Abstract
BackgroundThe Specialized Program of Research Excellence (SPORE) in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs) that provides semantic and syntactic interoperability of data sets.ResultsThe various components of this annotation tool include the Development of Common Data Elements (CDEs) that are derived from College of American Pathologists (CAP) Checklist and North American Association of Central Cancer Registries (NAACR) standards. The Data Entry Tool is a portable and flexible Oracle-based data entry device, which is an easily mastered web-based tool. The Data Query Tool helps investigators and researchers to search de-identified information within the warehouse/resource through a "point and click" interface, thus enabling only the selected data elements to be essentially copied into a data mart using a multi dimensional model from the warehouse's relational structure.The SPORE Head and Neck Neoplasm Database contains multimodal datasets that are accessible to investigators via an easy to use query tool. The database currently holds 6553 cases and 10607 tumor accessions. Among these, there are 965 metastatic, 4227 primary, 1369 recurrent, and 483 new primary cases. The data disclosure is strictly regulated by user's authorization.ConclusionThe SPORE Head and Neck Neoplasm Virtual Biorepository is a robust translational biomedical informatics tool that can facilitate basic science, clinical, and translational research. The Data Query Tool acts as a central source providing a mechanism for researchers to efficiently find clinically annotated datasets and biospecimens that are relevant to their research areas. The tool protects patient privacy by revealing only de-identified data in accordance with regulations and approvals of the IRB and scientific review committee.
Highlights
The Specialized Program of Research Excellence (SPORE) in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs) that provides semantic and syntactic interoperability of data sets
Standard for Subject Enrollment/Exclusion All participants enrolled in the SPORE Head and Neck Neoplasm Project (Epidemiology of Genetic Susceptibility to Head and Neck Cancer) are consented and enrollment criteria are based on following inclusion/exclusion protocols: Case definition The inclusion and exclusion criteria, used to define the case series, appear below
Multiple institute participation is a feature of several tissue banks including the Cooperative Prostate Cancer Tissue Resource (CPCTR) [21], Pennsylvania Cancer Alliance for Bioinformatics Consortium (PCABC) [18], Cooperative Breast Cancer Tissue Resource (CBCTR) [22], Cooperative Human Tissue Network (CHTN) [23], Cancer Family Registries (CFR), and the Early Detection Research Network (EDRN) []
Summary
The Specialized Program of Research Excellence (SPORE) in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs) that provides semantic and syntactic interoperability of data sets. Growth in translational research, focused on the identification and validation of disease biomarkers, has led to the development of biorepositories that are capable of providing high quality biospecimens with detailed clinical annotations. The development of tissue banking and informatics systems has been recognized as crucial to the pursuit of detailed translational cancer research. The recommendation in the RAND Corporation's Case Study of Existing Human Tissue repositories, "...the collection of consistent and high quality data associated with every biospecimen and employing a standardized set of common data element for annotation..." is broadly considered best practice: this general consensus reflects the need for such standardization [3,4,5]
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