Abstract: The present invention relates to methods and kits for identifying, diagnosing, prognosing, and monitoring cervical cancer. These methods include determining the methylation status or the expression levels of particular genes, or a combination thereof.

Abstract: Using a combination of analytic methods epigenetic silencing of markers in cancer have been determined. The cancers are generally those of the gastrointestinal tract including but not limited to esophageal, head and neck, gastric, pancreas, liver, and colon. The genes can be used for the early detection of cancer or can be used to identify adenomas that will likely progress to carcinomas. Therapeutic regimens based on the epigenetic silenced genes can be chosen and/or monitored. Kits for evaluating epigenetic silencing of these genes can be used for detection and monitoring.

Abstract: A real-time method of detecting the presence and/or amount of a methylated or unmethylated gene of interest in a DNA-containing sample, comprises the steps of: (a) contacting the DNA-containing sample with a reagent which selectively modifies unmethylated cytosine residues in the DNA to produce detectable modified residues but which does not modify methylated cytosine residues (b) amplifying at least a portion of the methylated or unmethylated gene of interest using at least one primer pair, at least one primer of which is designed to bind only to the sequence of methylated or unmethylated DNA following treatment with the reagent, wherein at least one primer in the primer pair is a primer containing a step loop structure carrying a donor and an acceptor moiety of a molecular energy transfer pair arranged such that in the absence of amplification, the acceptor moiety quenches fluorescence emitted by the donor moiety upon excitation and during amplification, the stem loop structure is disrupted so as to separat

Abstract: Methods and tools are provided for detecting and predicting lung cancer. The methods and tools are based on epigenetic modification due to methylation of genes in lung cancer or pre-lung cancer. The tools can be assembled into kits or can be used seperately. Genes found to be epigentically silenced in association with lung cancer include ACSL6, ALS2CL, APC2, ART-S1, BEX1, BMP7, BNIP3, CBR3, CD248, CD44, CHD5, DLK1, DPYSL4, DSC2, EDNRB, EPB41L3, EPHB6, ERBB3, FBLN2, FBN2, FOXL2, GNAS, GSTP1, HS3ST2, HPN, IGFBP7, IRF7, JAM3, LOX, LY6D, LY6K, MACF1, MCAM, NCBP1, NEFH, NID2, PCDHB15, PCDHGA12, PFKP, PGRMC1, PHACTR3, PHKA2, POMC, PRKCA, PSEN1, RASSF1A, RASSF2, RBP1, RRAD, SFRP1, SGK, SOD3, SOX17, SULF2, TIMP3, TJP2, TRPV2, UCHL1, WDR69, ZFP42, ZNF442, and ZNF655.

Abstract: Methods and kits for diagnosing and/or monitoring the progression of or otherwise staging a disease caused by a human papillomavirus (HPV) infection in a test sample obtained from a subject comprise determining the methylation status of a HPV genome. The presence of hypermethylation of the HPV genome indicates a positive diagnosis of the disease and/or an increased level of methylation of the HPV genome indicates the progression of the disease to a more advanced form. Suitable diseases linked to HPV infection include cancers such as cervical cancer. High risk HPV types such as HPV16 are generally assessed in the methods and using the kits of the invention. The HPV16 methylome is provided.

Abstract: An oligonucleotide, primer or probe comprises the nucleotide sequences of any of SEQ ID NO. 5, 6, 7, 2, 3, 4, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 25. The oligonucleotides are useful for the detection of the methylation status of a gene, in particular the MAGE-A3 gene. The oligonucleotides are useful in primer pairs, kits and methods for determining the methylation status of the MAGE-A3 gene and for diagnosing cancer, directing therapy and selecting subjects for treatment. The primer or probe can comprise a loop or hairpin structure and can be used in real-time methylation specific PCR.

Abstract: A method of detecting a predisposition to, or the incidence of, bladder cancer in a sample comprises detecting an epigenetic change in at least one gene selected from TWIST1, NID2, RUNX3, BMP7, CCNA1, PDLIM4, TNFRSF25, APC, RASSF1A, LOXL1, TUBB4, NTRK2, ARFGAP3, OSMR and TJP2. Detection of the epigenetic change is indicative of a predisposition to, or the incidence of, bladder cancer. The gene may be TWIST1 or a panel of genes such as TWIST1, NID2 and RUNX3 may be screened. The epigenetic change may be methylation. A kit for detecting a predisposition to, or the incidence of, bladder cancer in a sample comprises at least one primer pair for determining the methylation status of each of NID2, TWIST1 and RUNX3. A kit for detecting a predisposition to, or the incidence of, bladder cancer in a sample comprises means for detecting an epigenetic change in at least one gene selected from TWIST1, NID2, RUNX3, BMP7, CCNA1, PDLIM4, TNFRSF25, APC, RASSF1A, LOXL1, TUBB4, NTRK2, ARFGAP3, OSMR and TJP2.

