Abstract: The present invention relates to methods, devices, combinations, kits, and systems for predicting and treating clinically significant prostate cancer in a urine sample of an individual suspected of suffering from prostate cancer based on expression analysis of normalised prostate tumour markers. The present methods, devices, combinations, kits, and systems are especially suitable for predicting and treating prostate cancer with a Gleason score of seven or more in individuals with a serum prostate-specific antigen (sPSA) level lower than 15 ng/ml.

Abstract: The present invention relates to methods, devices, combinations, kits, and systems for predicting and treating clinically significant prostate cancer in a urine sample of an individual suspected of suffering from prostate cancer based on expression analysis of normalised prostate tumour markers. The present methods, devices, combinations, kits, and systems are especially suitable for predicting and treating prostate cancer with a Gleason score of seven or more in individuals with a serum prostate-specific antigen (sPSA) level lower than 15 ng/ml.

Abstract: Disclosed are methods and systems for detecting methylation of the promoter of O-6-methylguanine-DNA methyltransferase gene (MGMT). In particular, the methods and systems may be utilized to detect methylation in the MGMT promoter in a DNA sample from a glioblastoma and optionally in order to predict whether a subject having the glioblastoma will respond to treatment with an alkylating agent. The methods and systems typically include a step of deep-sequencing the DNA sample after the DNA sample has been treated with a reagent that converts unmethylated cytosine to uracil such as a bisulfite reagent.

Abstract: The present invention relates to methods, devices, combinations, kits, and systems for predicting and treating clinically significant prostate cancer in a urine sample of an individual suspected of suffering from prostate cancer based on expression analysis of normalised prostate tumour markers. The present methods, devices, combinations, kits, and systems are especially suitable for predicting and treating prostate cancer with a Gleason score of seven or more in individuals with a serum prostate-specific antigen (sPSA) level lower than 15 ng/ml.

Abstract: Disclosed are methods for determining one or more nucleotides at one or more nucleotide positions of a polynucleotide sample, the polynucleotide sample comprising heterogeneous polynucleotides having different nucleotides at the nucleotide positions. The disclosed methods may be utilized to control for sequencing bias during sequencing of the polynucleotide sample. Suitable samples may include patient samples for use in diagnosing, prognosing, and treating the patient.

Abstract: Disclosed are methods for determining the methylation status of the promoter region of the TWIST1 gene in genomic DNA from bladder cells, including bladder cells present in a urine sample. Also disclosed are kits for performing the disclosed methods, such as kits for determining the methylation status of the promoter region of the TWIST1 gene comprising at least one primer pair for determining the methylation status of TWIST1. The kits may contain means for processing a urine sample.

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 produces a detectable fluorescence signal during amplification which is detected in real-time (c) quantifying the results of the real-time detection against a standard curve for the methylated or unmethylated gene of interest to produce an output of gene copy number.

Abstract: Disclosed are methods for assessing the methylation and mutation status of nucleic acid in a sample. The methods provide for methylation-dependent modification of the nucleic acid in a sample, and subsequently nucleic acid amplification processes to distinguish between mutated and non-mutated target sequence.

Abstract: Disclosed are methods for determining the methylation status of the promoter region of the TWIST1 gene in genomic DNA from bladder cells, including bladder cells present in a urine sample. Also disclosed are kits for performing the disclosed methods, such as kits for determining the methylation status of the promoter region of the TWIST1 gene comprising at least one primer pair for determining the methylation status of TWIST1. The kits may contain means for processing a urine sample.

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 FOXE1 and GATA4. Detection of the epigenetic change is indicative of a predisposition to, or the incidence of, bladder cancer. The sample comprises nucleic acid molecules from bladder cells. The methods may be used to select treatments and patients for treatment. Related kits include primers allowing the methylation status of the genes to be determined.

Abstract: A method of detecting a predisposition to, or the incidence of, colorectal cancer in a fecal sample comprises, in a first step (a), detecting the presence of blood in the fecal sample, wherein detection of the presence of blood is indicative of a predisposition to, or the incidence of, colorectal cancer. The method additionally comprises, in second step (b), detecting an epigenetic modification in the DNA contained within the fecal sample, wherein detection of the epigenetic modification is indicative of a predisposition to, or the incidence of, colorectal cancer. Based upon a positive result obtained in either (a) or (b) or in both (a) and (b) a predisposition to, or the incidence of, colorectal cancer is detected. Related methods and kits involve detecting an epigenetic modification in a number of specific genes.

Abstract: Disclosed are methods of detecting a predisposition to, or the incidence of, bladder cancer in a sample comprising detecting an epigenetic change, such as methylation, in at least one gene selected from TWIST1, NID2, RUNX3, BMP7, CCNA1, PDLIM4, TNFRSF25, APC, RASSF1A, LOXL1, TUBB4, NTRK2, ARFGAP3, OSMR and TJP2, or a panel thereof. Also disclosed are kits for performing the disclosed methods, such as kits for detecting a predisposition to, or the incidence of, bladder cancer in a sample comprising at least one primer pair for determining the methylation status of each of NID2, TWIST1 and RUNX3. The kits may contain means for processing a urine sample.

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 produces a detectable fluorescence signal during amplification which is detected in real-time (c) quantifying the results of the real-time detection against a standard curve for the methylated or unmethylated gene of interest to produce an output of gene copy number.

Abstract: Disclosed are methods for detecting expression and/or aberrant methylation patterns in genes such as the gene DCR1 and their potential to diagnose or prognose a cancer or to predict drug resistance/susceptibility. More specifically, the disclosure relates to oligonucleotides, primers, probes, primer pairs and kits to detect genes such as the gene DCR1, and in particular, methylated forms of genes such as the gene DCR1. The disclosure also relates to pharmacogenetic methods to diagnose or prognose a cancer, to determine suitable treatment regimens for cancer, and to determine methods for treating cancer patients based on expression and/or aberrant methylation patterns in genes such as the gene DCR1.

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, TFPI2, BNIP3, FOXE1, SYNE1, SOX17, 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: 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 produces a detectable fluorescence signal during amplification which is detected in real-time (c) quantifying the results of the real-time detection against a standard curve for the methylated or unmethylated gene of interest to produce an output of gene copy number.

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, TFPI2, 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: Disclosed are methods for assessing the methylation and mutation status of nucleic acid in a sample. The methods provide for methylation-dependent modification of the nucleic acid in a sample, and subsequently nucleic acid amplification processes to distinguish between mutated and non-mutated target sequence.

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: An oligonucleotide, primer or probe comprises the nucleotide sequence of any of SEQ ID NO. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 61, 62 or 63. The oligonucleotide, primer or probe is useful for the detection of the methylation status of a gene. The oligonucleotides find application in the diagnosis and treatment of cancer.