Introduction and History

In early 2004, the 11 prostate cancer SPORE principal investigators (see Table 1) agreed to pilot the National Biospecimen Network (NBN) and appointed a Task Force on NBN implementation (the “Task Force”) chaired by Dr. Mark Rubin to accomplish this goal. Members of the current prostate SPORE NBN pilot Task Force and informatics representatives at participating sites are listed in Table 2 and Table 3, respectively.

At the July 10, 2005 inter-SPORE meeting in Baltimore, MD the Task Force and NCI representatives discussed the scope of the NBN pilot, framed the initiative relative to the prostate cancer SPORE programs and the Cancer Biomedical Informatics Grid (caBIG), and identified the critical need for an interoperable informatics system among the prostate SPOREs in order to create the NBN pilot.

To refine the scope of the proposed informatics platform, the Task Force agreed to use the Inter-SPORE Prostate Biomarker Study (IPBS) to focus the development of specific requirements for the NBN pilot standards, logistics, governance, and informatics infrastructure. The IPBS, which is based on strong science and approved by the SPORE programs, will initially help to focus the NBN pilot initiative. Ultimately, the NBN pilot will provide an ongoing platform for the prostate cancer SPOREs to test and validate biomarkers and will enhance the quality and availability of biospecimens to the scientific community.

The current challenge for the informatics group is to develop standards and systems that will allow 11 prostate cancer SPORE centers to successfully conduct the IPBS, and to accelerate the production of collaborative research by reducing barriers to leveraging the biospecimen, clinical data, and informatics resources across multiple centers. However, the informatics tools developed for the IPBS will also form the basis for an ongoing, interoperable informatics system that could be used for future retrospective studies and the development of new prospective protocols. Most SPORE programs need to utilize extramural resources for large projects. Although there are some examples of highly effective inter-institutional projects, systems, and resource sharing, numerous tedious steps are involved in collaboration, including regulatory approvals, preparation and merging of datasets, and negotiations for authorship/ acknowledgement. The amount of staff time consumed by these activities is staggering and would be mostly unnecessary with reasonable standardization of documents, data, and procedures, as well as implementation of information systems to automate standard procedures.

Progress on the NBN Pilot

National Biospecimen Network (NBN) Pilot:
Second Prostate Cancer SPORE Task Force Informatics Meeting

On January 30, 2005, the Second Prostate Cancer SPORE Task Force Informatics Meeting of the NBN Pilot was attended by informatics representatives from each Prostate Cancer SPORE to begin to address current challenges and to develop a strategy to successfully conduct the IPBS study and pilot the NBN. Specifically, the goals of the meeting were to:

• Lay the groundwork for NBN pilot development by sharing Prostate Cancer SPORE site visit information
• Define informatics requirements for the pilot
• Explore tools and compatibility issues for interfacing with the NCI Cancer Bioinformatics Grid (caBIG)
• Exchange Prostate Cancer SPORE system diagrams and/or data models via online informatics system demos
• Understand and appreciate the various extant resources for tissue annotation, storage, and analysis at the participating SPOREs
• Discuss ways that these individual resources can be mined and adapted to support the proposed NBN pilot
• Understand the scope of the resource that the team is engaged to build
• Establish further collaborations between Prostate Cancer SPOREs.

In particular, the Tissue Banks and Pathology Tools Workspace (TBPTW) will integrate, develop, and implement tissue and pathology tools to enable information sharing across Cancer Centers. These tissue banks and pathology tools will ultimately facilitate the integration of data from different studies and from different centers, provide a platform for rapidly surveying available tissue and pathology resources, and establish standards and interoperable tools for working with tissue and pathology resources. TBPTW activities involve the development of a basic tissue inventory tracking module that can be annotated with contemporary specimen resources. By building standard modules, caBIG can provide object models to query across different Cancer Centers, in a fashion similar to Microarray Gene Expression (MAGE), HL7, and other models.

Given the above information, it was determined that the Prostate SPORE Task Force for NBN Implementation could interact with caBIG in several key ways. For instance, caBIG could provide the backbone for plug-in applications as defined by use cases at the Prostate Cancer SPOREs. To facilitate this development, Prostate Cancer SPOREs would have to identify their needs and identify gaps in caBIG infrastructure. In turn, by working with caBIG to develop and share applications, the Task Force would ensure that caBIG will meet specified needs of the cancer research community.

January 31, 2005 Specimen Management and Biomarker Development Working Lunch

A working lunch to discuss specimen management and biomarker development in the context of the NBN Pilot was held on January 31, 2005 as part of the 2005 Inter-Prostate SPORE meeting in Houston, Texas. Drs. Mark Rubin and Angelo De Marzo summarized the progress made by the Prostate SPORE Task Force for NBN Implementation in the past six months. Prostate Cancer SPORE site visits had been conducted and an executive summary describing the existing informatics systems at each site had been developed. In addition, the scientific peer review of the IPBS study proposal was ongoing and a request for proposals (RFP) focusing on biospecimen collection and informatics aspects of the NBN pilot would be released in late March 2005. The scope of the contractor's role in the latter open competition would involve a repository management piece including the coordination of standard operating procedures (SOPs) and institutional review boards (IRBs) across Prostate Cancer SPOREs.

During this meeting, De Marzo also gave a presentation on the variability found in the processing of needle biopsies and radical prostatectomy tissue blocks across Prostate SPOREs. Great time and temperature variabilities were found in every step of the process. Dr. De Marzo emphasized the need for SOPs, but acknowledged the difficulty of implementing them across all 11 Prostate SPOREs. Several small studies to help demonstrate such variability and encourage changes in SOPs across Prostate SPORE sites were proposed.