Epigenomics AG Patent applications |
Patent application number | Title | Published |
20150031021 | METHODS AND NUCLEIC ACIDS FOR DETERMINING THE PROGNOSIS OF A CANCER SUBJECT - The invention provides methods, nucleic acids and kits for determining the prognosis of a subject having cancer. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients. | 01-29-2015 |
20140295445 | Method for the Carry-Over Protection in DNA Amplification Systems Targeting Methylation Analysis Achieved by a Modified Pre-Treatment of Nucleic Acids - Particular aspects provide methods for specific amplification of template DNA in the presence of potentially contaminating PCR products from previous amplification experiments. Particular embodiments comprise, in a first step, contacting DNA with a bisulfite solution, which sulfonates unmethylated (but not methylated) cytosines, resulting in cytosine deamination and generation of sulfonated uracil. Such sulfonation protects the template nucleic acid from being a target for the enzyme uracil-DNA-glycosylase (UNG), whereas any contaminating DNA, which contains unprotected unsulfonated or desulfonated uracils, is degraded enzymatically while the UNG is active. After UNG treatment and inactivation thereof, the sulfonated uracil bases are converted into uracil by desulfonation. Such aspects have substantial utility for decontamination of nucleic acid samples; e.g., for avoiding amplification of ‘carry over products’ in the context of DNA methylation analysis. In further aspects, the inventive methods can be generally used as simplified methods of bisulfite treatment. | 10-02-2014 |
20140179563 | Method and Nucleic Acids for the Analysis of Colorectal Cell Proliferative Disorders - The invention provides methods and nucleic acids for detecting, differentiating or distinguishing between colon cell proliferative disorders as well as therapy thereof by analysis of the gene EYA4 and its promoter and regulatory sequences. The invention further provides novel nucleic acid sequences useful for the cell proliferative disorder specific analysis of said gene as well as methods, assays and kits thereof. | 06-26-2014 |
20140087449 | 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, and 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. | 03-27-2014 |
20130190205 | 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. | 07-25-2013 |
20120258454 | Bisulfite conversion of DNA - The present invention relates to an improved method for the bisulfite conversion of DNA. In certain time-temperature ranges the efficacy of the bisulfite conversion is clearly improved. By combination with denaturating solvents, new reaction conditions and new purification methods the efficacy can be further increased The converted DNA can subsequently be analysed by different methods. The present invention facilitates the analysis of cytosine methylation. | 10-11-2012 |
20120184455 | Method and Nucleic Acids for the Improved Treatment of Breast Cell Proliferative Disorders - The present invention relates to modified and genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for predicting the response of a subject with a cell proliferative disorder of the breast tissues, to endocrine treatment. | 07-19-2012 |
20120129729 | Method for Determining the Methylation Pattern of a Polynucleic Acid - Particular aspects relate to a method for determining the methylation pattern of a polynucleic acid, comprising: a) preparing a solution comprising a mixture of fragments of the polynucleic acid; b) coupling the fragments with a substance being detectable with a detection method; c) contacting a solution comprising the fragments of b) with a DNA microarray having a plurality of different immobilized oligonucleotides, each comprising at least one methylation site, at respectively assigned different locations thereon, the contacting under conditions affording hybridization of fragments with correlated immobilized oligonucleotides under defined stringency, and wherein the immobilized oligonucleotides have a length of less than 200 bases; d) optionally performing a washing step; and e) detecting, using the physical detection method, such immobilized nucleic acids to which solution fragments are hybridized and/or to which solution fragments are not hybridized. | 05-24-2012 |
20110250601 | 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. | 10-13-2011 |
20110244458 | Methods and Nucleic Acids for Analyses of Cellular Proliferative Disorders - Aspects of the invention provide methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among liver cell proliferative disorders or for detecting, or for detecting and distinguishing between or among colorectal cell proliferative disorders. Particular aspects disclose and provide genomic sequences the methylation patterns of which have substantial utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 10-06-2011 |
