Abstract: 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.

Abstract: 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.

Abstract: A method is described for the amplification of nucleic acids, in which the segments to be amplified are first hybridized with at least two primer oligonucleotides that have two domains, wherein the sequence-specific domain found at the 3-end hybridizes to the segment to be amplified, while the generic domain found at the 5-end does not hybridize. Then an amplification reaction is conducted by means of a polymerase and subsequently a labeled primer oligonucleotide, which binds to the generic domain of the first primer, is hybridized to the amplificate which is formed. In the last step, the sequence of the amplificate is investigated.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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 which can be used as so-called “lead”-compounds for new and effective medicaments and treatment strategies of, in particular, human diseases.

Abstract: 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.

Abstract: 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.

Abstract: The following invention concerns a method for investigating cytosine methylation by means of DNA repair enzymes. Here, the DNA is first converted so that unmethylated cytosines are converted to uracil, while 5-methylcytosine remains unchanged. Then the DNA is hybridized to oligonucleotides, whereby hybrids will be formed with or without erroneous base pairings, in each case depending on the methylation status of the DNA. Following this, the erroneously paired hybrids will be cleaved by repair enzymes. Then the methylation status of the DNA can be determined in different ways. The method according to the invention is particularly suitable for the diagnosis and prognosis of cancer disorders and other diseases associated with a change of the methylation status as well as for predicting undesired drug effects.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.