The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

F1000Research, vol. 9, pp. 1229

Abstract

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established h uman CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

Authors 40

1. David Salgado

   Inserm · Aix-Marseille Université

   Affiliation as printed

   Aix Marseille Univ, INSERM, MMG, Marseille, France

   Aix Marseille University, Marseille

2. Irina M. Armean

   European Bioinformatics Institute · European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

   European Molecular Biology Laboratory, EMBL European Bioinformatics Institute, Wellcome Genome Campus, Hinxton

3. Michael Baudis

   SIB Swiss Institute of Bioinformatics · University of Zurich

   Affiliation as printed

   Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland

   Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Zurich

4. Sergi Beltrán

   Universitat Pompeu Fabra · Barcelona Institute of Science and Technology · Centre for Genomic Regulation · Centro Nacional de Análisis Genómico

   Affiliation as printed

   CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain

   Universitat Pompeu Fabra (UPF), Barcelona, Spain

   CNAG-CRG, Centre for Genomic Regulation (CRG), Center for Genomic Regulation, Barcelona, Baldiri Reixac 4, Barcelona 08028

   Universitat Pompeu Fabra (UPF), Barcelona

5. Salvador Capella-Gutiérrez

   Barcelona Supercomputing Center · ELIXIR

   Affiliation as printed

   Barcelona Supercomputing Center (BSC), Barcelona, Spain

   Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona, Spain

   Barcelona Supercomputing Center, Barcelona

   Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona

6. Denise Carvalho‐Silva

   European Bioinformatics Institute · Open Targets · European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

   Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK

   European Molecular Biology Laboratory, EMBL European Bioinformatics Institute, Wellcome Genome Campus, Hinxton

   Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD

7. Victoria Domínguez Del Angel

   Centre National de la Recherche Scientifique · Institut Français de Bioinformatique

   Affiliation as printed

   Institut Français de Bioinformatique, UMS3601-CNRS, CNRS, Paris, France

   Institut Français de Bioinformatique, UMS3601-CNRS, CNRS, Paris

8. Joaquı́n Dopazo

   Fundación Progreso y Salud · Hospital Universitario Virgen del Rocío

   Affiliation as printed

   Clinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocio, Sevilla, Spain

   Clinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocio, Sevilla

9. Laura Ines Furlong

   Universitat Pompeu Fabra · Hospital Del Mar · Hospital del Mar Research Institute

   Affiliation as printed

   Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain

   Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona

10. Bo Gao

    SIB Swiss Institute of Bioinformatics · University of Zurich

    Affiliation as printed

    Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland

    Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Zurich

11. Dietlind L. Gerloff

    University of Luxembourg · Luxembourg Centre for Systems Biomedicine

    Affiliation as printed

    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg

    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux

12. Ivo Glynne Gut

    Universitat Pompeu Fabra · Barcelona Institute of Science and Technology · Centre for Genomic Regulation · Centro Nacional de Análisis Genómico

    Affiliation as printed

    CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain

    Universitat Pompeu Fabra (UPF), Barcelona, Spain

    CNAG-CRG, Centre for Genomic Regulation (CRG), Center for Genomic Regulation, Barcelona, Baldiri Reixac 4, Barcelona 08028

    Universitat Pompeu Fabra (UPF), Barcelona

13. Attila Gyenesei

    University of Pecs

    Affiliation as printed

    Szentágothai Research Center, University of Pécs, Pécs, Hungary

    Szentágothai Research Center, University of Pecs, Pécs

14. John M. Hancock

    ELIXIR

    Affiliation as printed

    ELIXIR Hub, Hinxton, UK

    ELIXIR Hub, Hinxton

15. Marc Hanauer

    Inserm · Orphanet

    Affiliation as printed

    Orphanet, INSERM, Paris, France

    Orphanet, INSERM, Paris

16. Eivind J. Hovig

    Oslo University Hospital · University of Oslo

    Affiliation as printed

    Centre for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway

    Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway

    Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo

17. Lennart F. Johansson

    University Medical Center Groningen · University of Groningen

    Affiliation as printed

    Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands

    Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen

18. Thomas Keane

    European Bioinformatics Institute · European Molecular Biology Laboratory · European Molecular Biology Laboratory

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

    European Molecular Biology Laboratory, EMBL European Bioinformatics Institute, Wellcome Genome Campus, Hinxton

19. Jan O. Korbel

    European Molecular Biology Laboratory

    Affiliation as printed

    Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany

    Genome Biology, European Molecular Biological Laboratory, Heidelberg

20. Katharina B. Lauer

    ELIXIR

    Affiliation as printed

    ELIXIR Hub, Hinxton, UK

    ELIXIR Hub, Hinxton

21. Steven Laurie

    Barcelona Institute of Science and Technology · Centre for Genomic Regulation · Centro Nacional de Análisis Genómico