20110201005 | Methods and Nucleic Acids for the Detection of Metastasis of Colon Cell Proliferative Disorders - The invention provides methods, nucleic acids and kits for detecting metastasis of colon cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of metastasis of colon cell proliferative disorders, thereby enabling the improved diagnosis and treatment of patients. | 08-18-2011 |
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 |
20110136115 | METHODS AND NUCLEIC ACIDS FOR THE ANALYSIS OF GENE EXPRESSION ASSOCIATED WITH THE DEVELOPMENT OF PROSTATE CELL PROLIFERATIVE DISORDERS - The invention provides methods, nucleic acids and kits for detecting prostate cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients. | 06-09-2011 |
20110104695 | METHODS OF PREDICTING THERAPEUTIC EFFICACY OF CANCER THERAPY - The present invention relates to novel methods and kits for predicting, prognosing, and/or monitoring therapeutic efficacy of cancer therapy on a subject having malignant tumor or cell proliferative disorder. | 05-05-2011 |
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 |
20110046005 | METHOD AND NUCLEIC ACIDS FOR THE ANALYSIS OF COLON CELL PROLIFERATIVE DISORDERS - Provided are methods and nucleic acids for detecting, differentiating or distinguishing between colon cell proliferative disorders by analysis of one or more of the genes Versican, TPEF, H-Cadherin, Calcitonin, and EYA4. Further provided are novel nucleic acid sequences useful for the cell proliferative disorder specific analysis of said genes as well as methods, assays and kits thereof. | 02-24-2011 |
20110039719 | METHODS AND NUCLEIC ACIDS FOR THE ANALYSES OF CELLULAR PROLIFERATIVE DISORDERS - The invention provides methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among liver cell proliferative disorders or for detecting, or for detecting and distinguishing between or among colorectal cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 02-17-2011 |
20110027789 | METHODS FOR PRESERVATION OF GENOMIC DNA SEQUENCE COMPLEXITY - The present invention relates to methods and kits for preserving genomic DNA sequence complexity within chemically and/or enzymatically converted DNA by an enzyme or series of enzymes that adds a methyl group to a cytosine outside of CpG dinucleotide sequences of genomic DNA. Further, the present invention relates to methylation analysis of the genomic DNA. | 02-03-2011 |
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 |
20100184027 | METHODS AND NUCLEIC ACIDS FOR ANALYSES OF CELLULAR PROLIFERATIVE DISORDERS - The invention provides methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 07-22-2010 |
20100143902 | METHODS AND NUCLEIC ACIDS FOR ANALYSES OF CELLULAR PROLIFERATIVE DISORDERS - The invention provides methods, nucleic acids and kits for detecting colorectal cell proliferative disorders based on underexpression or methylation of a least one gene selected from RASSF2, TFAP2E, SND1, PCDHGC3, EDNRB, STOM, GLI3, RXFP3, LimK1, GPR73L1, PCDH1O, DOCKIO and MRPS21, and optionally Septin-9. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 06-10-2010 |
20100092953 | METHODS AND NUCLEIC ACIDS FOR ANALYSES FOR CELLULAR PROLIFERATIVE DISORDERS - The invention provides methods, nucleic acids and kits for detecting a cell proliferative disorder. The invention discloses genomic sequences of RASSF-2 the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients. | 04-15-2010 |
20100035242 | Methods and nucleic acids for the detection of metastasis of colon cell proliferative disorders - The invention provides methods, nucleic acids and kits for detecting metastasis of colon cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of metastasis of colon cell proliferative disorders, thereby enabling the improved diagnosis and treatment of patients. | 02-11-2010 |
20090317810 | METHODS AND NUCLEIC ACIDS FOR THE DETECTION OF COLORECTAL CELL PROLIFERATIVE DISORDERS - The invention provides methods, nucleic acids and kits for detecting, or for distinguishing between or among colorectal cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 12-24-2009 |
20090298054 | Epigenetic methods and nucleic acids for the detection of breast cell proliferative disorders - The present application provides methods and nucleic acids for the detection and differentiation of breast cell proliferative disorders. This is achieved by the analysis of the methylation of a panel of genes, or subsets thereof. The invention may be used for the detection and/or differentiation of a variety of tissue types including breast cancer and benign breast disorders as well as other cancers and tissue types. | 12-03-2009 |
20090269736 | Prognostic markers for prediction of treatment response and/or survival of breast cell proliferative disorder patients - Aspects of the present invention provide compositions and methods for prognosis of, and/or predicting the estrogen treatment outcome of breast cell proliferative disorder patients, and in particular of patients with breast carcinoma. In preferred embodiments, this is achieved, at least in part, by determining the expression level of PITX2, and/or the genetic or the epigenetic modifications of the genomic DNA associated with the gene PITX2. Additional aspects of the invention provide novel sequences, oligomers (e.g., oligonucleotides or peptide nucleic acid (PNA)-oligomers), and antibodies, which have substantial utility in the described inventive methods and compositions. | 10-29-2009 |
