Hypermethylated regions in LNCaP compared to PrEC cells can serve as biomarkers for prostate cancer. A, DNA methylation at representative regions identified as hypermethylated in LNCaP cells compared to PrEC cells was measured in prostate cell lines using the COMPARE-MS assay as described previously . The extent of methylation at each region is color scaled from white to red as shown, with white representing absence of detectable methylation, and red representing nearly complete methylation of all input copies. M.SssI-treated, completely-methylated, WBC DNA served as a positive control. All of the prostate cancer cell lines showed a high degree of methylation at multiple regions, while the PrEC normal prostate cells did not show any detectable methylation at these regions as expected. B, COMPARE-MS analysis of DNA methylation at three of the five regions from (A) showed significant methylation of at least one of the three regions in every tumor sample with very low or undetectable methylation in the matched normal tissue samples.