title: Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research.
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.
authors: Department of Medical Epidemiology and Biostatistics, Swedish e-Science Research Centre, Karolinska Institutet, Stockholm, Sweden.|Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors: Ola
authors: O
authors: Spjuth
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.|Uniquer Sarl, rue de la Mercerie, Lausanne, Switzerland.
authors: Maria
authors: M
authors: Krestyaninova
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.
authors: Janna
authors: J
authors: Hastings
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Biomedicum Helsinki 2U, Helsinki, Finland.
authors: Huei-Yi
authors: HY
authors: Shen
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Biomedicum Helsinki 2U, Helsinki, Finland.
authors: Jani
authors: J
authors: Heikkinen
authors: Institute of Epidemiology II, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.|Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
authors: Melanie
authors: M
authors: Waldenberger
authors: Department of Public Health and General Practice, HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway.
authors: Arnulf
authors: A
authors: Langhammer
authors: Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Lund, Sweden.|Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden.
authors: Claes
authors: C
authors: Ladenvall
authors: Estonian Genome Center, University of Tartu, Tartu, Estonia.
authors: Tõnu
authors: T
authors: Esko
authors: Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Lund, Sweden.|Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden.
authors: Mats-Åke
authors: MÅ
authors: Persson
authors: Department of Public Health and General Practice, HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway.
authors: Jon
authors: J
authors: Heggland
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.
authors: Joern
authors: J
authors: Dietrich
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.
authors: Sandra
authors: S
authors: Ose
authors: Institute of Epidemiology II, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.|Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
authors: Christian
authors: C
authors: Gieger
authors: Institute of Genetic Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg.
authors: Janina S
authors: JS
authors: Ried
authors: Institute of Epidemiology II, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.|Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
authors: Annette
authors: A
authors: Peters
authors: McGill University Health Centre, Montreal, Quebec, Canada.
authors: Isabel
authors: I
authors: Fortier
authors: Department of Biological Psychology, FGB, VU University, Amsterdam, The Netherlands.
authors: Eco J C
authors: EJ
authors: de Geus
authors: Latvian Genome Data Base (LGDB), Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, Latvia.
authors: Janis
authors: J
authors: Klovins
authors: Latvian Genome Data Base (LGDB), Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, Latvia.
authors: Linda
authors: L
authors: Zaharenko
authors: Department of Biological Psychology, FGB, VU University, Amsterdam, The Netherlands.
authors: Gonneke
authors: G
authors: Willemsen
authors: Department of Biological Psychology, FGB, VU University, Amsterdam, The Netherlands.
authors: Jouke-Jan
authors: JJ
authors: Hottenga
authors: Department of Medical Epidemiology and Biostatistics, Swedish e-Science Research Centre, Karolinska Institutet, Stockholm, Sweden.|BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, Graz, Austria.
authors: Jan-Eric
authors: JE
authors: Litton
authors: National Institute for Health and Welfare, Helsinki, Finland.|University of Jyvaskyla, Jyväskylä, Finland.
authors: Juha
authors: J
authors: Karvanen
authors: Department of Biological Psychology, FGB, VU University, Amsterdam, The Netherlands.
authors: Dorret I
authors: DI
authors: Boomsma
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Biomedicum Helsinki 2U, Helsinki, Finland.|Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, Lund, Sweden.
authors: Leif
authors: L
authors: Groop
authors: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK.|Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
authors: Johan
authors: J
authors: Rung
authors: Department of Medical Epidemiology and Biostatistics, Swedish e-Science Research Centre, Karolinska Institutet, Stockholm, Sweden.|Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Biomedicum Helsinki 2U, Helsinki, Finland.
authors: Juni
authors: J
authors: Palmgren
authors: Department of Medical Epidemiology and Biostatistics, Swedish e-Science Research Centre, Karolinska Institutet, Stockholm, Sweden.
authors: Nancy L
authors: NL
authors: Pedersen
authors: Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.|Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.
authors: Mark I
authors: MI
authors: McCarthy
authors: Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors: Cornelia M
authors: CM
authors: van Duijn
authors: Department of Public Health and General Practice, HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway.
authors: Kristian
authors: K
authors: Hveem
authors: Estonian Genome Center, University of Tartu, Tartu, Estonia.
authors: Andres
authors: A
authors: Metspalu
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Biomedicum Helsinki 2U, Helsinki, Finland.|Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
authors: Samuli
authors: S
authors: Ripatti
authors: Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.|Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK.
authors: Inga
authors: I
authors: Prokopenko
authors: Division of Epidemiology, Department of Genes and Environment, The Norwegian Institute of Public Health, Oslo, Norway.
authors: Jennifer R
authors: JR
authors: Harris
mesh_terms: D018070:Biological Specimen Banks; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000941:ethics / Q000379:methods* / Q000592:standards; D018907:Privacy