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Background  Early screening for prostate cancer (PCA) remains controversial because of overdiagnosis and overtreatment of clinically insignificant cancers. Even though a number of diagnostic tests have been developed to improve on PSA testing, there remains a need for a more informative non-invasive test for PCA. The objective of this study is to identify a panel of DNA methylation markers suitable for a non-invasive diagnostic test from urine DNA collected following a digital rectal exam (DRE) and/or from first morning void (FV). A secondary objective is to determine if the cumulative methylation is indicative of biopsy findings.    Methods  DRE and FV urine samples were prospectively collected from 94 patients and analyzed using 24 methylation-specific quantitative PCR assays derived from 19 CpG islands. The methylation of individual markers and various combinations of markers was compared to biopsy results. A methylation threshold for cancer classification was determined using a target specificity of 70%. The average methylation and the number of positive markers were also compared to the result of the biopsy, and the area under the receiver operating characteristic curves (AUCs) were calculated.    Results  Methylation of all 19 markers was detected in FV and DRE DNAs. Combining the methylation of two or more markers improved on individual marker results. Using  6of19  methylated markers as the threshold for cancer classification yielded a specificity of 71% (95% CI, 0.57–0.86) from both DRE and FV and a sensitivity of 89% (95% CI, 0.79–0.97) from DRE and 94% (95% CI, 0.84–1.0) from FV. The negative predictive value at the 6of19 threshold was ≥ 90 for both DNA types.    Conclusions  PCA-specific methylation was detected in both FV and DRE DNA. There was no significant difference in diagnostic accuracy at the 6of19 threshold between DRE and FV urine DNA. The results support the development of a non-invasive diagnostic test to reduce unnecessary biopsies in men with elevated PSA. The test can also provide patients with personalized recommendations based on their own methylation profile.    Electronic supplementary material  The online version of this article (10.1186/s13148-018-0524-x) contains supplementary material, which is available to authorized users.

A panel of DNA methylation markers for the detection of prostate cancer from FV and DRE urine DNA