Making sense of big data in health research: Towards an EU action plan

Charles Auffray^{1

2}, Rudi Balling³, Inês Barroso⁴, László Bencze⁵, Mikael Benson⁶, Jay Bergeron⁷, Enrique Bernal-Delgado⁸, Niklas Blomberg⁹, Christoph Bock^{10

11

12}, Ana Conesa^{13

14}, Susanna Del Signore¹⁵, Christophe Delogne¹⁶, Peter Devilee¹⁷, Alberto Di Meglio¹⁸, Marinus Eijkemans¹⁹, Paul Flicek²⁰, Norbert Graf²¹, Vera Grimm²², Henk-Jan Guchelaar²³, Yi-Ke Guo²⁴, Ivo Glynne Gut²⁵, Allan Hanbury²⁶, Shahid Hanif²⁷, Ralf-Dieter Hilgers²⁸, Ángel Honrado²⁹, D Rod Hose³⁰, Jeanine Houwing-Duistermaat³¹, Tim Hubbard^{32

33}, Sophie Helen Janacek²⁰, Haralampos Karanikas³⁴, Tim Kievits³⁵, Manfred Kohler³⁶, Andreas Kremer³⁷, Jerry Lanfear³⁸, Thomas Lengauer¹², Edith Maes³⁹, Theo Meert⁴⁰, Werner Müller⁴¹, Dörthe Nickel⁴², Peter Oledzki⁴³, Bertrand Pedersen⁴⁴, Milan Petkovic⁴⁵, Konstantinos Pliakos⁴⁶, Magnus Rattray⁴¹, Josep Redón I Màs⁴⁷, Reinhard Schneider⁴⁸, Thierry Sengstag⁴⁹, Xavier Serra-Picamal⁵⁰, Wouter Spek⁵¹, Lea A I Vaas³⁶, Okker van Batenburg⁵¹, Marc Vandelaer⁵², Peter Varnai⁵³, Pablo Villoslada⁵⁴, Juan Antonio Vizcaíno²⁰, John Peter Mary Wubbe⁵⁵, Gianluigi Zanetti^{56

