Abstract: A method for deparaffinizing an FFPE tissue sample comprises mixing the FFPE tissue sample with an organic solvent to form a first mixture (10). A surfactant is added to the first mixture (10) to form a second mixture. The second mixture is separated into an organic solvent layer (11) and a surfactant layer (12). The surfactant layer (12) comprises a deparaffinized tissue sample from the FFPE tissue sample. The method also comprises adding water or an aqueous solution to the separated second mixture to form an organic solvent layer (11), a water or aqueous solution layer (13) and a surfactant layer (12). This surfactant layer comprises the deparaffinized tissue sample.

Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.

Abstract: Methods of screening a sample for a predisposition for forming an EGFR-associated cancer and the presence of EGFR (v3) contained therein are described. The methods include the steps of obtaining a sample containing a plurality of cells and hybridizing a first set of labeled chromosomal probes and a second set of labeled chromosomal probes to the sample. The first set of labeled chromosomal probes specific to chromosome 7, and the second set of labeled chromosomal probes is a labeled EGFR(v3)-probe. The first and second sets of labeled chromosomal probes include different labels to permit identification of the first and second sets of labeled chromosomal probes hybridized to the sample. The method includes calculating the number of signals of the first and second sets labeled chromosomal probes on an individual cell basis and determining a predisposition for forming an EGFR-associated cancer and the presence of EGFR (v3) contained therein based upon those calculations.

Abstract: The present invention provides an artificial exogenous reference molecule for type and abundance comparison among different species of microorganisms. The artificial exogenous reference molecule includes several species detection regions and several linker sequence regions, where the species detection regions and the linker sequence regions are arranged alternately; at least two species detection regions are provided and are species detection regions for different species; and the linker sequence regions are random sequences different from species sequences to be detected. The species detection region includes a primer sequence region and a specific recognition region; the sequence length of the specific recognition region simulates the characteristic detection sequence length of the corresponding species to be detected; and the sequence of the specific recognition region has obviously specific difference from the DNA sequence of a genome in the species to be detected without homology.

Abstract: The present invention relates to methods for the identification of methylated cytosines in a population of double stranded DNA molecules. The invention also relates to adapters and kits for synthesizing said adapters as well as to double stranded DNA libraries obtained by the methods of the invention.

Abstract: The present invention concerns cancer biomarkers. In particular, the invention concerns HGF as a biomarker for patient selection and patient prognosis in cancer, as well as methods of therapeutic treatment, articles of manufacture and methods for making them, diagnostic kits, methods of detection and methods of advertising related thereto.

Abstract: The invention relates to a method for in vitro diagnosis or prognosis of testicular cancer which comprises a step of detecting the presence or absence of at least one expression product from at least one nucleic acid sequence selected from the sequences identified in SEQ ID NOS: 1 to 6 or from the sequences which exhibit at least 99% identity with one of the sequences identified in SEQ ID NOS: 1 to 6, to isolated nucleic acid sequences and to the use thereof as a testicular cancer marker.

Abstract: The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation—, e.g., the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides—combined with detection of levels of particular genomic regions using array hybridization.

Abstract: The inventions provided herein relate to detection reagents, compositions, methods, and kits comprising the detection reagents for use in detection, identification, and/or quantification of analytes in a sample. Such detection reagents and methods described herein allow multiplexing of many more labeled species in the same procedure than conventional methods, in which multiplexing is limited by the number of available and practically usable colors.

Abstract: A method for identifying any of the presence, location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.

Abstract: A method for characterising a DNA analyte comprised of one or more polynucleotide types characteristic of a site of nucleotide polymorphism each of which includes a target region having the formula -X-Y-Z- wherein X and Z are respectively first and second characteristic flanking oligonucleotide regions and Y is one of the variants constituting the site is provided.

Abstract: The present invention is directed to methods for identifying the presence of one or more methylated or unmethylated target nucleotide sequences in a sample that involve coupled methylation sensitive restriction enzyme digestion-ligation and/or extension processes. In some embodiments, the ligation and primary extension products formed in the reaction processes of the present invention are subsequently amplified using a polymerase chain reaction. The ligation products or primary extension products are detected, and the presence of one or more methylated or unmethylated target nucleotide sequences in the sample is identified based on the detection.

