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Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab. (Spjuth)ORCID iD: 0000-0002-8083-2864
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2016 (English)In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 24, no 4, 521-528 p.Article in journal (Refereed) Published
Abstract [en]

A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase.

Place, publisher, year, edition, pages
2016. Vol. 24, no 4, 521-528 p.
National Category
Bioinformatics (Computational Biology)
Research subject
URN: urn:nbn:se:uu:diva-261092DOI: 10.1038/ejhg.2015.165ISI: 000374124800007PubMedID: 26306643OAI: diva2:849646
Swedish e‐Science Research CentereSSENCE - An eScience CollaborationScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceEU, FP7, Seventh Framework Programme, HEALTH-F4-2010-261433

De två första författarna delar förstaförfattarskapet.

Available from: 2015-08-29 Created: 2015-08-29 Last updated: 2016-08-08Bibliographically approved

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Spjuth, OlaRung, Johan
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Department of Pharmaceutical BiosciencesScience for Life Laboratory, SciLifeLabDepartment of Immunology, Genetics and Pathology
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European Journal of Human Genetics
Bioinformatics (Computational Biology)

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