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Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

Authors :
Tõnu Esko
Ola Spjuth
Huei-Yi Shen
Eco J. C. de Geus
Mats-Ake Persson
Andres Metspalu
Jon Heggland
Leif Groop
Sandra Ose
Isabel Fortier
Johan Rung
Claes Ladenvall
Dorret I. Boomsma
Cornelia M. van Duijn
Samuli Ripatti
Linda Zaharenko
Arnulf Langhammer
Jouke-Jan Hottenga
Annette Peters
Janis Klovins
Christian Gieger
Jennifer R. Harris
Joern Dietrich
Kristian Hveem
Inga Prokopenko
Juni Palmgren
Melanie Waldenberger
Mark I. McCarthy
Jani Heikkinen
Nancy L. Pedersen
Janina S. Ried
Janna Hastings
Jan-Eric Litton
Juha Karvanen
Gonneke Willemsen
Maria Krestyaninova
Epidemiology
Biological Psychology
Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep
Source :
European Journal of Human Genetics, Spjuth, O, Krestyaninova, M, Hastings, J, Shen, H Y, Heikkinen, J, Waldenberger, M, Langhammer, A, Ladenvall, C, Esko, T, Persson, M Å, Heggland, J, Dietrich, J, Ose, S, Gieger, C, Ried, J S, Peters, A, Fortier, I, de Geus, E J C, Klovins, J, Zaharenko, L, Willemsen, G, Hottenga, J J, Litton, J E, Karvanen, J, Boomsma, D I, Groop, L, Rung, J, Palmgren, J, Pedersen, N L, McCarthy, M I, van Duijn, C M, Hveem, K, Metspalu, A, Ripatti, S, Prokopenko, I & Harris, J R 2016, ' Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research ', European Journal of Human Genetics, vol. 24, no. 4, pp. 521-528 . https://doi.org/10.1038/ejhg.2015.165, European Journal of Human Genetics, 24(4), 521-528. Nature Publishing Group, Eur. J. Hum. Genet. 24, 521-528 (2015), European Journal of Human Genetics; (2015)
Publication Year :
2016

Abstract

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. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Details

Language :
English
ISSN :
10184813 and 14765438
Volume :
24
Issue :
4
Database :
OpenAIRE
Journal :
European Journal of Human Genetics
Accession number :
edsair.doi.dedup.....b8b72203de9508f6be731677dda026a9