# Presentation: 180565

## The Prostate SPORE 
National Biospecimen Network Pilot and caBIG

**The Prostate SPORE **
**National Biospecimen Network Pilot and caBIG**

- caBIG Tissue Banks and Pathology Tools Workspace Meeting
- May 5, 2005
- Washington University
- St. Louis, Missouri

## Prostate SPORE NBN Pilot Overview

**Paul Fearn, Memorial Sloan-Kettering Cancer Center**

## NBN Concept Developed with Extensive Input from the Cancer Community

- National Biospecimen Network Blueprint
- 	(http://www.ndoc.org/about_ndc/reports)

## Prostate SPORE Programs and Principal Investigators

| Program | Principal Investigator |
| --- | --- |
| Baylor College of Medicine | Timothy Thompson, Ph.D.  |
| Dana-Farber/Harvard | Philip Kantoff, M.D.*  |
| Johns Hopkins University | William Nelson, M.D., Ph.D.  |
| Mayo Clinic | Donald Tindall, Ph.D. |
| MD Anderson Cancer Center | Christopher Logothetis, M.D.  |
| Memorial Sloan-Kettering Cancer Center | Peter Scardino, M.D.* |
| Northwestern University | Chung Lee, Ph.D.  |
| University of California, Los Angeles | Jean deKernion, M.D.  |
| University of California, San Francisco | Marc Shuman, M.D.  |
| University of Michigan | Kenneth Pienta, M.D.  |
| University of Washington / FHCRC | Paul Lang, M.D.  |

- *Designated by Prostate SPORE PIs as primary points of contact for the NBN pilot

## Prostate SPORE Task Force for NBN Implementation

- Mark Rubin, Chair, Dana-Farber
- Larry True, FHCRC
- Timothy McDonnell, MD Anderson
- Gustavo Ayala, Baylor
- Angelo De Marzo, Johns Hopkins

- Pathology/Tissue Processing

- Paul Lang, Co-Chair, FHCRC
- James Montie, University of Michigan
- Alan Partin, Johns Hopkins
- Bruce Trock, Johns Hopkins

- Clinical and Epidemiology

- George Klee, Mayo Clinic
- Herbert Fritsche, MD Anderson

- Laboratory Medicine

- Paul Fearn, Memorial Sloan-Kettering
- Borko Javanovic, Northwestern

- Bioinformatics

- Teri Mielese, UCSF

- Regulatory Affairs

## Prostate SPORE NBN Pilot Overview

## Prostate SPORE NBN Pilot Overview, continued

## Prostate SPORE NBN Pilot / caBIG Timeline

| January 2004 | Prostate SPORE Principal Investigators (PIs) agree to pilot NBN concept and establish a Task Force |
| --- | --- |
| July 2004 | First meeting of NBN pilot Task Force |
| August 2004 | Informatics site visits begin |
| January 2005 | First meeting of the NBN pilot Informatics Group |
| February 2005 | Meeting of NBN pilot Informatics Group and CaBIG representatives; regular teleconferences initiated |
| March 2005 | Prostate SPOREs apply for Year 2 caBIG Funding |
| March 2005 | Prostate SPORE NBN pilot RFP released |
| April 2005 | NBN pilot Informatics Group and caBIG representatives discuss Workflow and Use Cases |

## Inter-Prostate SPORE Biomarkers Study Overview

## IPBS Research Question

- Do promising biomarkers improve upon existing models to predict aggressive cancers that will progress following surgery or radiotherapy?

**Notes:**
- Before we go down the path that breast cancer research did with erbB-2 . . .

## Common Underlying Needs ofIPBS and NBN

- dispersed network of contributors & users
- use of standardized/optimized methods:
**annotation, common or exchangeable data structures**
**“****best practices” tissue processing, storage, disbursement, quality control**
**Identify ****tolerances**** if standardization is not possible**
- tissue linked to clinical, pathology & outcome data
- sustainable and scalable infrastructure
- control of pre-analytical error

**Notes:**
- This problem (from previous slide) really underlies the motivation for both the IPBS and the NBN

**Consent ****(CCE)****, QA ****(CDE)**

**Biopsy****	**		      **Blood**
**Standardize:**		      **Standardize:**
- - processing time, temp	      - tubes (plain, citrate, EDTA, heparin)
- - paraffin temp		      - time from phlebotomy to processing
- - fixation time		      - centrifuge time, temp, speed
- - sectioning, sign-out		      - multiple aliquots

