Methods for Detecting Epigenetic Modifications

2-8. (canceled)

11-17. (canceled)

19-27. (canceled)

(canceled)

33-40. (canceled)

42-45. (canceled)

47-53. (canceled)

A method for determining the histopathological stage of cancer and in particular a gastrointestinal cancer in a sample comprising 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 the histopathological stage of the cancer.

55-64. (canceled)

A method for predicting the likelihood of successful treatment or resistance to treatment of cancer and in particular a gastrointestinal cancer with a DNA demethylating agent or a DNA methyltransferase inhibitor or HDAC inhibitor comprising 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 that the likelihood of successful treatment is higher than if the epigenetic modification is not detected and wherein detection of the epigenetic change is indicative that the likelihood of resistance to treatment is lower than if the epigenetic modification is not detected.

66-78. (canceled)

A method of selecting a suitable treatment regimen for cancer in particular a gastrointestinal cancer comprising 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 results in selection of a DNA demethylating agent or a DNA methyltransferase inhibitor or a HDAC inhibitor for treatment and wherein if the epigenetic change is not detected, a DNA demethylating agent or a DNA methyltransferase inhibitor or a HDAC inhibitor is not selected for treatment.

80-86. (canceled)

88-98. (canceled)

A kit for detecting a predisposition to, or the incidence of a gastrointestinal cancer and in particular colorectal cancer in a sample comprising:

• (a) means for detecting an epigenetic change in at least one gene selected from GATA4, OSMR, NDRG4, GATA5, SFRP1, ADAM23, JPH3, SFRP2, APC and MGMT, or at least one gene selected from TFPI2, BNIP3, FOXE1, SYNE1, SOX17, PHACTR3 and JAM3, and
• (b) a homogenization buffer for processing a faecal sample.

100-111. (canceled)

A kit for detecting a predisposition to, or the incidence of, gastrointestinal cancer and in particular colorectal cancer in a sample comprising:

• (a) means for detecting an epigenetic change in at least one gene selected from OSMR, SFRP1, NDRG4, GATA5, ADAM23, JPH3, SFRP2 and APC, or at least one gene selected from TFPI2, BNIP3, FOXE1, SYNE1, SOX17, PHACTR3 and JAM3, and
• (b) a kit specifically adapted for isolating DNA form a blood sample or derivative thereof or a stabilizer for stabilizing a blood sample or derivative thereof.

113-135. (canceled)

A method of determining the methylation status of at least one gene in a blood plasma or serum sample, comprising:

• (a) isolating DNA from a blood plasma or serum sample,
• (b) subjecting the isolated DNA to treatment with a reagent which selectively modifies unmethylated cytosine residues in the DNA contained in the sample to produce detectable modified residues but which does not modify methylated cytosine residues, and
• (c) amplifying the treated isolated DNA in order to determine the methylation status of at least one gene, characterised in that 0.07 to 0.72 ml blood plasma or serum sample equivalent of DNA is used per amplification reaction.

137-156. (canceled)

159-163. (canceled)

A method of processing a faecal sample to isolate and prepare DNA for use in detecting a predisposition to, or the incidence of, colorectal cancer in a faecal sample comprising:

• (a) isolating DNA from the faecal samples
• (b) subjecting at least 2.5 μg of the isolated DNA per amplification reaction required to treatment with a reagent which selectively modifies unmethylated cytosine residues in the DNA contained in the sample to produce detectable modified residues but which does not modify methylated cytosine residues, and
• (c) amplifying the treated isolated DNA.

165-170. (canceled)

A primer pair selected from the primer pairs comprising the nucleotide sequences set forth in tables 2 to 18.

A probe selected from the probes comprising the nucleotide sequences set forth in tables 2 to 18.

A kit comprising a primer pair selected from the primer pairs comprising the nucleotide sequences set forth in tables 2 to 18 and corresponding probe selected from the probes comprising the nucleotide sequences set forth in tables 2 to 18.