Detecting neoplasm
View Patent ↗Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as pancreatic and colorectal cancer. Accordingly, provided herein is technology for pancreatic cancer screening markers and other gastrointestinal cancer screening markers that provide a high signal to-noise ratio and a low background level when detected from samples taken from a subject (e.g., stool sample). As described herein, the technology provides a number of methylated DNA markers and subsets thereof (e.g., sets of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more markers) with high discrimination for G1 neoplasms overall and/or at individual tumor sites.
1. A method for measuring the methylation level of one or more CpG sites in CLEC11A comprising:
a) extracting genomic DNA from a biological sample of a human individual suspected of having or having a gastrointestinal neoplasm, a pancreas neoplasm, a stomach neoplasm and/or an esophagus neoplasm,
b) treating the extracted genomic DNA with bisulfite,
c) amplifying the bisulfite-treated genomic DNA with primers consisting of a pair of primers specific for CLEC11A, and
d) measuring the methylation level of one or more CpG sites in CLEC11A by methylation-specific PCR, quantitative methylation-specific PCR, methylation sensitive DNA restriction enzyme analysis or bisulfite genomic sequencing PCR.
2. The method of claim 1 wherein the sample is a stool sample, an esophageal tissue sample, a tissue sample, a pancreatic juice sample, a pancreatic cyst fluid sample, a blood sample, or a urine sample.
3. The method of claim 1 wherein the pair of primers specific for CLEC11A consists of SEQ ID Nos: 47 and 48.