Proteomic Genetic and Longitudinal Pathways to Ovarian Cancer Biomarkers

Abbreviated Name
Ovarian Cancer Biomarker Discovery
Lead Investigator
Skates, StevenMassachusetts General Hospital
Coordinating Investigator
Skates, Steven Massachusetts General Hospital
Involved Investigators


Discovery and verification of early detection ovarian cancer plasma/serum biomarkers.


1.   Candidate discovery via a.   LC/MS in ovarian cyst fluid b.   LC/MS in vibratome sliced fresh tissue (fallopian tube vs ovarian cancer) c.   LC/MS in conditioned media from phenocopy model fallopian tube system d.   Affy arrays in fallopian/ovarian tissue filtered by secretome 2.   Integrated prioritization of candidates for verification by systems biology/pathway analysis 3.   Verification of 50 candidates in plasma from 50 cases & 50 benign adnexal masses, and in longitudinal plasma from ovarian cancer screening trial 4.   Longitudinal change-point analysis to determine candidates with earliest significant rise above baseline

Analytic Method

Phase 1 will consist of the proteomic analysis of proximal fluids (ovarian cyst fluid, conditioned media from FTE or ex-vivo phenocopy system if needed) and genomic analysis of ovarian/fallopian tube tissue and will occur during years 0-2.5, and produce a list of candidate discovery biomarkers. The ovarian cyst fluid follows the PRoBE design since at time the fluid is obtained the pathological diagnosis has not been made, and therefore the design will be a nested case-control one. However, the conditioned media will be from known cases and control subjects, so will not be PRoBE compliant – as there is no feasible way to achieve this goal in this setting. Quantitative criteria for phase 1 genomic and proteomic over-expression are that the ratio exceeds 5 with a p-value < 0.001 assessed by the permutation test (false discovery rate FDR < 10%). Phase 2 will consist of the AIMS experiments to determine which discovery candidates are detectable in multiple pools of plasma, and SISCAPA-MRM experiments in plasma biospecimens obtained prior to surgery in patients with pelvic masses, to determine which candidates differentiate malignant from benign disease. The pools of plasma will be from the same set of patients as from which the cyst fluid was obtained, while the plasma samples will be from the same patients and patients with a pelvic mass but without a cyst, which is the case for the majority of patients with a pelvic mass. Therefore the plasma specimens will be from a patient set which is a super-set of the cyst fluid patients. SISCAPA-MRM over-expression are that the 95% probability intervals for sensitivity at 98% specificity exceed 5%, that is, there is evidence that there is at least 5% sensitivity contributed to ovarian cancer detection by a candidate biomarker before going on to phase 3. Phase 3 will consist of SISCAPA-MRM experiments to measure the best 50 candidates in longitudinal samples from a pilot screening trial, and will occur from years 3-5. Screening samples automatically comply with the PRoBE design as they are collected prospectively before diagnosis is known and will be evaluated without knowledge of their case/control status. The quantitative criterion for the next phase is that the longitudinal algorithm for a given candidate provides a sensitivity of at least 10% at 1-2 years prior to detection at 98% specificity.


  • 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
Jul 1 2010
Estimated Finish Date
Jun 30 2015
Protocol ID
Protocol Type
Field of Research
Collaborative Group
Breast and Gynecologic Cancers Research Group
Cancer Types
  • Malignant neoplasm of ovary

Associated Forms