Research article

The development and deployment of Common Data Elements for tissue banks for translational research in cancer – An emerging standard based approach for the Mesothelioma Virtual Tissue Bank

Sambit K Mohanty¹ , Amita T Mistry¹ , Waqas Amin¹ , Anil V Parwani^1,2 , Andrew K Pople¹ , Linda Schmandt¹ , Sharon B Winters¹ , Erin Milliken³ , Paula Kim³ , Nancy B Whelan¹ , Ghada Farhat⁴ , Jonathan Melamed⁵ , Emanuela Taioli⁴ , Rajiv Dhir³ , Harvey I Pass⁶ and Michael J Becich^1,2

¹Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

²Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

³Translating Research Across Communities, USA

⁴Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

⁵Department of Pathology, New York University School of Medicine, New York, NY, USA

⁶Department of Cardiothoracic Surgery, Division of Thoracic Surgery and Thoracic Oncology, New York University School of Medicine, New York, NY, USA

author email corresponding author email

BMC Cancer 2008, 8:91doi:10.1186/1471-2407-8-91

Published:	8 April 2008

Abstract

Background

Recent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) – compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).

Methods

The purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).

Results

Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.

Conclusion

The CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.