The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved]
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...
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F1000 Research Ltd
2020-10-01
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| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/9-1229/v1 |
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| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
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 |
| spellingShingle |
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 The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] F1000Research |
| author_facet |
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 |
| author_sort |
David Salgado |
| title |
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] |
| title_short |
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] |
| title_full |
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] |
| title_fullStr |
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] |
| title_full_unstemmed |
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] |
| title_sort |
elixir human copy number variations community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved] |
| publisher |
F1000 Research Ltd |
| series |
F1000Research |
| issn |
2046-1402 |
| publishDate |
2020-10-01 |
| description |
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. |
| url |
https://f1000research.com/articles/9-1229/v1 |
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doaj-ce2c79f73a854618a434aa5e5c6bd6722021-07-26T13:57:24ZengF1000 Research LtdF1000Research2046-14022020-10-01910.12688/f1000research.24887.127459The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved]David Salgado0Irina M. Armean1Michael Baudis2Sergi Beltran3Salvador Capella-Gutierrez4Denise Carvalho-Silva5Victoria Dominguez Del Angel6Joaquin Dopazo7Laura I. Furlong8Bo Gao9Leyla Garcia10Dietlind Gerloff11Ivo Gut12Attila Gyenesei13Nina Habermann14John M. Hancock15Marc Hanauer16Eivind Hovig17Lennart F. Johansson18Thomas Keane19Jan Korbel20Katharina B. Lauer21Steve Laurie22Brane Leskošek23David Lloyd24Tomas Marques-Bonet25Hailiang Mei26Katalin Monostory27Janet Piñero28Krzysztof Poterlowicz29Ana Rath30Pubudu Samarakoon31Ferran Sanz32Gary Saunders33Daoud Sie34Morris A. Swertz35Kirill Tsukanov36Alfonso Valencia37Marko Vidak38Cristina Yenyxe González39Bauke Ylstra40Christophe Béroud41Aix Marseille Univ, INSERM, MMG, Marseille, FranceEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UKDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, SwitzerlandCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, SpainBarcelona Supercomputing Center (BSC), Barcelona, SpainEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UKInstitut Français de Bioinformatique, UMS3601-CNRS, CNRS, Paris, FranceClinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocio, Sevilla, SpainResearch Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, SpainDepartment of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, SwitzerlandEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UKLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, LuxembourgCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, SpainSzentágothai Research Center, University of Pécs, Pécs, HungaryGenome Biology, European Molecular Biological Laboratory, Heidelberg, GermanyELIXIR Hub, Hinxton, UKOrphanet, INSERM, Paris, FranceCentre for bioinformatics, Department of Informatics, University of Oslo, Oslo, NorwayDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The NetherlandsEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UKGenome Biology, European Molecular Biological Laboratory, Heidelberg, GermanyELIXIR Hub, Hinxton, UKCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, SpainFaculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, SloveniaELIXIR Hub, Hinxton, UKInstitute of Evolutionary Biology (UPF-CSIC), Catalan Institution for Research and Advanced Studies, Barcelona, SpainSequencing Analysis Support Core, Leiden University Medical Center, Leiden, The NetherlandsInstitute of Enzymology, Research Centre for Natural Sciences, Budapest, HungaryResearch Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, SpainCentre for Skin Sciences, University of Bradford, Bradford, UKOrphanet, INSERM, Paris, FranceDepartment of Medical Genetics, Oslo University Hospital, Oslo, NorwayResearch Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, SpainELIXIR Hub, Hinxton, UKDepartment of Clinical Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The NetherlandsEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UKCatalan Institution of Research and Advanced Studies, Barcelona, SpainFaculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, SloveniaEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UKDepartment of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The NetherlandsAix Marseille Univ, INSERM, MMG, Marseille, FranceCopy 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.https://f1000research.com/articles/9-1229/v1 |