Abstract: The present invention provides an epigenetic haemogram, also referred to as an epigenetic blood cell count that identifies the quantitative, comprehensive picture of cellular composition in a biological sample, wherein advantageously a normalization standard is used. The normalization standard is a nucleic acid molecule comprising at least one marker-region being specific for each of the blood cells to be detected, and at least one control-region being cell-unspecific, wherein said regions are present in the same number of copies on said molecule and/or a natural blood cell sample of known composition. Furthermore, the present invention relates to a kit and the use of a kit for performing the epigenetic assessment of comprehensive, quantitative cellular composition of a biological sample. The biological sample is derived from e.g.

Abstract: Methods and genetic sequences are described for use in determining the diagnosis, subtype, prognosis, and disease course of high-grade gliomas, such as glioblastoma multiforme. One such method includes determining increased expression of at least one gene on a chromosome segment in cells of the glioma, the segment being 17:57,851,812-17:57,973,757; 7:127,892,509-7:127,947,649; 12:33,854-12:264,310; or 19:33,329,393-19:35,322,055; and estimating, based on the expression, a predicted length of survival, a probability of survival, or a predicted response to a therapy for the glioma.

Abstract: A gene expression signature of colon cancer, microarrays including them and methods of using the colon gene expression signature are provided. The gene expression signature is especially useful for determining the prognosis of a patient diagnosed with colon cancer, such as stage II colon cancer. The gene signature described herein is also useful for determining effectiveness of surgical resection with or without adjuvant chemotherapy, and determining possibility of cancer recurrence in patients with colon cancer.

Abstract: The present invention relates to a kit comprising a DNA-dependant DNA polymerase and at least one natural deoxynucleoside and to a kit comprising a DNA-dependent DNA polymerase and a detection system comprising a DNA template molecule, a DNA primer molecule, and a fluorescent moiety capable of being displaced from, or bound to, dsDNA synthesized by said DNA-dependent polymerase.

Abstract: Described herein are methods, compositions and kits for identifying modifications that could lead to false positive detections in nucleic acid sequencing. In some embodiments, the methods, compositions and kits provided herein are useful for reducing potential of false positive detection of variants caused by errors during sample preparation or sequencing.

Abstract: Methods of testing HIV viral load are described. The methods comprise detecting HIV viral RNA in a sample of leukocyte-depleted blood. Such methods can be carried out on low-volume samples obtained without the need for venipuncture or a centrifuge. The methods are particularly suited for HIV viral load testing in resource-limited settings. Methods for monitoring HIV infection are also described, as well as kits for carrying out the methods.

Abstract: A method for the integrated and automated analysis of DNA or protein, including a single-use cartridge, with an analysis device having a control device, and devices for capturing and processing signals, the control device carrying out a completely automatic process and evaluation of molecular diagnostic analysis via single-use cartridges (Lab-on-a-Chip). Controlling of an analysis process, which occurs in the cartridge, involve the subsequent displacement and thermostatisation of liquids with a first device, and with a second device the signals which are obtained during the analysis are processed. The first and the second devices are synchronized in such a manner that the analysis process of the sample can be carried out in a totally integrated manner thus producing an immediate result.

Abstract: Disclosed is nucleic acid preserving compositions and methods of manufacturing and using the same. Compositions include a carrier, a chaotropic agent, a buffering agent, a chelating agent, a surfactant, an alcohol, an acid, and a mucolytic agent. Compositions as aqueous solutions can include water as a carrier. Preferred embodiments include water, guanidine thiocyanate, Tris, EDTA, SLS, SDA 3C, HCl, and N-acetyl-L-cysteine. Some embodiments include a colored dye as a visual indicator. Methods of manufacturing include combining the components into a mixture, such as an aqueous solution. Methods of use include providing a biological sample that includes nucleic acid and contacting the biological sample with the composition. Kits include the composition disposed in a portion of a biological sample collection apparatus.