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, 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.

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: 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.

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, 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.

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, 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.

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 the analysis of cytosine methylations in DNA is described. Here, the DNA to be investigated is first chemically or enzymatically converted. Then a promoter is introduced into the DNA. After this, the DNA is converted to RNA. The methylation pattern of the DNA can be concluded in different ways by means of an analysis of the RNA. The RNA is preferably fragmented chemically or enzymatically prior to the analysis, whereby the fragmenting results depend on the methylation pattern of the DNA. The method according to the invention is particularly suitable for the diagnosis and prognosis of cancer disorders and other diseases associated with a modification of the methylation pattern.

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: 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: 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: Particular aspects of the present invention provide a method for quantification of two different variations of a DNA sequence. Particularly, the invention relates to a quantification of methylated DNA, and for this purpose, the test DNA is converted so that cytosine is converted to uracil, while 5-methylcytosine remains unchanged. The converted DNA is amplified by means of a real-time PCR, wherein two labeled real-time probe types are utilized: one specific for methylated DNA; and one for unmethylated DNA. Preferably, the degree of methylation of the test DNA is calculated from the ratio of the signal intensities of the probes or from the Ct values. The inventive methods have substantial utility for diagnosis and prognosis of cancer and other disorders associated with altered or characteristic DNA methylation status, as well as having substantial utility for analysis of SNPs, allelic expression, and prediction of drug response, drug interactions, among other uses.

Abstract: The present invention relates to promoters which permit a caryopsis-specific expression or suppression of genes in genetically modified plants, to methods for the tissue-specific gene expression or gene suppression in plants, expression cassettes, recombinant vectors and host cells containing such promoters, to transgenic plant cells and plants transformed with said promoters, and to methods for generating such plant cells and plants.

Abstract: The present invention provides promoters which bring about a caryopsis-specific expression of coding nucleotide sequences controlled by them, and to expression cassettes, recombinant vectors and host cells containing such promoters. Transformed transgenic plant cells and plants and methods for generating them, are also described.

Abstract: The present invention relates to promoters which permit a caryopsis-specific expression or suppression of genes in genetically modified plants, to methods for the tissue-specific gene expression or gene suppression in plants, expression cassettes, recombinant vectors and host cells containing such promoters, to transgenic plant cells and plants transformed with said promoters, and to methods for generating such plant cells and plants.

Abstract: The present invention provides promoters which bring about a caryopsis-specific expression of coding nucleotide sequences controlled by them, and to expression cassettes, recombinant vectors and host cells containing such promoters. Transformed transgenic plant cells and plants and methods for generating them, are also described.