57}

Affiliations

¹ European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010, Paris, France. cauffray@eisbm.org.
² CIRI-UMR5308, CNRS-ENS-INSERM-UCBL, Université de Lyon, 50 avenue Tony Garnier, 69007, Lyon, France. cauffray@eisbm.org.
³ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg. rudi.balling@uni.lu.
⁴ Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
⁵ Health Services Management Training Centre, Faculty of Health and Public Services, Semmelweis University, Kútvölgyi út 2, 1125, Budapest, Hungary.
⁶ Centre for Personalised Medicine, Linköping University, 581 85, Linköping, Sweden.
⁷ Translational & Bioinformatics, Pfizer Inc., 300 Technology Square, Cambridge, MA, 02139, USA.
⁸ Institute for Health Sciences, IACS - IIS Aragon, San Juan Bosco 13, 50009, Zaragoza, Spain.
⁹ ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
¹⁰ CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.
¹¹ Department of Laboratory Medicine, Medical University of Vienna, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.
¹² Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany.
¹³ Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera 3, 46012, Valencia, Spain.
¹⁴ University of Florida, Institute of Food and Agricultural Sciences (IFAS), 2033 Mowry Road, Gainesville, FL, 32610, USA.
¹⁵ Bluecompanion Ltd, 6 London Street (second floor), London, W2 1HR, UK.
¹⁶ Technology, Data & Analytics, KPMG Luxembourg, Société Coopérative, 39 Avenue John F. Kennedy, 1855, Luxembourg, Luxembourg.
¹⁷ Department of Human Genetics, Department of Pathology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
¹⁸ Information Technology Department, European Organization for Nuclear Research (CERN), 385 Route de Meyrin, 1211, Geneva 23, Switzerland.
¹⁹ Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands.
²⁰ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
²¹ Department of Pediatric Oncology/Hematology, Saarland University, Campus Homburg, Building 9, 66421, Homburg, Germany.
²² Project Management Jülich, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
²³ Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
²⁴ Data Science Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK.
²⁵ CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08029, Barcelona, Spain.
²⁶ Institute of Software Technology and Interactive Systems, TU Wien, Favoritenstrasse 9-11/188, 1040, Vienna, Austria.
²⁷ The Association of the British Pharmaceutical Industry, 7th Floor, Southside, 105 Victoria Street, London, SW1E 6QT, UK.
²⁸ Department of Medical Statistics, RWTH-Aachen University, Universitätsklinikum Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.
²⁹ SYNAPSE Research Management Partners, Diputació 237, Àtic 3ª, 08007, Barcelona, Spain.
³⁰ Department of Infection, Immunity and Cardiovascular Disease and Insigneo Institute for In-Silico Medicine, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK.
³¹ Department of Statistics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
³² Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK.
³³ Genomics England, London, EC1M 6BQ, UK.
³⁴ National and Kapodistrian University of Athens, Medical School, Xristou Lada 6, 10561, Athens, Greece.
³⁵ Vitromics Healthcare Holding B.V., Onderwijsboulevard 225, 5223 DE, 's-Hertogenbosch, The Netherlands.
³⁶ Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.
³⁷ ITTM S.A., 9 avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
³⁸ Research Business Technology, Pfizer Ltd, GP4 Building, Granta Park, Cambridge, CB21 6GP, UK.
³⁹ Health Economics & Outcomes Research, Deloitte Belgium, Berkenlaan 8A, 1831, Diegem, Belgium.
⁴⁰ Janssen Pharmaceutica N.V., R&D G3O, Turnhoutseweg 30, 2340, Beerse, Belgium.
⁴¹ Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK.
⁴² UMR3664 IC/CNRS, Institut Curie, Section Recherche, Pavillon Pasteur, 26 rue d'Ulm, 75248, Paris cedex 05, France.
⁴³ Linguamatics Ltd, 324 Cambridge Science Park Milton Rd, Cambridge, CB4 0WG, UK.
⁴⁴ PwC Luxembourg, 2 rue Gerhard Mercator, 2182, Luxembourg, Luxembourg.
⁴⁵ Philips, HighTechCampus 36, 5656AE, Eindhoven, The Netherlands.
⁴⁶ Department of Public Health and Primary Care, KU Leuven Kulak, Etienne Sabbelaan 53, 8500, Kortrijk, Belgium.
⁴⁷ INCLIVA Health Research Institute, University of Valencia, CIBERobn ISCIII, Avenida Menéndez Pelayo 4 accesorio, 46010, Valencia, Spain.
⁴⁸ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
⁴⁹ Swiss Institute of Bioinformatics (SIB) and University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.
⁵⁰ Agency for Health Quality and Assessment of Catalonia (AQuAS), Carrer de Roc Boronat 81-95, 08005, Barcelona, Spain.
⁵¹ EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands.
⁵² Integrated BioBank of Luxembourg, 6 rue Nicolas-Ernest Barblé, 1210, Luxembourg, Luxembourg.
⁵³ Technopolis Group, 3 Pavilion Buildings, Brighton, BN1 1EE, UK.
⁵⁴ Hospital Clinic of Barcelona, Institute d'Investigacions Biomediques August Pi Sunyer (IDIBAPS), Rosello 149, 08036, Barcelona, Spain.
⁵⁵ European Platform for Patients' Organisations, Science and Industry (Epposi), De Meeûs Square 38-40, 1000, Brussels, Belgium.
⁵⁶ CRS4, Ed.1 POLARIS, 09129, Pula, Italy.
⁵⁷ BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria.

PMID: 27338147
PMCID: PMC4919856
DOI: 10.1186/s13073-016-0323-y

Making sense of big data in health research: Towards an EU action plan

Charles Auffray et al. Genome Med. 2016.

