title: A panel of DNA methylation markers reveals extensive methylation in histologically benign prostate biopsy cores from cancer patients.
abstract: BACKGROUND
  Men with a negative first prostate biopsy will undergo one or more additional biopsies if they remain at high suspicion of prostate cancer. To date, there are no diagnostic tests capable of identifying patients at risk for a positive diagnosis with the predictive power needed to eliminate unnecessary repeat biopsies. Efforts to develop clinical tests using the epigenetic signature of cores recovered from first biopsies have been limited to a few markers and lack the sensitivity and specificity needed for widespread clinical adoption.
  
  
  METHODS
  We developed methylation-specific quantitative polymerase chain reaction assays for a panel of 24 markers that are preferentially methylated in prostate cancer. We modified the bisulfite conversion conditions to allow the integration of the methylation information from multiple markers. We determined the methylation status of the 24 markers in 213 prostate biopsy cores from 104 patients, 37 prostate cancer patients and 67 controls. We performed logistic regression on combinations of markers as well as the entire panel of 24 markers to identify the best candidates for a diagnostic test.
  
  
  RESULTS
  The marker panel differentiated between cancer cores and benign cores from non-cancer patients with 100% sensitivity and 97% specificity. Furthermore, the panel detected significant methylation in benign cores from prostate cancer patients that was not present in controls. Using methylation of 5 out of 24 to define a cancer case, the analysis of a single benign biopsy core identified 62% of prostate cancer patients undergoing repeat biopsies. ROC curve analysis showed that markers commonly methylated in benign cores from cancer patients are the best candidates for a diagnostic test. The results suggest that 5 to 10 markers will be needed to achieve optimal predictive power.
  
  
  CONCLUSIONS
  This study shows that epigenetic field effects differ significantly between cancer patients and controls. Their detection in benign biopsy cores can form the basis of diagnostic tests to identify patients in need of repeat biopsies, reducing the cost of continued PCA screening by up to 40%. They could also be used to identify prostate cancer patients with low grade disease who are likely candidates for active surveillance or focal therapy.
authors.affiliation: Euclid Diagnostics LLC, Crown Point, Indiana USA.
authors.forename: Igor
authors.initials: I
authors.lastname: Brikun
authors.affiliation: Euclid Diagnostics LLC, Crown Point, Indiana USA.
authors.forename: Deborah
authors.initials: D
authors.lastname: Nusskern
authors.affiliation: Department of Statistics, University of California Irvine, Irvine, California USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gillen
authors.affiliation: Consultants in Laboratory Medicine, Toledo, Ohio USA.
authors.forename: Amy
authors.initials: A
authors.lastname: Lynn
authors.affiliation: Promedica Genitourinary Surgeons, Toledo, Ohio USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Murtagh
authors.affiliation: Pathology Consultants, Michigan City, Indiana USA.
authors.forename: John
authors.initials: J
authors.lastname: Feczko
authors.affiliation: Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland USA.
authors.forename: William G
authors.initials: WG
authors.lastname: Nelson
authors.affiliation: Euclid Diagnostics LLC, Crown Point, Indiana USA.
authors.forename: Diha
authors.initials: D
authors.lastname: Freije
keywords: Atypical small acinar proliferation; DNA methylation; Early cancer diagnostics; High grade prostatic intraepithelial lesions; Prostate cancer; Repeat biopsies