Abstract: The invention relates to, among others, a method for assessing a prognosis of a patient with a malignant disease and/or for predicting the response of a patient with a malignant disease to immunotherapy. For this purpose, a DNA methylation analysis is carried out on at least one immunoregulatory gene of cells of the malignant disease and/or T lymphocytes which interact with the cells of the malignant disease, said gene coding for an immune checkpoint selected from B7 proteins and the receptors thereof, MHC-peptide complex-binding co-receptors, the members of the tumor necrosis factor receptor superfamily TNFRSF9, CD40, TNFRSF4, TNFRSF18, and CD27, the members of the immunoglobulin superfamily TIGIT, BTLA, HAVCR2, BTNL2 and CD48, and the andenosine-binding adenosine 2A receptor.

Abstract: A method for determining a mutation in genomic DNA is described. The method is characterized in that the mutation analysis is performed with genomic DNA, in which at least a part of the cytosines contained therein has previously been converted into uracil or another base with a base pairing behavior or molecular weight distinguishable from that of cytosine.

Abstract: The invention relates to methods for predicting the response of a patient with a malignant disease to immunotherapy with a pharmaceutical compound that is designed to inhibit an immunoregulatory effect of an immune checkpoint selected from cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and its ligands Cluster of differentiation 80 (CD80) and Cluster of Differentiation 86 (CD86). The methods are based on a DNA methylation analysis of the CTLA4 gene of cells of the malignant disease and/or T lymphocytes interacting with said cells of the malignant disease.

Abstract: The invention relates to, among others, a method for assessing a prognosis of a patient with a malignant disease and/or for predicting the response of a patient with a malignant disease to immunotherapy. For this purpose, a DNA methylation analysis is carried out on at least one immunoregulatory gene of cells of the malignant disease and/or T lymphocytes which interact with the cells of the malignant disease, said gene coding for an immune checkpoint selected from B7 proteins and the receptors thereof, MHC-peptide complex-binding co-receptors, the members of the tumor necrosis factor receptor superfamily TNFRSF9, CD40, TNFRSF4, TNFRSF18, and CD27, the members of the immunoglobulin superfamily TIGIT, BTLA, HAVCR2, BTNL2 and CD48, and the andenosine-binding adenosine 2A receptor.

Abstract: A method for determining a mutation in genomic DNA is described. The method is characterized in that the mutation analysis is performed with genomic DNA, in which at least a part of the cytosines contained therein has previously been converted into uracil or another base with a base pairing behavior or molecular weight distinguishable from that of cytosine.

Abstract: The invention relates to methods for predicting the response of a patient with a malignant disease to immunotherapy with a pharmaceutical compound that is designed to inhibit an immunoregulatory effect of an immune checkpoint selected from cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and its ligands Cluster of differentiation 80 (CD80) and Cluster of Differentiation 86 (CD86). The methods are based on a DNA methylation analysis of the CTLA4 gene of cells of the malignant disease and/or T lymphocytes interacting with said cells of the malignant disease.

Abstract: A method is useful for predicting a response of a malignant disease to an immunotherapy which inhibits the PD-1 immune checkpoint signaling pathway. The method is characterized in that at least a part of an immunoregulatory gene selected from CTLA4, CD86, CD28, CD80 and/or ICOS of cells of the malignant disease and/or of immune cells interacting with cells of the malignant disease is subjected to a DNA methylation analysis, and the result is used to predict the response of the malignant disease to the immunotherapy.

Abstract: 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. Other aspects provide methods for determining the presence or absence of methylation of at least one cytosine, or a series of cytosines in cis, in human DNA of a blood sample, a plasma sample, a serum sample or a urine sample from a human individual.

Abstract: The invention relates to, among others, a method for assessing a prognosis of a patient with a malignant disease and/or for predicting the response of a patient with a malignant disease to immunotherapy. For this purpose, a DNA methylation analysis is carried out on at least one immunoregulatory gene of cells of the malignant disease and/or T lymphocytes which interact with the cells of the malignant disease, said gene coding for an immune checkpoint selected from B7 proteins and the receptors thereof, MHC-peptide complex-binding co-receptors, the members of the tumor necrosis factor receptor superfamily TNFRSF9, CD40, TNFRSF4, TNFRSF18, and CD27, the members of the immunoglobulin superfamily TIGIT, BTLA, HAVCR2, BTNL2 and CD48, and the andenosine-binding adenosine 2A receptor.

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, SNDI, PCDHGC3, EDNRB, STOM, GLI3, RXFP3, LimK1, GPR73L1, PCDH1O, DOCKIO and MRPS21, and optionally Septin-9.

Abstract: The present invention relates to the field of pharmacogenomics and in particular to assessing the response of a cancer patient to a treatment by analysing CpG methylation in the shox2 gene. Depending on the result of the analysis, the treatment can be continued or altered, thereby exploiting the therapeutic window better than conventional methods of assessing a treatment response.

Abstract: Provided herein are methods, nucleic acids and kits for detecting a cell proliferative disorder. Also provided herein are genomic sequences of RASSF?-2, the methylation patterns of which have utility for the improved detection of cell proliferative disorders, thereby enabling the improved diagnosis and treatment of patients.

Abstract: The invention provides methods, nucleic acids and kits for detecting lung carcinoma. 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.

Abstract: The invention provides methods, nucleic acids and kits for determining the prognosis of a subject having cell proliferative disorder, preferably 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.

Abstract: 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.

Abstract: 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.

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: The invention provides methods, nucleic acids and kits for detecting lung carcinoma. 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.

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.