of nucleic acid hybridization probes for detecting a nucleic acid target sequence and methods for their production are described. In one preferred embodiment, the nucleic acid hybridization probe includes a hybridization domain, an adaptor, a linker, and a signaling domain. The hybridization domain includes a nucleic acid sequence having complementarity to the nucleic acid target sequence. The adaptor is a nucleic acid sequence. The linker includes a moiety having at least one abasic site, such that the moiety blocks extension by an elongating polymerase on a nucleic acid template containing the moiety. The signaling domain comprises a nucleic acid having at least one label or a nucleic acid having at least one nucleic acid domain for binding at least one additional nucleic acid.

Abstract: A method of detecting high-grade dysplasia, pancreatobiliary cancer, or metastatic cancer to the pancreatobiliary tract or inferring an increased risk thereof, comprising obtaining a sample of pancreatobiliary cells from a patient with a set of detectably labeled probes comprising a locus-specific probe for MCL1 (myeloid cell leukemia sequence 1), a locus-specific probe for EGFR (epidermal growth factor receptor), a locus-specific probe for MYC, and a locus-specific probe for P16 under hybridization conditions and determining the presence of chromosomal abnormalities; a set of probes comprising a locus-specific probe for MCL1, a locus-specific probe for EGFR, a locus-specific probe for MYC, and a locus-specific probe for P16; and a kit comprising the set of probes and instructions for detecting high-grade dysplasia, pancreatobiliary cancer, or metastatic cancer to the pancreatobiliary tract, or inferring an increased risk thereof, in a patient.

Abstract: Method and compositions for screening for the presence of Epidermal Growth Factor Receptor variant 3 (EGFR(v3)) in a sample are described. The method comprises obtaining a sample containing a plurality of cells; hybridizing a set of chromosomal probes to the sample, wherein the set comprises an EGFR(v3)-probe and a probe to chromosome 7 different from an EGFR(v3)-probe; and visualizing the hybridization pattern of the set of chromosomal probes in the plurality of cells of the sample, wherein the presence of at least one copy of chromosome 7 lacking a hybridization signal of the EGFR(v3)-probe in at least one cell is indicative of the presence of the EGFR(v3) in the sample. The method and compositions are suitable for diagnosing the therapeutic outcome for treating a patient having a cancer with an anti-EGFR therapeutic agent and for screening a sample for a predisposition for forming an EGFR-associated cancer.

Abstract: A method of diagnosing bladder cancer in a patient comprising contacting a sample of urothelial cells obtained from the patient with a set of detectably labeled probes comprising locus-specific probes for c-myc and AURKA and centromeric probes for chromosomes 7 and 17 under hybridization conditions, and determining the presence of chromosomal abnormalities, wherein the presence of chromosomal abnormalities involving at least two of the detectably labeled probes indicates that the patient has bladder cancer; a method of monitoring recurrence of bladder cancer in a patient; a set of probes comprising locus-specific probes for c-myc and AURKA and centromeric probes for chromosomes 7 and 17; and a kit comprising (a) the set of probes and (b) instructions for diagnosing bladder cancer, or monitoring the recurrence thereof, in a patient.

Abstract: Chemical reaction vessels are disclosed herein. An example method includes forming a reaction chamber between two pliable sheets and dividing the reaction chamber into a plurality of chambers. The reaction chamber is to have a substantially planar base, and the reaction chamber is to hold a fluid for a chemical reaction.

Abstract: A method to detect prostate cancer comprising contacting a sample of prostate cells from the patient with a set of detectably labeled probes under hybridization conditions and determining the presence of chromosomal abnormalities in prostate tumor tissue, PIN (intra-epithelial neoplasia), histologically benign tissue and benign prostatic hyperplasia (BPH); a method to combine immunofluorescence and FISH (IF-FISH) to facilitate the assessment of chromosomal abnormalities; a set of probes; and a kit comprising the set of probes and instructions for diagnosing prostate cancer in a patient.

Abstract: Methods, probes and kits for diagnosing malignant melanoma and prognosing metastasis thereof in a patient.

Abstract: A method is disclosed for rapid molecular profiling of tissue or other cellular specimens by placing a donor specimen in an assigned location in a recipient array, providing copies of the array, and performing a different biological analysis of each copy. The results of the different biological analyses are compared to determine if there are correlations between the results of the different biological analyses at each assigned location. In some embodiments, the specimens may be tissue specimens from different tumors, which are subjected to multiple parallel molecular (including genetic and immunological) analyses. The results of the parallel analyses are then used to detect common molecular characteristic of the genetic disorder type, which can subsequently be used in the diagnosis or treatment of the disease. The biological characteristics of the tissue can be correlated with clinical or other information, to detect characteristics associated with the tissue.

Abstract: A method and/or system for making determinations regarding samples from biologic sources including statistical methods for making meaning grouping of observed data and/or for pre-selecting endpoints.

Abstract: Probe sets and methods of using probes and probe sets for the detection of cancer are described. Methods for detecting cancer that include hybridizing a set of chromosomal probes to a biological sample obtained from a patient, and identifying if cancer cells are present the sample. Also included are methods of selecting a combination of probes for the detection of cancer.

Abstract: A method and/or system for making determinations regarding samples from biologic sources including statistical methods for making meaning grouping of observed data and/or for determining an overall quality measure of an assay.