Abstract
BACKGROUND: Our knowledge of childhood diseases has been greatly expanded by research on biologic specimens. Clinical researchers commonly collect multiple specimens per patient and use genomics and proteomics to study disease processes and to predict the response to treatment. The ability of such studies to generate meaningful results is dependent on a well–annotated biospecimen repository, which combines pathology data and experimental data from high throughput technologies and structured clinical data. We present the architecture and approach of an evolving information service at Indiana University for specimen collections with clinical and research data annotations. The services to be provided include: specimen inventory, clinical data annotations, experimental data annotations, analysis toolbox and data visualizationAPPROACH: A virtual specimen inventory was created for tracking specimens based on the National Cancer Institute's Cancer Bioinformatics Grid's (CaBIG) Tissue Banking and Pathology Taskforce's tool for specimen storage and distribution, CaTISSUE. Clinical data annotations are to be done through customized data entry forms. Customized data entry forms for pediatric oncology based on the College of American Pathology (CAP) cancer protocols are to be created and linked to SNOMED and LOINC concept codes suitable for standard data interchange. Additional clinical data from the Regenstrief Medical Records System can also be used through the applications generated for the Shared Pathology Information Network. The experimental data annotation currently consists of gene expression data and proteomics mass spectroscopy data. The analysis toolbox consists of commonly used algorithms hosted on a scalable computing server platform. All analysis workflows are catalogued and are available for reuse for future research projects. Temporal and multidimensional visualization tools allow clinicians to better explore and understand large datasets. This standardized information system can be expanded to a campus wide or inter-campus resource.CONCLUSION: An integrated specimen information system can greatly enhance our ability to identify key factors leading to childhood diseases by using powerful computational and visualization tools for co-analyses of high throughput data with clinical data. This standardized system will facilitate intra- and inter-campus collaboration, data sharing, and the gain of greater knowledge.
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
