Abstract: 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.

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: 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: 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: 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 a method for detecting the presence of one or more methylation patterns. It comprises the conversion of nucleic acids and a catalytic nucleic acid activity. Here, the conversion of the nucleic acid is characterized such that the 5-methylcytosine remains unchanged while the unmethylated cytosine is converted into uracil or another base, which can be distinguished from cytosine in its base-pairing behavior.

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.

Abstract: Aspects of the present invention relate to compositions and methods of identifying at least one biological sample in the field of methylation analysis. In particular aspects at least one biological sample is provided, at least one identifier is applied for each sample, the applied identifier(s) are detected or quantified, and the methylation analysis is performed. Additional aspects provide a methods for testing an experimental procedure. Additional aspects provide kits suitable for realizing the aspects of the invention.

Abstract: A method is described for the detection of 5-methylcytosine in genomic DNA samples. First, a genomic DNA from a DNA sample is chemically converted with a reagent, whereby 5-methylcytosine and cytosine react differently. Then the pretreated DNA is amplified with the use of a polymerase with primers of different sequence. In the next step, the amplified genomic DNA is hybridized to an oligonucleotide array and PCR products are obtained, which must be provided with a label. Alternatively, the PCR products can be extended in a primer extension reaction, wherein the extension products are also provided with a label. In the last step, the extended oligonucleotides are investigated for the presence of the label.

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: A method is described for distinguishing 5-position methylation changes of cytosine bases and cytosine-to-thymine mutations and for the detection of single nucleotide polymorphisms (SNPs) or point mutations in genomic DNA, in which: a) a genomic DNA sample is treated with sulfite or disulfite in such a way that all of the cytosine bases that are not methylated in the 5-position of the base are changed in such a way that a base is formed that is different in its base-pairing behavior, whereas the cytosines methylated at the 5-position remain unchanged, and b) an aliquot of the same genomic DNA sample is quantitatively methylated with Sss1 or another methyltransferase prior to the chemical treatment according to a) and c) both of the DNA samples treated in this way are investigated for the presence of cytosine by means of the same analytical method, and d) the cytosine positions that are determined are matched with a reference DNA sequence.

Abstract: The present invention concerns a method for the detection of cytosine methylation in DNA samples, wherein the following steps are conducted: (a) a genomic DNA sample, which comprises the DNA to be investigated and background DNA, is chemically treated in such a way that all of the unmethylated cytosine bases are converted to uracil, whereas the 5-methylcytosine bases remain unchanged; (b) the chemically treated DNA sample is amplified with the use of at least 1 primer oligonucleotide as well as a polymerase, whereby the DNA to be investigated is preferred as the template over the background DNA, and (c) the amplified products are analyzed and the methylation status in the DNA to be investigated is concluded from the presence of an amplified product and/or from the analysis of additional positions.

Abstract: Chemically modified genomic sequences of genes associated with gene regulation, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genes associated with gene regulation which are directed against the sequence are disclosed. In addition, a method for ascertaining genetic and/or epigenetic parameters of genes associated with gene regulation is disclosed.

Abstract: A method is described for distinguishing 5-position methylation changes of cytosine bases and cytosine-to-thymine mutations and for the detection of single nucleotide polymorphisms (SNPs) or point mutations in genomic DNA, in which: a) a genomic DNA sample is treated with sulfite or disulfite in such a way that all of the cytosine bases that are not methylated in the 5-position of the base are changed in such a way that a base is formed that is different in its base-pairing behavior, whereas the cytosines methylated at the 5-position remain unchanged, and b) an aliquot of the same genomic DNA sample is quantitatively methylated with Sss1 or another methyltransferase prior to the chemical treatment according to a) and c) both of the DNA samples treated in this way are investigated for the presence of cytosine by means of the same analytical method, and d) the cytosine positions that are determined are matched with a reference DNA sequence.

Abstract: The invention describes a set of oligonucleotides as probes for the detection of relevant variations of DNA methylation in a target group of genes, the use thereof for the detection of gene variants with respect to DNA methylation, a medical device which uses a set of oligonucleotides, a method for investigating the methylation state of an individual as well as a method for creating a model for evaluating the probability of occurrence of a health problem of an individual.

Abstract: A method is described for the relative quantification of the methylation of cytosine bases in DNA samples, wherein the following method steps are conducted: a) a genomic DNA sample is chemically converted with a reagent, wherein 5-methylcytosine and cytosine react differently and show a different base pairing behavior in the DNA duplex after the reaction; b) the DNA sample is amplified, whereby a fluorescently labeled dCTP or dGTP derivative is added; c) the amplified products are separated spatially from each other; and d) the fluorescence of the separated amplified products is measured quantitatively.

Abstract: The present invention concerns a method for the detection of cytosine methylation in DNA samples, in which the following steps are conducted: a genomic DNA sample which comprises target DNA and background DNA is chemically treated such that all unmethylated cytosine bases are converted to uracil, while the 5-methylcytosine bases remain unchanged; the chemically treated DNA sample is amplified with the use of at least 2 primer oligonucleotides as well as a polymerase and a nucleotide mixture, the composition of which leads to a preference for the target DNA over the background DNA as the template; and the methylation state in the target DNA is concluded from the presence of an amplificate or its quantity.

Abstract: A method is described for the detection of 5-methylcytosine in genomic DNA samples. First, a genomic DNA from a DNA sample is chemically converted with a reagent, whereby 5-methylcytosine and cytosine react differently. Then the pretreated DNA is amplified with the use of a polymerase with primers of different sequence. In the next step, the amplified genomic DNA is hybridized to an oligonucleotide array and PCR products are obtained, which must be provided with a label. Alternatively, the PCR products can be extended in a primer extension reaction, wherein the extension products are also provided with a label. In the last step, the extended oligonucleotides are investigated for the presence of the label.

Abstract: 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 contacing 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 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.