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Pre-PLCO Phase II Dataset

Dataset Abstract:

Pre-PLCO Phase II Analysis Files

The following additional information has been defined for this dataset. The information has been provided by the Principal Investigator or staff from his or her laboratory.

Pre-PLCO Phase II Dataset
Daniel Cramer
Allison Vitonis
Pre PLCO datasets (Phase II):
This phase II set consisted of 160 cases of epithelial ovarian cancer with specimens obtained from FHCRC,
Fox Chase Cancer Center (FCCC, AKG), MDACC, and Partners. Approximately half of the cases were early stage (I, II)
and half late stage (III, IV). Also included was a benign disease group of 160 cases. There were 480 general population
controls assembled from the four sites. The healthy controls were recruited in the context of selection from the
general population as controls for an ovarian cancer case-control study or from attendees at mammographic screening
clinics. Forty paired serial specimens from healthy controls were obtained from women participating in regular mammography
screening (FHCRC) and 84 replicates were constructed from pooled female sera available for laboratory standardization (ProMedDX,
Norton, MA). All cases had blood drawn prior to surgery or chemotherapy and processed for serum generally within four hours of
draws. The serum was stored in aliquots at -80 C. Controls had blood drawn, processed, and stored under conditions similar to
the cases at each contributing sites. All subjects were accrued between 1998 and 2006 under IRB approved protocols.

All of the common phase II specimens were banked at the individual sites contributing specimens. Two ml aliquots of blood for all
subjects selected were assembled from the sites listed above and sent to FCCC for separation into aliquots and re-labeling to blind
their source and case or control status. Four aliquots were prepared: 0.3 ml to go to FHCRC, 0.1 ml to go MDACC, and 1.4 ml to go
to Partners, and 0.2 ml to go to UPCI. Specimens for each set were organized so there would be similar ratios of cases, benign disease
controls, general population controls, paired serial, and quality control specimens in batch sizes of 96. Aliquots were express-shipped
on dry ice.

Laboratory Assays

Laboratory assays for the phase II study were conducted at the four separate laboratories by individuals who were blind to case or control
status for the phase II specimens. Assays included single- or multi-plex Luminex bead assays, plate-based ELISA assays, platform-based
(Roche E170) assays, and a mass spectroscopy-based system using surface enhanced antibody chips. With the exceptions noted below, the assays
used for the phase III specimens were also used for the phase II specimens.

At FHCRC single-plex Luminex bead assays were used for all markers, details of which can be found in (Shah CA, Lowe KA, Paley P, Wallace E, Anderson
GL, McIntosh MW, Andersen MR, Scholler N, Bergan LA, Thorpe JD, Urban N, and Drescher CW, Influence of ovarian cancer risk status on the diagnostic
performance of the serum biomarkers mesothelin, HE4, and CA125. Cancer Epidemiol Biomarkers Prev, 2009. 18(5): p. 1365-72.). MDACC used a
mass spectroscopy based system for its markers, described in (Zhang Z, Bast RC, Jr., Yu Y, Li J, Sokoll LJ, Rai AJ, Rosenzweig JM, Cameron B, Wang YY,
Meng XY, Berchuck A, Van Haaften-Day C, Hacker NF, de Bruijn HW, van der Zee AG, Jacobs IJ, Fung ET, and Chan DW, Three biomarkers identified from
serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res, 2004. 64(16): p. 5882-90.). Partners used plate-based
assay for B7-H4(Diadexus), DcR3(Diadexus), CA72.4, IGF 2, Mesothelin, HE4, and Kallikrein 6 (as described in (Diamandis EP, Scorilas A, Fracchioli S,
Van Gramberen M, De Bruijn H, Henrik A, Soosaipillai A, Grass L, Yousef GM, Stenman UH, Massobrio M, Van Der Zee AG, Vergote I, and Katsaros D,
Human kallikrein 6 (hK6): a new potential serum biomarker for diagnosis and prognosis of ovarian carcinoma. J Clin Oncol, 2003. 21(6): p. 1035-43)).
Platform-based assays (Roche) were used for CA125, CA15.3, CA19.9, and CEA. Unless the volume was insufficient assays were run in duplicate and
averaged. Seven markers were carried over to phase III and these included B7H4, CA125, CA15.3, CA19.9, CA72.4, HE4, and HK 6. The same assays were used
except that a platform-based assay was available for CA72.4. The two 0.3 aliquots were first combined and homogenized. UPCI used a multi-plex bead assay
system was used to evaluate 34 markers in phase II. This technique is described in (Nolen B, Marrangoni A, Velikokhatnaya L, Prosser D, Winans M, Gorelik E,
and Lokshin A, A serum based analysis of ovarian epithelial tumorigenesis. Gynecol Oncol, 2009. 112(1): p. 47-54). For the phase II markers included in the
Yale panel, these markers were evaluated using a multi-plex bead system described in (Visintin I, Feng Z, Longton G, Ward DC, Alvero AB, Lai Y, Tenthorey J,
Leiser A, Flores-Saaib R, Yu H, Azori M, Rutherford T, Schwartz PE, and Mor G, Diagnostic markers for early detection of ovarian cancer. Clin Cancer Res, 2008.
14(4): p. 1065-72).
The Pre-PLCO datasets contain 59 markers measured by 4 sites (Partners, FHCRC, MD Anderson, and Pittsburgh). The best performers were selected to be measured in PLCO samples.
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