Detecting neoplasm
This document relates to methods and materials for detecting premalignant and malignant neoplasms. For example, methods and materials for determining whether or not a stool sample from a mammal contains nucleic acid markers or polypeptide markers of a neoplasm are provided.
1. A method for characterizing a biological sample comprising:
(a) obtaining a biological sample from a human individual;
(b) measuring a K-ras mutation score within the obtained biological sample through exposing a portion of the biological sample to one or more K-ras specific primers and determining the K-ras mutation score by performing a digital melt curve analysis or quantitative allele-specific PCR, wherein the K-ras specific primers comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 2, 3, 4, 5, 6, 7 and 8;
(c) measuring a methylation level of a CpG site for BMP3 in a portion of the obtained biological sample through
treating genomic DNA in the biological sample with bisulfite;
amplifying the bisulfite-treated genomic DNA using primers specific for BMP3, and determining the methylation level of the CpG site by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR;
(d) comparing the K-ras mutation score and the BMP3 methylation level to a corresponding set of control samples without colorectal cancer; and
(e) determining that the individual has colorectal cancer when 1) the measured K-ras mutation score is higher than in the control sample, and 2) the measured BMP3 methylation level is higher than in the control sample.
2. The method of claim 1 , wherein the biological sample is a stool sample, a tissue sample, a blood sample, or a urine sample.