AN INFORMATICS-DRIVEN TISSUE BANKING EFFORT FOR MESOTHELIOMA - THE MESOTHELIOMA VIRTUAL BANK (MVB) MODEL TO ACCELERATE TRANSLATIONAL RESEARCH: AN UPDATE
Electronic Poster - Honorable MentionMichael Feldman MD; University of Pennsylvania; Anil V Parwani MD; University Of Pittsburgh; Sharon B Winters MA; University Of Pittsburgh; Linda Schmandt MBA; University Of Pittsburgh; Michael J Becich MD; University Of Pittsburgh; Ghada Farhat PhD; University Of Pittsburgh; Amita Mistry MD; University Of Pittsburgh; Smbit K. Mohanty MD; University Of Pittsburgh; Waqas Amin MD; University Of Pittsburgh; Emanuela Taioli MD; University Of Pittsburgh;
Content:
Advances in molecular pathology, systems biology, genomics, proteomics, clinical trails, and biomarker development studies have lead to the need for standardized and well annotated biospecimen for research. Mesothelioma Virtual Biorepository (MVB) drives together information from epidemiological, clinical, pathological, and molecular areas to develop sets of Common Data Elements to annotate the tissue specimens, providing useful and vital information for the end-users. The MVB project is supported by the Centers for Disease Control and Prevention (CDC), and associated with the National Institute for Occupational Safety and Health (NIOHS).
Technology:
The MVB web-based tool is based upon the caTISSUE Clinical Annotation Engine (CAE), originally developed by the University of Pittsburgh as part of the National Cancer Institutes (NCI) Cancer Biomedical Grid (caBIG) program. It provides a mechanism for entering, importing and searching for biospecimen annotation. In the latest released version of this software (version 1.3), clinical annotations are attached to either a participant/patient, a tissue accession or a specimen (part) or sub-specimen (block). Altogether these entities form a hierarchy or backbone that encapsulates all of the annotation data for a case. Annotations can be entered manually using the provided user interface or imported using an XML format. The application provides a mechanism for making mesothelioma cases searchable via a user-friendly web interface. The resulting system has been made available publicly on the Department of Biomedical Informatics (DBMI) website (www.mesotissue.org). Information models for MVB are constructed as Unified Modeling Language (UML) class diagrams constructing, visualizing, and documenting the artifacts of software engineering. A UML class diagram is one that depicts a collection of static model elements such as physical or conceptual entities and their relationships. Enterprise Architect (EA) (developed by Sparx System) has been utilized as the UML modeling tool for this project due to its low cost and high performance. High-level UML classes were then joined by relations representing the logical relationships between classes.
Design:
DESIGN The MVB architecture is based on three major components that work in succession to rationalize the process of data annotation. Common Data Element (CDE) The entire set of information regarding CDEs is gathered during the routine work of medical center, so these data sets can be easily configured and maintained. The Common Data Elements were built upon the College of American Pathologists (CAP) checklists, the Association of Directors of Anatomic and Surgical pathology (ADASP) guidelines, and the North American Association of Central Cancer Registries (NAACR), core elements. The final set of data elements thus formed provides sufficient and comprehensive information. Data Entry The Data Entry tool is mobile, adjustable and web based. Data entered is de-identified before being made available in the database. Data Query Tool The Data Query Tool runs on a point and click query system, thereby facilitating researchers to search through de-identified data, while at the same time only allowing specific data to be copied and transferred. The level of query is dependent on the access level granted to the investigators.
Results:
The database contains standardized sets of clinical (demographic and epidemiologic data) and pathological information, follow-up information, and genotypes data. These are available to investigators via an easy to use query tool so they can maximally utilize tissue samples. The data disclosed are tightly regulated depending upon users authorization. Such a secure and easily navigated database provides access to vast source of information related to biospecimens for the end-users.
Conclusion:
The Mesotheleoma Virtual Biorepository acts as a central resource allowing researchers to access well annotated high quality biospecimen. It protects patient privacy by disclosing only de-identified data and biospecimen can be accessible to researchers only with Institutional Review Board (IRB) and Scientific Review Board Committee approval. The integration of heterogeneous datasets along with an efficient statistical analysis provides user with standardized biospecimen to support their research.