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 |
20090203011 | METHODS AND NUCLEIC ACIDS FOR ANALYSES OF CELL PROLIFERATIVE DISORDERS - Particular aspects provide methods, nucleic acids and kits for detecting cell proliferative disorders. Preferred aspects provide genomic sequences, the methylation patterns of which have substantial utility for the improved detection of said disorders, providing for improved diagnosis and treatment of same in patients. | 08-13-2009 |
20090197250 | METHODS AND NUCLEIC ACIDS FOR THE ANALYSIS OF GENE EXPRESSION ASSOCIATED WITH THE PROGNOSIS OF PROSTATE CELL PROLIFERATIVE DISORDERS - Particular aspects provide novel methods and compositions (e.g., nucleic acids, kits, etc.) having substantial utility for providing a prognosis of prostate cell proliferative disorders. In particular aspects, this is achieved by the analysis of the expression status of a panel of genes, or subsets thereof. | 08-06-2009 |
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 |
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 |
20090162836 | Prognostic and Diagnostic Markers for Cell Proliferative Disorders of The Breast Tissues - The present invention relates to prognostic and diagnostic markers for cell proliferative disorders of the breast tissues. The present invention therefore provides methods and nucleic acids for the analysis of biological samples for features associated with the development of breast cell proliferative disorders. Furthermore, the invention provides for prognosis of treatment effects relating to drug therapy, in particular hormonal/antihormonal therapy, chemotherapy and/or adjuvant therapy. | 06-25-2009 |
20090111707 | MARKERS FOR THE PREDICTION OF OUTCOME OF ANTHRACYCLINE TREATMENT - The present invention relates to methods for predicting the outcome of anthracycline treatment of cell proliferative disorder patients. This is achieved by determining the expression level of at least one gene selected from the group consisting of PITX2; TFF1 and PLAU. The invention also relates to sequences, oligonucleotides and antibodies which can be used within the described methods. | 04-30-2009 |
20090075260 | Methods and Nucleic Acids For Analysis of Cellular Proliferative Disorders - Aspects of the invention provide methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among liver cell proliferative disorders or for detecting, or for detecting and distinguishing between or among colorectal cell proliferative disorders. Particular aspects disclose and provide genomic sequences the methylation patterns of which have substantial utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 03-19-2009 |
20090047666 | Methods and nucleic acids for the analysis of colon proliferative disorders - The invention provides methods, nucleic acids and kits for detecting colon cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients. | 02-19-2009 |
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 |
20090004646 | Method for Quantifying Methylated Dna - The inventive method makes it possible to quantify methylated DNA by combining the restricted digestion and real-time PCR. For this purpose, the inventive method consists in isolating the examined DNA from a biological sample, in reacting the isolated AND with a methylation specific restriction enzyme, in amplifying by means of a real-time PCR, wherein the amplified products are formed only when the DNA is precut-off and, afterwards, in calculated the methylated and unmethylated DNA proportion in the initial sample with the aid of a reference measurement. Said method is particularly suitable for diagnosis and prognosis cancer and other diseases associated with a methylation state modification and for predicting the drug effects. | 01-01-2009 |
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 |
20080286761 | Methods and Nucleic Acids for the Analysis of Gene Expression Associated with the Development of Prostate Cell Proliferative Disorders - The following application provides methods and nucleic acids for the detection of and/or differentiation between prostate cell proliferative disorders. This is achieved by the analysis of the expression status of a panel of genes, or subsets thereof. | 11-20-2008 |
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 |
20080254447 | Method and Nucleic Acids for the Improved Treatment of Breast Cell Proliferative Disorders - The present invention relates to modified and genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for predicting the disease free survival and/or response of a subject with a cell proliferative disorder of the breast tissues, to endocrine treatment. | 10-16-2008 |