. 2016 Jun 23;8(1):71.

doi: 10.1186/s13073-016-0323-y.

Authors

Affiliations

¹ European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010, Paris, France. cauffray@eisbm.org.
² CIRI-UMR5308, CNRS-ENS-INSERM-UCBL, Université de Lyon, 50 avenue Tony Garnier, 69007, Lyon, France. cauffray@eisbm.org.
³ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg. rudi.balling@uni.lu.
⁴ Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
⁵ Health Services Management Training Centre, Faculty of Health and Public Services, Semmelweis University, Kútvölgyi út 2, 1125, Budapest, Hungary.
⁶ Centre for Personalised Medicine, Linköping University, 581 85, Linköping, Sweden.
⁷ Translational & Bioinformatics, Pfizer Inc., 300 Technology Square, Cambridge, MA, 02139, USA.
⁸ Institute for Health Sciences, IACS - IIS Aragon, San Juan Bosco 13, 50009, Zaragoza, Spain.
⁹ ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
¹⁰ CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.
¹¹ Department of Laboratory Medicine, Medical University of Vienna, Lazarettgasse 14, AKH BT25.2, 1090, Vienna, Austria.
¹² Max Planck Institute for Informatics, Campus E1 4, 66123, Saarbrücken, Germany.
¹³ Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera 3, 46012, Valencia, Spain.
¹⁴ University of Florida, Institute of Food and Agricultural Sciences (IFAS), 2033 Mowry Road, Gainesville, FL, 32610, USA.
¹⁵ Bluecompanion Ltd, 6 London Street (second floor), London, W2 1HR, UK.
¹⁶ Technology, Data & Analytics, KPMG Luxembourg, Société Coopérative, 39 Avenue John F. Kennedy, 1855, Luxembourg, Luxembourg.
¹⁷ Department of Human Genetics, Department of Pathology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
¹⁸ Information Technology Department, European Organization for Nuclear Research (CERN), 385 Route de Meyrin, 1211, Geneva 23, Switzerland.
¹⁹ Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands.
²⁰ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
²¹ Department of Pediatric Oncology/Hematology, Saarland University, Campus Homburg, Building 9, 66421, Homburg, Germany.
²² Project Management Jülich, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
²³ Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
²⁴ Data Science Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK.
²⁵ CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08029, Barcelona, Spain.
²⁶ Institute of Software Technology and Interactive Systems, TU Wien, Favoritenstrasse 9-11/188, 1040, Vienna, Austria.
²⁷ The Association of the British Pharmaceutical Industry, 7th Floor, Southside, 105 Victoria Street, London, SW1E 6QT, UK.
²⁸ Department of Medical Statistics, RWTH-Aachen University, Universitätsklinikum Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.
²⁹ SYNAPSE Research Management Partners, Diputació 237, Àtic 3ª, 08007, Barcelona, Spain.
³⁰ Department of Infection, Immunity and Cardiovascular Disease and Insigneo Institute for In-Silico Medicine, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK.
³¹ Department of Statistics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
³² Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK.
³³ Genomics England, London, EC1M 6BQ, UK.
³⁴ National and Kapodistrian University of Athens, Medical School, Xristou Lada 6, 10561, Athens, Greece.
³⁵ Vitromics Healthcare Holding B.V., Onderwijsboulevard 225, 5223 DE, 's-Hertogenbosch, The Netherlands.
³⁶ Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.
³⁷ ITTM S.A., 9 avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
³⁸ Research Business Technology, Pfizer Ltd, GP4 Building, Granta Park, Cambridge, CB21 6GP, UK.
³⁹ Health Economics & Outcomes Research, Deloitte Belgium, Berkenlaan 8A, 1831, Diegem, Belgium.
⁴⁰ Janssen Pharmaceutica N.V., R&D G3O, Turnhoutseweg 30, 2340, Beerse, Belgium.
⁴¹ Faculty of Life Sciences, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK.
⁴² UMR3664 IC/CNRS, Institut Curie, Section Recherche, Pavillon Pasteur, 26 rue d'Ulm, 75248, Paris cedex 05, France.
⁴³ Linguamatics Ltd, 324 Cambridge Science Park Milton Rd, Cambridge, CB4 0WG, UK.
⁴⁴ PwC Luxembourg, 2 rue Gerhard Mercator, 2182, Luxembourg, Luxembourg.
⁴⁵ Philips, HighTechCampus 36, 5656AE, Eindhoven, The Netherlands.
⁴⁶ Department of Public Health and Primary Care, KU Leuven Kulak, Etienne Sabbelaan 53, 8500, Kortrijk, Belgium.
⁴⁷ INCLIVA Health Research Institute, University of Valencia, CIBERobn ISCIII, Avenida Menéndez Pelayo 4 accesorio, 46010, Valencia, Spain.
⁴⁸ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
⁴⁹ Swiss Institute of Bioinformatics (SIB) and University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.
⁵⁰ Agency for Health Quality and Assessment of Catalonia (AQuAS), Carrer de Roc Boronat 81-95, 08005, Barcelona, Spain.
⁵¹ EuroBioForum Foundation, Chrysantstraat 10, 3135 HG, Vlaardingen, The Netherlands.
⁵² Integrated BioBank of Luxembourg, 6 rue Nicolas-Ernest Barblé, 1210, Luxembourg, Luxembourg.
⁵³ Technopolis Group, 3 Pavilion Buildings, Brighton, BN1 1EE, UK.
⁵⁴ Hospital Clinic of Barcelona, Institute d'Investigacions Biomediques August Pi Sunyer (IDIBAPS), Rosello 149, 08036, Barcelona, Spain.
⁵⁵ European Platform for Patients' Organisations, Science and Industry (Epposi), De Meeûs Square 38-40, 1000, Brussels, Belgium.
⁵⁶ CRS4, Ed.1 POLARIS, 09129, Pula, Italy.
⁵⁷ BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria.

