Clinical Annotation and Integration of Datasets Utilizing Current Technologies: The Informatics Approach for a Tissue Banking Initiative for the Gynecologic Disease Program
Sambit K. Mohanty MD; Postdoctoral Fellow;
Content:
Sambit K Mohanty1 MD DNB, Waqas Amin1 MD , Amita T. Mistry1 MD, Lindsay Mock2 BS, John T. Milnes1 BS, Linda Schmandt1MA MS, Andrew K. Pople1 BS, Michelle Bisceglia2 BS, Anil V. Parwani1&2 MD Phd, Rajiv Dhir2 MD, Michael J. Becich1&2 MD PhD. 1 Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA. 2 Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA.
Technology:
Technology: The bioinformatics core for GDP is devised to (1) create a well-characterized and standard-based biospecimen repository for Ovarian and Endometrial malignancies; (2) facilitate the collection and transfer of well annotated datasets to the Central Data warehouse; and (3) create an internal storage system of transferred data using java-based Clinical Trial Management Application (CTMA).
Design:
Design: The major sources of data include Questionnaire data (HOPE Ovarian and Endometrial), Pathology and Cancer Registry core elements. Data collection is performed at the respective sites by specific personnel and gathered into a single platform before sending to the centralized data center. Additionally, data is stored internally in the CTMA.
Results:
Result: Since November 2003, as a part of GDP study protocol, we have been consenting patients and collecting biospecimens. The pre-operative (Case/Control) questionnaire and the CTMA fields are filled out by the Research Nurse Coordinator (RNC) on the first encounter once they are consented. The RNC then assigns a de-identified number to each case. Subsequently, the specimen is accessioned for pathologic examination (generating coPATH Data). The RNC then completes the Post-operative questionnaire. She sends copies of the entire of questionnaire data to the Data Manager, Department of Epidemiology, Department of Biomedical Informatics (DBMI) and Cancer Registry Team. Finally, datasets are transferred to the centralized data warehouse as electronic files of Questionnaire Data utilizing Scansoft Processing Unit , and Pathology and Cancer Registry Data as Excel Workbook. Corresponding datasets are stored internally in the CTMA.
Conclusion:
Conclusion: The repository for Ovarian and Endometrial malignancies can provide a platform for the GDP as well as non-GDP researchers. This resource has the potential to expedite progress in the research initiatives related to gynecological malignancies research by forming a multi-institutional bioinformatics network linking the participating institutions and individuals to enable the sharing of annotated data, standards and biospecimens.