Abstract: A method of detecting a predisposition to, or the incidence of, cancer in a sample comprises detecting an epigenetic change in at least one gene selected from an NDRG4/NDRG2 subfamily gene, GATA4, OSMR, GATA5, SFRP1, ADAM23, JPH3, SFRP2, APC, MGMT, 11112, BNIP3, FOXE1, SYNE1, S0X17, PHACTR3 and JAM3, wherein detection of the epigenetic change is indicative of a predisposition to, or the incidence of, cancer. Also described are pharmacogenetic methods for determining suitable treatment regimens for cancer and methods for treating cancer patients, based around selection of the patients according to the methods of the invention. The present invention is also concerned with improved methods of collecting, processing and analyzing samples, in particular body fluid samples. These methods may be useful in diagnosing, staging or otherwise characterizing various diseases.

Abstract: Two hundred ten markers are provided which are epigenetically silenced in one or more cancer types. The markers can be used diagnostically, prognostically, therapeutically, and for selecting treatments that are well tailored for an individual patient. Restoration of expression of silenced genes can be useful therapeutically, for example, if the silenced gene is a tumor-suppressor gene. Restoration can be accomplished by supplying non-methylated copies of the silenced genes or polynucleotides encoding their encoded products. Alternatively, restoration can be accomplished using chemical demethylating agents or methylation inhibitors. Kits for testing for epigenetic silencing can be used in the context of diagnostics, prognostics, or for selecting “personalized medicine” treatments.

Abstract: Two hundred ten markers are provided which are epigenetically silenced in one or more cancer types. The markers can be used diagnostically, prognostically, therapeutically, and for selecting treatments that are well tailored for an individual patient. Restoration of expression of silenced genes can be useful therapeutically, for example, if the silenced gene is a tumor-suppressor gene. Restoration can be accomplished by supplying non-methylated copies of the silenced genes or polynucleotides encoding their encoded products. Alternatively, restoration can be accomplished using chemical demethylating agents or methylation inhibitors. Kits for testing for epigenetic silencing can be used in the context of diagnostics, prognostics, or for selecting “personalized medicine” treatments.

Abstract: Two hundred ten markers are provided which are epigenetically silenced in one or more cancer types. The markers can be used diagnostically, prognostically, therapeutically, and for selecting treatments that are well tailored for an individual patient. Restoration of expression of silenced genes can be useful therapeutically, for example, if the silenced gene is a tumor-suppressor gene. Restoration can be accomplished by supplying non-methylated copies of the silenced genes or polynucleotides encoding their encoded products. Alternatively, restoration can be accomplished using chemical demethylating agents or methylation inhibitors. Kits for testing for epigenetic silencing can be used in the context of diagnostics, prognostics, or for selecting “personalized medicine” treatments.

Abstract: Twenty-three markers are provided which are epigenetically silenced in ovarian cancers. The markers can be used diagnostically, prognostically, therapeutically, and for selecting treatments that are well tailored for an individual patient. Restoration of expression of silenced genes can be useful therapeutically, for example, if the silenced gene is a tumor-suppressor gene. Restoration can be accomplished by supplying non-methylated copies of the silenced genes or polynucleotides encoding their encoded products. Alternatively, restoration can be accomplished using chemical demethylating agents or methylation inhibitors. Kits for testing for epigenetic silencing can be used in the context of diagnostics, prognostics, or for selecting “personalized medicine” treatments.

Abstract: Genes for thirteen DNA damage repair or DNA damage response enzymes can be epigenetically silenced in cancers. The silencing of nucleic acids encoding a DNA repair or DNA damage response enzyme can be used prognostically and for selecting treatments that are well tailored for an individual patient. Combinations of these markers can also be used to provide prognostic information. Kits for testing epigenetic silencing can be used to determine a prognosis or a therapeutic regimen.

Abstract: We have developed a transcriptome-wide approach to identify genes affected by promoter CpG island hypermethylation and transcriptional silencing in colorectal cancer (CRC). By screening cell lines and validating tumor specific hypermethylation in a panel of primary human CRC samples, we estimate that nearly 5% of all known genes may be promoter methylated in an individual tumor. When directly compared to gene mutations, we find a much larger number of genes hypermethylated in individual tumors, and much higher frequency of hypermethylation within individual genes harboring either genetic or epigenetic changes. Thus, to enumerate the full spectrum of alterations in the human cancer genome, and facilitate the most efficacious grouping of tumors to identify cancer biomarkers and tailor therapeutic approaches, both genetic and epigenetic screens should be undertaken. The genes we identified can be used inter alia diagnostically to detect cancer, pre-cancer, and likelihood of developing cancer.