**biopsy results**

** ****Annotate (CDEs)**
**Send to IPBS Core**

**Cancer - not**
**eligible**

**Cancer - eligible**

**Not**
**cancer**

## Prospective Study Schema (5 Years)

- Prostate Ca
- Diagnosis

- Radical
- Prostatectomy

- Radiation
- Therapy

**PSA**
**Recurrence**

**Treatment**
**(Pt choice)**

**Cancer**
**Outcome**

**BM**

**BM**

**PSA**
**Recurrence**

**Notes:**
- BM = Biomarker.  Biomarkers would be tested to see if they predict biochemical recurrence following RRP and/or XRT.
- Epidemiology Working Group can identify research questions to be addressed using patients and samples from the prospective study.

## 700 PC Patients

**from 11 SPOREs**

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

**Centralized processing, annotation**
**distribution, storage, data linkage**

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

**Centralized processing, annotation**
**distribution, storage, data linkage**

**700 bx**

**700 bx**

**700 bx**

**700 S/P**

**700 S/P**

**100 frozen bx**

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**PSA Recurrence**

**Correlate 5 individual biomarkers with Prognosis**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

**Centralized processing, annotation**
**distribution, storage, data linkage**

**700 bx**

**700 bx**

**700 bx**

**700 S/P**

**700 S/P**

**100 frozen bx**

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**PSA Recurrence**

**Correlate 5 individual biomarkers with Prognosis**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

**Centralized processing, annotation**
**distribution, storage, data linkage**

**700 bx**

**700 bx**

**700 bx**

**700 S/P**

**700 S/P**

**100 frozen bx**

- Microarray BM Discovery

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**PSA Recurrence**

**Correlate 5 individual biomarkers with Prognosis**

**Correlate BM**
**to Tx Response**

**Recurrent pts**
**enter trials**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

**Centralized processing, annotation**
**distribution, storage, data linkage**

**700 bx**

**700 bx**

**700 bx**

**700 S/P**

**700 S/P**

**100 frozen bx**

- Microarray BM Discovery

## 700 PC Patients

**700 PC Patients**
**from 11 SPOREs**

**PSA Recurrence**

**Correlate 5 individual biomarkers with Prognosis**

**Correlate BM**
**to Tx Response**

**Recurrent pts**
**enter trials**

**Dynamic**
**Data**
**&**
**Tissue**
**Resource**

**●**** ****15 paraffin slides**
**●   ****3 serum & 3 plasma tubes**
**●  ****(2 frozen core biopsies)**

**Centralized processing, annotation**
**distribution, storage, data linkage**

**700 bx**

**700 bx**

**700 bx**

**700 S/P**

**700 S/P**

**100 frozen bx**

- Microarray BM Discovery

## The Prostate SPORE NBN Pilot and caBIG Tools, Principles and  Infrastructure

**John Speakman, Memorial Sloan-Kettering Cancer Center**

## NBN: Contributing to Prostate Pathology CDEs

- Each pilot site will contribute existing data elements
- The data elements and definitions will be harmonized and agreed upon by the pilot sites
- Those harmonized definitions will be contributed to the VCDE workspace for harmonization and acceptance to the caDSR

## NBN: Making Use of the caTISSUE Object Model

- The caTISSUE OM will be used to connect the NBN pilot sites repositories to a caBIG grid-compliant communications layer
- The caTISSUE OM will either be connected to existing biospecimen systems at the local system or caTISSUE-Core will be used to house the specimen data locally

## NBN : Making Use of the caTISSUE Object Model

- The communications layer will provide the basis for a general biospecimen ‘virtual broker’ module
- The very defined nature of the NBN Pilot is an ideal ‘real world’ application for the caTISSUE and caGRID

