Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

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: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: The present application provides methods and nucleic acids for providing a prognosis of cell proliferative disorders, most preferably cancer but not breast cancer.

Abstract: 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.

Abstract: 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.

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 two oligonucleotides, the latter being joined by inserting at least one oligonucleotide. In the ligation product, one nucleotide carries a detectable label, and the elongation depends 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: The invention provides methods, nucleic acids and kits for detecting, classifying and/or distinguishing between or among lung 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: Chemically modified nucleic acid sequences of genomic DNA, oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA. In addition, a method for ascertaining genetic and/or epigenetic parameters of genes for the characterization, classification, differentiation, grading, staging, treatment and diagnosis of oligodendrogliomas, astrocytomas and oligoastrocytomas.

Abstract: The present invention relates to chemically modified genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for ascertaining genetic and/or epigenetic parameters of genes for use in characterisation, classification, differentiation, diagnosis and therapy of prostate lesions.

Abstract: Chemically modified genomic sequences, oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA. In addition, a method for ascertaining genetic and/or epigenetic parameters of genes for use in the characterization, classificaiton, differrentiation, grading, staging, treatment and/or diagnosis of astrocytomas, or the predisposition to astrocytomas.