| Patent application number | Description | Published |
|---|
| 20080206760 | Method for detecting DNA methylation using labelled S-adenosylmethionine analogs - The invention relates to a method for detecting the methylation status in DNA samples. According to the invention, a DNA methyl transferase and a labeled S-adenosylmethionine derivative allow a detectable label to be covalently bonded to the DNA, in accordance with the respective methylation status of the DNA sample. | 08-28-2008 |
| 20080220418 | Method For Providing Dna Fragments Derived From An Archived Sample - Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, an are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable. | 09-11-2008 |
| 20080254470 | Methods and Nucleic Acids For the Analysis of Gene Expression Associated With the Prognosis of Cell Proliferative Disorders - The present application provides methods and nucleic acids for providing a prognosis of cell proliferative disorders, most preferably cancer but not breast cancer. | 10-16-2008 |
| 20080311627 | Compositions and Methods for Preventing Carry-Over Contamination in Nucleic Acid Amplification Reactions - Particular aspects provide methods for the specific amplification of template DNA in the presence of potentially contaminating PCR products from previous amplification experiments, but wherein the contaminating prior reaction amplificates (carry-over contaminants) are rendered non-amplifiable, based on use of particular contaminant degradation enzymes, and use of at least one primer that is fully complementary to any contaminating prior reaction amplificate nucleic acid, but contains a mismatch with the correspond sequence of the sample template nucleic acid. Additional aspects provide a method for the specific amplification of single-stranded sample template DNA in the presence of potentially double-stranded carry-over products. Further aspects provide methods comprising use of a template-dependent thermostable DNA polymerase enzyme suitable for incorporating ribonucleotides as well as deoxy-nucleotides to provide a chimeric amplificate. After digestion with an RNase, any contaminating prior chimeric amplificate, the RNase is inactivated. These aspects are surprisingly effective alternatives to the carry over protection system known as UNG system, and other art-recognized methods. | 12-18-2008 |
| 20090005268 | Compositions and Methods for Cancer Diagnostics Comprising Pan-Cancer Markers - The present invention relates to compositions and methods for cancer diagnostics, including but not limited to, so-called “pan cancer markers”. In particular, the present invention provides methods of identifying methylation patterns in genes associated with specific cancers, and their related uses. In another aspect, the present invention provides methods of selecting and combining useful sets of pan cancer markers. | 01-01-2009 |
| 20090170089 | METHODS AND COMPOSITIONS FOR DIFFERENTIATING TISSUES OR CELL TYPES USING EPIGENETIC MARKERS - The present invention provides, inter alia, a method for generating a genome-wide epigenomic map, comprising a correlation between methylation variable CpG positions (MVP) and genomic DNA sample types. MVP are those CpG positions that show a variable quantitative level of methylation between sample types. Particular genomic regions of interest (ROI) provide preferred marker sequences that comprise multiple, and preferably proximate MVP, and that have novel utility for distinguishing sample types. The epigenic maps have broad utility, for example, in identifying sample types, or for distinguishing between and among sample types. In a preferred embodiment the epigenomic map is based on methylation variable regions (MVP) within the major histocompatibility complex (MHC), and has utility, for example, in identifying the cell or tissue source of a genomic DNA sample, or for distinguishing one or more particular cell or tissue types among other cell or tissue types. Analysis of epigenetic characteristics of one, or of a set of nucleic acid sequences, in the context of an inventive epigenomic map, allows for the determination of an origin of the nucleic acids. | 07-02-2009 |
| 20090191548 | METHODS AND NUCLEIC ACIDS FOR THE ANALYSIS OF GENE EXPRESSION ASSOCIATED WITH TISSUE CLASSIFICATION - The present application provides methods and nucleic acids the classification of a biological sample. This is achieved by the analysis of the expression status of at least one of the genes selected from Table 1 as disclosed. | 07-30-2009 |
| 20090208941 | Method for investigating cytosine methylations in dna - A method for sensitive and specific detection of cytosine methylation is described wherein the DNA to be analyzed is subjected to initial enrichment. More specifically, said enrichment can be effected in a methylation-specific, sequence-specific or origin-specific fashion. Thereafter, the enriched DNA is converted in a methylation-specific fashion. The converted DNA can be analyzed using various methods, particularly real-time PCR methods. | 08-20-2009 |
| 20090253584 | Method for the determination of the DNA methylation level of a CPG position in identical cells within a tissue sample - Aspects of the present invention relate to the determination of the DNA methylation level at one or more CpG position within cells of a defined type in a tissue sample. This methylation level is deduced from the total DNA methylation level of all cells of the sample and from the content of said cells of interest. In aspects of the invention, the cell content is determined by means of histopatholoy, staining methods, antibodies, expression analysis or DNA methylation analysis. | 10-08-2009 |