## NBN: Making Use of caGRID

**legacy**

***caBIG grid infrastructure***

**caBIG**
**Compatible**
**Object**
**Model**
**Adapter**

**caBIG **
**Compatible**
**System**

**Registration**
**Subscription/publication**
**Federation**
**Security**

## Prostate SPORE NBN Pilot Preliminary Workflow Diagrams

**Paul Fearn, Memorial Sloan-Kettering Cancer Center**

## Biomarker Experiments Workflow:Prospective and Retrospective Studies

## Biomarker Experiments Workflow:Prospective and Retrospective Studies (continued)

## Main Workflow – Prospective Study

## Main Workflow – Prospective Study (continued)

## Main Workflow – Prospective Study (continued)

## Main Workflow – Retrospective Study

## High-Level Use Cases: Prospective Study Actor/Action 

## High-Level Use Cases: Retrospective Study Actor/Action 

## Timeline, Next Steps and Opportunities for Additional Interaction with caBIG

## Next Steps for Prostate SPORE NBN Pilot / caBIG Collaboration

| May 2005 | Revise workflows, use cases, and CDEs |
| --- | --- |
| May 2005 | Proposals due for Prostate SPORE NBN pilot RFP |
| June 2005 | Obtain feedback on workflow, use cases and CDEs from Prostate SPORE clinicians and pathologists |
| June 2005 | Decisions made about Year 2 caBIG Funding |
| June 2005 | Update NBN Pilot Executive Summary with information about workflows, use cases and CDEs |
| July 2005 | NBN Task Force meeting at 13th SPORE Workshop |
| July 2005 | Final submission of CDEs to NCICB caDSR |
| September 2005 | Prostate SPORE NBN pilot RFP contract award (anticipated); initiation of prospective and retrospective IPBS |

## Draft Joint Timeline for Prostate SPORE NBN Pilot & caBIG 

**Submit NBN Pilot Specimen & Clinical CDEs to caDSR (Jul 15)**

**Initiate IPBS Prospective & Retrospective Studies (Sept 1)**

- Draft Joint Timeline for Prostate SPORE NBN Pilot & caBIG

**NCI Selects Contractor for Prostate SPORE Biospecimen Coordination**
** ****System RFP (late September)**

**Finalize Specimen & Clinical CDEs with Prostate SPORE clinicians (Mar 1 – May 27)**

**Release of caBIG Adopter RFP to Prostate SPOREs (Feb 18)**

**Complete caTISSUE Annotations Specifications ( Mar 15)**

**Prostate SPORE institutions apply  for caBIG Adopter RFP: caTISSUE Adopter (Mar 18)**

**Select caTISSUE Adopters (Apr 14) **

**Complete caTISSUE Prototype (Jun 30)**

- Prostate SPORE NBN Pilot

- caBIG

**Finalize NBN Pilot Informatics Executive Summary and distribute to Prostate SPORE PI’s (Apr 15)**

**Organ Systems Branch Completes IPBS Proposal Review  (Mar 15)**

**Organ Systems Branch Funds IPBS biomarker validation activities  (Jul 1)**

**Organ Systems Branch Distributes draft MTAs, Informed Consent Forms, & SOPs to Prostate SPOREs (Apr 30)**

**NCICB/caBIG**

**Organ Systems Branch, NCI**

**Office of the Director, NCI**

**Finalize Use Cases with Prostate SPORE clinicians (Mar 1 – May 27)**

**Debrief Prostate SPORE Informatics Representatives & PIs about Biospecimen Coordination System RFP (Apr 1)**

**Annual SPORE Workshop  (Jul 9-12)**

**Annual caBIG Meeting (Apr 12-13) **

**TBPTW Meeting (May 4-5)**

**NCI Releases Prostate SPORE Biospecimen Coordination System RFP (late March)**

**Finalize MTAs, Informed Consent Forms, & SOPs  (August 31)**

**Prostate SPOREs begin mapping individual systems to **
**common CDE set (Sept 1)**

**Q1**

**Q2**

**Q3**

**Q4**

**2005**

**Complete caTISSUE Alpha Release (Oct 15)**

**Complete caTISSUE Annotations Module Alpha****(Oct 31)**

## Possible Future Interactions between the Prostate SPORE NBN Pilot and caBIG

- Participation of Prostate SPORE NBN Pilot representatives in caBIG TBPTW and other workspace teleconferences
- Participation of caBIG TBPTW representatives in Prostate SPORE NBN Pilot teleconference

## Additional Information about the Prostate SPORE NBN Pilot Project

- Prostate SPORE NBN Pilot Website
- _prostateNBNpilot.nci.nih.gov_
- RFP Information
- _http://rcb.cancer.gov/rcb-internet/appl/rfp/published_rfps.jsp_