Gene methylation based colorectal cancer diagnosis

A method of identifying a colorectal cancer in a sample comprising:

• obtaining DNA from a subject;
• determining a methylation status of one or more genes further defined as PTGS2, TFPI2, TWIST1, TMEFF2, BOLL, CDX1, CLIC4, DCC, ESR1, GATA4, GDNF, HLA-G, JUB, MYOD1, NKX2-1, PENK, PITX2, RARB, S100A2, SALL3, SEZ6L, SFRP2, SPARC, TCEB2, THBD, TJP2, TP53, or WT1;
• and
• comparing the methylation status with a control, thereby identifying colorectal cancer DNA in the sample.

A set of nucleic acid primers or hybridization probes being specific for a potentially methylated region of marker genes being suitable to diagnose or predict colorectal cancer, with the set comprising probes or primers for genes:

• a) BOLL, CDX1, CLIC4, DCC, ESR1, GATA4, GDNF, HLA-G, JUB, MYOD1, NKX2-1, PENK, PITX2, PTGS2, RARB, S100A2, SALL3, SEZ6L, SFRP2, SPARC, TCEB2, TFPI2, THBD, TJP2, TMEFF2, TP53, TWIST1 and WT1;
• b) ESR1, TFPI2, WT1, TMEFF2, PENK, MYOD1, TWIST1, DCC, PTGS2, TJP2, SPARC, PITX2, SEZ6L, TP53, GDNF, CDX1, CLIC4, SFRP2, HLA-G, GATA4, BOLL, THBD, RARB, NKX2-1, SALL3 and JUB;
• c) TFPI2 and TJP2;
• d) TMEFF2, PITX2, TWIST1, ESR1, BOLL, TFPI2, WT1, GDNF, HLA-G, PENK, SEZ6L, SFRP2, TCEB2 and RARB;
• e) TMEFF2, TWIST1, PITX2 and TFPI2;
• f) TWIST1, TMEFF2, ESR1, WT1, PITX2, TFPI2, HLA-G, PENK, BOLL, DCC, TP53, GATA4, GDNF, RARB, CLIC4, SEZ6L, SFRP2, PTGS2, THBD, TJP2, SPARC, TCEB2, MYOD1 and S100A2;
• g) TFPI2, TMEFF2, TWIST1, ESR1, PITX2, DCC, WT1, SEZ6L, BOLL and SFRP2;
• h) TFPI2, DCC, PTGS2, TJP2, and PITX2;
• i) TFPI2, DCC, PTGS2, and TJP2;
• j) TFPI2, DCC, and PTGS2;
• k) TFPI2 and PTGS2;
• l) TMEFF2, PITX2, TWIST1, SFRP2, RARB, ZNF256, SPARC, DAPK1, CALCA, and S100A2;
• m) TMEFF2, PITX2, TWIST1, SFRP2, ZNF256, SPARC, and DAPK1;
• n) TMEFF2, PITX2, TWIST1, SPARC, and S100A2;
• o) TMEFF2 and TWIST1;
• p) GATA4, WT1, TFPI2, SEZ6L, TMEFF2, DCC, BOLL, PITX2, and GDNF;
• q) TMEFF2, PITX2, and TWIST1;
• r) TMEFF2, TWIST1, PTX2, and S100A2;
• s) DAPK1, TMEFF2, PITX2, S100A2, ZNF256, RARB, and SFRP2;
• t) DAPK1, TMEFF2, PITX2, S100A2, SPARC, CALCA, TWIST1, ZNF256, RARB, and SFRP2;
• or probes or primers for at least 50%, preferably at least 60%, at least 70%, at least 80%, at least 90%, 100% of the genes of anyone of the above a) to t), with the proviso that at least 2 genes are represented, and any of these sets comprises not more than 350 probes or primer pairs.