| 20090263810 | BISULFITE CONVERSION OF DNA - The present invention provides an improved method for the bisulfite conversion of DNA, and facilitates the analysis of cytosine methylation of genomic DNA. Novel combinations of denaturing solvents, new reaction conditions and new purification methods provide surprisingly efficacious methods for bisulfite conversion of DNA relative to prior art methods. The converted DNA may subsequently be analyzed by many different methods. | 10-22-2009 |
| 20090280494 | Method for the detection of cytosine methylations in immobilized DNA samples - A method is described for the analysis of cytosine methylation patterns in genomic DNA samples. In the first method step, the genomic DNA is isolated from cells or other accompanying materials and bound essentially irreversibly to a surface. Then the DNA bound to the surface is treated, preferably with a bisulfite, in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged. Then the reagents that were used are removed in a washing step. Finally, selected segments of the immobilized DNA are amplified in a polymerase reaction and the amplified products are investigated with respect to their sequence. | 11-12-2009 |
| 20100143893 | Method for detection of cytosine methylation - Herein described is a method for the detection of cyto-sine methylation in a nucleic acid sample, comprising the steps of: a) treating a nucleic acid sample with an agent convert-ing unmethylated cytosine bases into uracil bases and not converting methylated cytosine bases within said nucleic acid sample, b) amplifying selected segments of the treated nucleic acid sample, by providing two first oligonucleotide primers (A and B) that are capable of producing an amplificate under certain chosen amplification conditions inde-pendently of the methylation status of the nucleic acid before treatment in step a), and further providing at least two additional second oligonucleotide primers (C and D) that can each produce a product with one of the first primers (A or B) under said same amplification conditions, wherein at least one of the second primers binds to the nucleic acid in a methylation specific manner, thereby distinguishing between unconverted initially methylated and converted unmethylated nucleic acids and/or blocking molecules are provided that hinder the binding of at least one of the second primers to the nucleic acid in a methylation specific manner, thereby distinguishing between unconverted initially methylated and converted unmethylated nucleic acids, c) detecting the amplificates of the treated nucleic acid. | 06-10-2010 |
| 20100233722 | Methods for determining the biological effect and/or activity of r pharmaceutical compositions based on their effect on the methylation status of the DNA - This invention is related to methods, systems and computer program products for determining the biological effect and/or activity of drugs, chemical substances and/or pharmaceutical compositions using their effect on DNA methylation as a marker for their biological effect(s). The invention is further related to the use of the inventive methods, systems and computer program products in obtaining new biologically active compounds for new and effective medicaments and treatment strategies of, in particular, human diseases. | 09-16-2010 |
| 20110059432 | METHOD FOR PROVIDING DNA FRAGMENTS DERIVED FROM A REMOTE SAMPLE - Aspects of the present invention relate to compositions and methods for providing DNA fragments from a remote sample. In particular aspects a remote sample comprising DNA is provided, DNA is isolated from the remote sample, and the isolated DNA is treated in a way which allows differentiation of methylated and unmethylated cytosine. Additional, particular embodiments provide compositions and methods for methylation analysis of DNA derived from a remote sample. Other aspects provide for compositions and methods of whole genome amplification of bisulfite treated DNA. | 03-10-2011 |
| 20110136687 | METHOD FOR DETERMINING THE DEGREE OF METHYLATION OF DEFINED CYTOSINES IN GENOMIC DNA IN THE SEQUENCE CONTEXT OF 5'-CpG-3' - A method is described for the detection of the degree of methylation of a specific cytosine in the sequence context 5′-CpG-3′ of a genomic DNA sample. In the first step, the genomic DNA is chemically treated in such a way that the cytosine bases are converted to uracil, but not the 5-methylcytosine bases. Then segments of the genomic DNA which contain the said specific cytosine are amplified, whereby the amplified products are given a detectable label and in the following steps the extent of hybridization of the amplified products on two classes of oligonucleotides is determined by detection of the label of the amplified products, and a conclusion is made on the extent of methylation of said specific cytosine in the genomic DNA sample from the ratio of the labels detected on the two classes of oligonucleotides as a consequence of the hybridization. | 06-09-2011 |
| 20110159491 | Method for detecting cytosine methylation in DNA samples - Described is a method for detecting 5-methylcytosine in genomic DNA samples. First, a genomic DNA from a DNA sample is chemically converted with a reagent, 5-methylcytosine and cytosine reacting differently, and the pretreated DNA is subsequently amplified using a polymerase and at least one primer. In the next step, the amplified genomic DNA is hybridized to at least one oligonucleotide, forming a duplex, and said oligonucleotide is elongated by at least one nucleotide, the nucleotide carrying a detectable label, and the elongation depending on the methylation status of the specific cytosine in the genomic DNA sample. In the next step, the elongated oligonucleotides are analyzed for the presence of the label. | 06-30-2011 |