PMID: 27338147
PMCID: PMC4919856
DOI: 10.1186/s13073-016-0323-y

Erratum in

Erratum to: Making sense of big data in health research: towards an EU action plan.
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Auffray C, et al. Genome Med. 2016 Nov 7;8(1):118. doi: 10.1186/s13073-016-0376-y. Genome Med. 2016. PMID: 27821178 Free PMC article. No abstract available.

Abstract

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans.

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Figures

**Fig. 1**
Making sense of complex data and overcoming the hairball syndrome using systems biology algorithms and visualization tools. a Visualization of the topology of clinical data from the U-BIOPRED consortium adult severe asthma cohorts (courtesy of Ratko Djukanovic, University of Southampton, UK and Peter Sterk, Amsterdam Medical Center, The Netherlands) [126] using Topology Data Analysis from Ayasdi [127, 128]. b Network obtained though integration of genome, transcriptome, and proteome data from the SysCLAD consortium lung transplantation cohorts (courtesy of Johann Pellet, EISBM, France) [129, 130] using Ingenuity® Variant Analysis [131]. c Typical static representation of a molecular pathway in Thomson Reuters GeneGo MetaCore™ [132]. d An example of a detailed representation of biochemical reactions in the LCSB Parkinson’s molecular map [133]. e A cellular-level representation of biological interactions in the EISBM AsthmaMap (courtesy of Alexander Mazein, EISBM, France) [134, 135]. f A network representation of data and statements developed as part of a biocentric knowledge base within the eTRIKS consortium (courtesy of Mansoor Saqi and Irina Balaur, EISBM, France) [67]

See this image and copyright information in PMC

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Making sense of big data in health research: Towards an EU action plan

Affiliations

Making sense of big data in health research: Towards an EU action plan

Authors

Affiliations

Erratum in

Abstract

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References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical