F1000Research (Oct 2020)
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved]
- David Salgado,
- Irina M. Armean,
- Michael Baudis,
- Sergi Beltran,
- Salvador Capella-Gutierrez,
- Denise Carvalho-Silva,
- Victoria Dominguez Del Angel,
- Joaquin Dopazo,
- Laura I. Furlong,
- Bo Gao,
- Leyla Garcia,
- Dietlind Gerloff,
- Ivo Gut,
- Attila Gyenesei,
- Nina Habermann,
- John M. Hancock,
- Marc Hanauer,
- Eivind Hovig,
- Lennart F. Johansson,
- Thomas Keane,
- Jan Korbel,
- Katharina B. Lauer,
- Steve Laurie,
- Brane Leskošek,
- David Lloyd,
- Tomas Marques-Bonet,
- Hailiang Mei,
- Katalin Monostory,
- Janet Piñero,
- Krzysztof Poterlowicz,
- Ana Rath,
- Pubudu Samarakoon,
- Ferran Sanz,
- Gary Saunders,
- Daoud Sie,
- Morris A. Swertz,
- Kirill Tsukanov,
- Alfonso Valencia,
- Marko Vidak,
- Cristina Yenyxe González,
- Bauke Ylstra,
- Christophe Béroud
Affiliations
- David Salgado
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- Irina M. Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Michael Baudis
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain
- Salvador Capella-Gutierrez
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Victoria Dominguez Del Angel
- Institut Français de Bioinformatique, UMS3601-CNRS, CNRS, Paris, France
- Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocio, Sevilla, Spain
- Laura I. Furlong
- 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
- Bo Gao
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Leyla Garcia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Dietlind Gerloff
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain
- Attila Gyenesei
- Szentágothai Research Center, University of Pécs, Pécs, Hungary
- Nina Habermann
- Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany
- John M. Hancock
- ELIXIR Hub, Hinxton, UK
- Marc Hanauer
- Orphanet, INSERM, Paris, France
- Eivind Hovig
- Centre for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Lennart F. Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Jan Korbel
- Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany
- Katharina B. Lauer
- ELIXIR Hub, Hinxton, UK
- Steve Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain
- Brane Leskošek
- Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia
- David Lloyd
- ELIXIR Hub, Hinxton, UK
- Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
- Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Janet Piñero
- 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
- Krzysztof Poterlowicz
- Centre for Skin Sciences, University of Bradford, Bradford, UK
- Ana Rath
- Orphanet, INSERM, Paris, France
- Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Ferran Sanz
- 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
- Gary Saunders
- ELIXIR Hub, Hinxton, UK
- Daoud Sie
- Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Morris A. Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Alfonso Valencia
- Catalan Institution of Research and Advanced Studies, Barcelona, Spain
- Marko Vidak
- Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia
- Cristina Yenyxe González
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- DOI
- https://doi.org/10.12688/f1000research.24887.1
- Journal volume & issue
-
Vol. 9
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 human 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.
