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

Our plain-English summary of 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, by S.K. Mohanty, A.T. Mistry, W. Amin, et al (BMC Cancer, 2008).

The study

• Authors: S.K. Mohanty, A.T. Mistry, W. Amin, A.V. Parwani, A.K. Pople, L. Schmandt, S.B. Winters, E. Milliken, P. Kim, N.B. Whelan, G. Farhat, J. Melamed, E. Taioli, R. Dhir, H.I. Pass, M.J. Becich
• Journal: BMC Cancer
• Published: 2008;8:91
• Cited by: 31 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

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.

In plain English

This article described how the authors built a standard set of data fields, called Common Data Elements, for the Mesothelioma Virtual Bank, a research tissue bank shared by the Universities of Pennsylvania and Pittsburgh and New York University. It described an information system. It was not a study of patients' health or of asbestos exposure. The data fields drew on existing pathology and cancer registry standards. They covered demographics, epidemiology, clinical history, pathology down to individual tissue blocks, and follow-up on treatment, recurrence and vital status. When the article was written, over 400 annotated cases of pleural, peritoneal and pericardial mesothelioma were available. Most were archival paraffin blocks from surgical patients treated between 1981 and 2006. A tissue microarray held samples from 41 patients, and DNA and blood samples had been collected in 136 cases. The authors concluded that their approach can successfully lead to robust mesothelioma-related data elements. They noted that evaluation of the data elements was ongoing.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Description of the development of a data standard and database for a multi-institution mesothelioma tissue bank (informatics methods report). It is not an epidemiological or clinical study.
• Who was studied: Mesothelioma tissue bank cases at participating institutions (Universities of Pennsylvania and Pittsburgh, and New York University), including pleural, peritoneal and pericardial mesothelioma specimens
• Main results:
  • Over 400 annotated cases of pleural, peritoneal and pericardial mesothelioma specimens were available to researchers at the time of writing
  • Most cases were archival paraffin blocks from surgical patients treated between 1981 and 2006
  • A tissue microarray included samples from 41 patients
  • DNA and blood samples with clinical annotation were collected in 136 cases
  • The data elements included annotation down to individual tissue blocks, as well as follow-up information
  • The data elements were built to comply with the ISO/IEC metadata standard
• The authors' conclusion: The authors concluded that their development process showed this approach can successfully lead to robust mesothelioma-related data elements that guide collection of high-quality research data.
• Limitations the authors state:
  • The de-identification software used to protect patient privacy removes a small amount of clinical information
  • Evaluation of the data elements was still ongoing

Topics

The National Library of Medicine indexes this study under subjects our site covers: Mesothelioma.

Medical terms in this study, explained in our Lexicon: Mesothelioma, Biomarker, Pathology, Cancer Registry, Epidemiology, NIOSH.

Related studies

• National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research — W. Amin, A.V. Parwani, et al. (2008)
• National Mesothelioma Virtual Bank: A Platform for Collaborative Research and Mesothelioma Biobanking Resource to Support Translational Research — W. Amin, A.V. Parwani, et al. (2013)
• A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research — W. Amin, H. Singh, et al. (2010)
• Factors influencing malignant mesothelioma survival: a retrospective review of the National Mesothelioma Virtual Bank cohort — W. Amin, F. Linkov, et al. (2018)
• Industry, occupation, and exposure history of mesothelioma patients in the U.S. National Mesothelioma Virtual Bank, 2006-2022 — Y. Gao, J.M. Mazurek, et al. (2023)
• Emerging translational therapies for mesothelioma — H.I. Pass, B.W. Robinson, et al. (1999)

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