Upgrading Reference Set (URS) Application: Paul Boutros-UCLA (2020)

Abbreviated Name
URS Reference Set App: Boutros (2020)
Lead Investigator
Boutros, PaulThe University of California, Los Angeles
Coordinating Investigator
Feng, Ziding Fred Hutchinson Cancer Center
Involved Investigators


Same as Objectives


Aim 1: Collect tissue, blood, and urine specimens to obtain 195 complete specimen sets under the URS protocol. We have recruited 146 complete sample sets with updated SOPs suitable for biomarker validation studies. An additional 74 subjects have been recruited under the SOPs but Based on historical completion and eligibility rates for recruited subjects, we estimate 186 complete sample sets will be in-hand when these subjects complete treatment (Table 1 below). We are seeking support to gather these in-queue specimens and to recruit an additional 30 subjects to ensure we have a large enoughcomplete sample set to evaluate candidate biomarkers, both those developed within the EDRN and by the broader scientific community. Aim 2: Perform Germline whole-genome sequencing for each subject in the cohort to validate the PRS markers with respect to upgrading as previously reported. Our second aim will attempt to validate an established PRS and assess its ability to predict upgrading. This will simultaneously create a resource to enrich the characterization of the cohort for all future studies and enable low-cost validation of any future germline-based risk markers

Analytic Method

For validation, the primary null hypothesis is H0: ROC-1(0.98) ≥ 0.98 for lower threshold and the secondary hypothesis is H0: ROC (0.02) ≤0.25 for higher threshold. If the true false positive rate, ROC-1(0.98) ≤ 0.65 using this threshold, the study will have 90% power if we have 195 biopsy GS=6 patients. We will use the final study sample of n=240 to account for various factors (lower than 60% upgrading rate, inadequate biospecimen for assay, missing radical prostatectomy outcome). The power calculation used the formula for testing ROC-1(p) in [Pepe]. Assuming 60% upgrading prevalence, 35% specificity at threshold corresponding to 98% sensitivity leads to NPV=92.1%, judged adequate for patients with GS=3+3 to avoid radical prostatectomy and adopt active surveillance. Of particular interest are the comparisons of the performance of clinical predictors alone, and clinical predictors combined with blood, urine, or tumor-tissue based biomarkers.


Same as Objectives


  • No publications available at this time for this protocol.


  • No biomarkers available at this time for this protocol.

Data Collections

  • No data collections available at this time for this protocol.
 Team Project
Start Date
Apr 1 2020
Estimated Finish Date
Mar 31 2021
Finish Date
Jun 15 2023
Protocol ID
Protocol Type
Reference Set
Field of Research
Collaborative Group
Prostate and Urologic Cancers Research Group
Cancer Types
  • Malignant neoplasm of prostate
Phased Status

Associated Forms