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Amin W, Parwani AV, Melamed J, Flores R, Pennathur A, Valdivieso F, Whelan NB, Landreneau R, Luketich J, Feldman M, Pass HI, Becich MJ. National Mesothelioma Virtual Bank: A Platform for Collaborative Research and Mesothelioma Biobanking Resource to Support Translational Research. Lung Cancer Int 2013; 2013:765748. [PMID: 26316942 PMCID: PMC4437393 DOI: 10.1155/2013/765748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/23/2022]
Abstract
The National Mesothelioma Virtual Bank (NMVB), developed six years ago, gathers clinically annotated human mesothelioma specimens for basic and clinical science research. During this period, this resource has greatly increased its collection of specimens by expanding the number of contributing academic health centers including New York University, University of Pennsylvania, University of Pittsburgh Medical Center, and Mount Sinai School of Medicine. Marketing efforts at both national and international annual conferences increase awareness and availability of the mesothelioma specimens at no cost to approved investigators, who query the web-based NMVB database for cumulative and appropriate patient clinicopathological information on the specimens. The data disclosure and specimen distribution protocols are tightly regulated to maintain compliance with participating institutions' IRB and regulatory committee reviews. The NMVB currently has over 1120 annotated cases available for researchers, including paraffin embedded tissues, fresh frozen tissue, tissue microarrays (TMA), blood samples, and genomic DNA. In addition, the resource offers expertise and assistance for collaborative research. Furthermore, in the last six years, the resource has provided hundreds of specimens to the research community. The investigators can request specimens and/or data by submitting a Letter of Intent (LOI) that is evaluated by NMVB research evaluation panel (REP).
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Affiliation(s)
- Waqas Amin
- Department of Biomedical Informatics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anil V. Parwani
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jonathan Melamed
- Department of Pathology, New York University Medical Center, New York, NY, USA
| | - Raja Flores
- Department of Cardiothoracic Surgery, Mount Sinai School of Medicine, New York, NY, USA
| | - Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Nancy B. Whelan
- Department of Biomedical Informatics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Rodeny Landreneau
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - James Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael Feldman
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Medical Center, New York, NY, USA
| | - Michael J. Becich
- Department of Biomedical Informatics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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Amin W, Parwani AV, Schmandt L, Mohanty SK, Farhat G, Pople AK, Winters SB, Whelan NB, Schneider AM, Milnes JT, Valdivieso FA, Feldman M, Pass HI, Dhir R, Melamed J, Becich MJ. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer 2008; 8:236. [PMID: 18700971 PMCID: PMC2533341 DOI: 10.1186/1471-2407-8-236] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2008] [Accepted: 08/13/2008] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. METHODS The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid (caBIG, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. RESULT The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. CONCLUSION The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers.
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Affiliation(s)
- Waqas Amin
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Anil V Parwani
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, PA, USA
| | - Linda Schmandt
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Sambit K Mohanty
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Ghada Farhat
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrew K Pople
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Sharon B Winters
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Nancy B Whelan
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Althea M Schneider
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - John T Milnes
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
| | - Federico A Valdivieso
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Michael Feldman
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery and Thoracic Oncology, New York University School of Medicine, New York, NY, USA
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh School of Medicine, PA, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michael J Becich
- Departments of Biomedical Informatics, University of Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, PA, USA
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Mohanty SK, Mistry AT, Amin W, Parwani AV, Pople AK, Schmandt L, Winters SB, Milliken E, Kim P, Whelan NB, Farhat G, Melamed J, Taioli E, Dhir R, Pass HI, Becich MJ. 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. BMC Cancer 2008; 8:91. [PMID: 18397527 PMCID: PMC2329649 DOI: 10.1186/1471-2407-8-91] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2007] [Accepted: 04/08/2008] [Indexed: 11/17/2022] Open
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.
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Affiliation(s)
- Sambit K Mohanty
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amita T Mistry
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Waqas Amin
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anil V Parwani
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrew K Pople
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Linda Schmandt
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sharon B Winters
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Paula Kim
- Translating Research Across Communities, USA
| | - Nancy B Whelan
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ghada Farhat
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan Melamed
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Emanuela Taioli
- Department of Epidemiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rajiv Dhir
- Translating Research Across Communities, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery and Thoracic Oncology, New York University School of Medicine, New York, NY, USA
| | - Michael J Becich
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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