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Open Access Methodology

Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register

Imad Abugessaisa1, David Gomez-Cabrero1, Omri Snir24, Staffan Lindblad3, Lars Klareskog2, Vivianne Malmström2 and Jesper Tegnér1*

Author Affiliations

1 Department of Medicine, The Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden

2 Department of Medicine, The Rheumatology Unit, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden

3 Rheumatology clinic, Karolinska University Hospital, Solna, Sweden

4 Current affiliation: Department of Immunology, Centre for Immune Regulation, Oslo University Hospital-Rikshospitalet, University of Oslo, Oslo, Norway

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Journal of Translational Medicine 2013, 11:85  doi:10.1186/1479-5876-11-85

Published: 2 April 2013

Abstract

Background

Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet.

Methods

Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system.

Results

We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features.

Conclusions

Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort.

Keywords:
Swedish Rheumatology Quality Register (SRQ); Translational medicine platform; Secondary use of clinical data; Patient de-identification