    Affiliation as printed

    CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain

    CNAG-CRG, Centre for Genomic Regulation (CRG), Center for Genomic Regulation, Barcelona, Baldiri Reixac 4, Barcelona 08028

22. Brane L. Leskošek

    University of Ljubljana

    Affiliation as printed

    Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia

    Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana

23. David Lloyd

    ELIXIR

    Affiliation as printed

    ELIXIR Hub, Hinxton, UK

    ELIXIR Hub, Hinxton

24. Tomàs Marquès‐Bonet

    Institució Catalana de Recerca i Estudis Avançats · Consejo Superior de Investigaciones Científicas · Institut de Biologia Evolutiva

    Affiliation as printed

    Institute of Evolutionary Biology (UPF-CSIC), Catalan Institution for Research and Advanced Studies, Barcelona, Spain

    Institute of Evolutionary Biology (UPF-CSIC), Catalan Institution for Research and Advanced Studies, Barcelona

25. Hailiang Mei Aachen Sequencing Analysis Support Core

    Leiden University Medical Center

    Affiliation as printed

    Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands

    Sequencing Analysis Support Core, Leiden University Medical Center, Leiden

26. Katalin Monostory

    Institute of Molecular Life Sciences · Hungarian Academy of Sciences · HUN-REN Research Centre for Natural Sciences

    Affiliation as printed

    Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary

    Hungarian Academy of Sciences, Budapest

27. Janet Piñero

    Universitat Pompeu Fabra · Hospital Del Mar · Hospital del Mar Research Institute

    Affiliation as printed

    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain

    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona

28. Krzysztof Poterlowicz

    University of Bradford

    Affiliation as printed

    Centre for Skin Sciences, University of Bradford, Bradford, UK

    Centre for Skin Sciences, University of Bradford, Bradford

29. Ana Rath

    Inserm · Orphanet

    Affiliation as printed

    Orphanet, INSERM, Paris, France

    Orphanet, INSERM, Paris

30. Pubudu Saneth Samarakoon

    Oslo University Hospital

    Affiliation as printed

    Department of Medical Genetics, Oslo University Hospital, Oslo, Norway

    Department of Medical Genetics, Oslo University Hospital, Oslo

31. Ferrán Sanz

    Universitat Pompeu Fabra · Hospital Del Mar · Hospital del Mar Research Institute

    Affiliation as printed

    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain

    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona

32. Gary Ian Saunders

    ELIXIR

    Affiliation as printed

    ELIXIR Hub, Hinxton, UK

    ELIXIR Hub, Hinxton

33. Daoud Sie

    Amsterdam University Medical Centers · Cancer Center Amsterdam · Vrije Universiteit Amsterdam · Amsterdam UMC Location Vrije Universiteit Amsterdam

    Affiliation as printed

    Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Medical Centre, Amsterdam

34. Morris A. Swertz

    University Medical Center Groningen · University of Groningen

    Affiliation as printed

    Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands

    Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen

35. Kirill Tsukanov

    European Bioinformatics Institute · European Molecular Biology Laboratory · European Molecular Biology Laboratory

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

    European Molecular Biology Laboratory, EMBL European Bioinformatics Institute, Wellcome Genome Campus, Hinxton

36. Alfonso Valencia

    Institució Catalana de Recerca i Estudis Avançats · Barcelona Supercomputing Center · ELIXIR

    Affiliation as printed

    Barcelona Supercomputing Center (BSC), Barcelona, Spain

    Catalan Institution of Research and Advanced Studies, Barcelona, Spain

    Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona, Spain

    Barcelona Supercomputing Center, Barcelona

    Catalan Institution of Research and Advanced Studies, Barcelona

    Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona

37. Marko Vidak

    University of Ljubljana

    Affiliation as printed

    Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia

    Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana

38. Cristina González

    European Bioinformatics Institute · European Molecular Biology Laboratory · European Molecular Biology Laboratory

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

    European Molecular Biology Laboratory, EMBL European Bioinformatics Institute, Wellcome Genome Campus, Hinxton

39. Bauke Ylstra

    Amsterdam University Medical Centers · Cancer Center Amsterdam · Vrije Universiteit Amsterdam · Amsterdam UMC Location Vrije Universiteit Amsterdam

    Affiliation as printed

    Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

    Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Medical Centre, Amsterdam

40. Christophe Béroud

    Inserm · Aix-Marseille Université · Assistance Publique Hôpitaux de Marseille · Hôpital de la Timone

    Affiliation as printed

    Aix Marseille Univ, INSERM, MMG, Marseille, France

    Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'enfants de la Timone, 13385 Marseille, France

    Aix Marseille University, Marseille

    Département de Génétique Médicale et de Biologie Cellulaire, APHM, Public Assistance - Hospitals of Marseille, 13385 Marseille