Design and utilization of the colorectal and pancreatic neoplasm virtual biorepository: An early detection research network initiative

Abstract

Background: The Early Detection Research Network (EDRN) colorectal and pancreatic neoplasm virtual biorepository is a bioinformatics-driven system that provides high-quality clinicopathology-rich information for clinical biospecimens. This NCI-sponsored EDRN resource supports translational cancer research. The information model of this biorepository is based on three components: (a) development of common data elements (CDE), (b) a robust data entry tool and (c) comprehensive data query tools.

Methods: The aim of the EDRN initiative is to develop and sustain a virtual biorepository for support of translational research. High-quality biospecimens were accrued and annotated with pertinent clinical, epidemiologic, molecular and genomic information. A user-friendly annotation tool and query tool was developed for this purpose. The various components of this annotation tool include: CDEs are developed from the College of American Pathologists (CAP) Cancer Checklists and North American Association of Central Cancer Registries (NAACR) standards. The CDEs provides semantic and syntactic interoperability of the data sets by describing them in the form of metadata or data descriptor. The data entry tool is a portable and flexible Oracle-based data entry application, which is an easily mastered, web-based tool. The data query tool facilitates investigators to search deidentified information within the warehouse through a "point and click" interface thus enabling only the selected data elements to be essentially copied into a data mart using a dimensional-modeled structure from the warehouse's relational structure.

Results: The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository database contains multimodal datasets that are available to investigators via a web-based query tool. At present, the database holds 2,405 cases and 2,068 tumor accessions. The data disclosure is strictly regulated by user's authorization. The high-quality and well-characterized biospecimens have been used in different translational science research projects as well as to further various epidemiologic and genomics studies.

Conclusions: The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository with a tangible translational biomedical informatics infrastructure facilitates translational research. The data query tool acts as a central source and provides a mechanism for researchers to efficiently query clinically annotated datasets and biospecimens that are pertinent to their research areas. The tool ensures patient health information protection by disclosing only deidentified data with Institutional Review Board and Health Insurance Portability and Accountability Act protocols.

Keywords: Colorectal and pancreatic neoplasm; tissue banking informatics.

Figure 1

An overview of the early detection research network colon and pancreatic virtual biorepository system designed for central database as a multi-tiered application using Oracle 9i

Figure 2

Work flow data collection and transfer at end user interface in the clinical and research environments

Figure 3

The early detection research network colon and pancreatic virtual biorepository statistics on colon and pancreatic tissue collection

Figure 4

(a) The Early Detection Research Network (EDRN) colon data entry application that allows honest brokers to enter data on web-based data entry interface. (b) The EDRN colon data entry application

Figure 5

The early detection research network colorectal and pancreatic virtual biorepository query tool criteria selection page: users can select the specific criteria for searching the central database

Figure 6

Approved investigator query tool: the approved investigator query tool shows a detailed annotation of the cases available. Users of this level can view data in multiple predefined views

Figure 7

(a–b) Detailed deidentified clinical data of an individual case that is accessible to an approved investigator

Figure 8

(a–b) Users with administrative rights that can customize their own data view and description but also edit and customize the “standard” and “extended” views for the rest of the user community