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Jiménez-Huete A, Patiño-García A, Guillén EF, Porta JM, Martin-Bastida A, Suárez-Vega V, Pérez N. Brain 18F-FDG PET findings and sequential vestibular testing in SCA27B: a case report. J Neurol 2024; 271:1015-1018. [PMID: 37831126 DOI: 10.1007/s00415-023-12032-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Affiliation(s)
- Adolfo Jiménez-Huete
- Department of Neurology, Clínica Universidad de Navarra, C/ Marquesado de Sta. Marta, 1, 28027, Madrid, Spain.
| | - Ana Patiño-García
- Department of Pediatrics and Medical Genetics Unit, Clínica Universidad de Navarra, Pamplona, Madrid, Spain
| | | | | | - Antonio Martin-Bastida
- Department of Neurology, Clínica Universidad de Navarra, C/ Marquesado de Sta. Marta, 1, 28027, Madrid, Spain
| | - Víctor Suárez-Vega
- Department of Radiology, Clínica Universidad de Navarra, Pamplona, Madrid, Spain
| | - Nicolás Pérez
- Department of Otolaryngology, Clínica Universidad de Navarra, Pamplona, Madrid, Spain
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2
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Corvò A, Matalonga L, Spalding D, Senf A, Laurie S, Picó-Amador D, Fernandez-Callejo M, Paramonov I, Romero AF, Garcia-Rios E, Ciges JI, Mohan A, Thomas C, Silva Valencia AF, Halmagyi C, Freeberg MA, Töpf A, Horvath R, Saunders G, Gut I, Keane T, Piscia D, Beltran S. Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases. CELL GENOMICS 2023; 3:100246. [PMID: 36819661 PMCID: PMC9932977 DOI: 10.1016/j.xgen.2022.100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/04/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023]
Abstract
The Solve-RD project objectives include solving undiagnosed rare diseases (RD) through collaborative research on shared genome-phenome datasets. The RD-Connect Genome-Phenome Analysis Platform (GPAP), for data collation and analysis, and the European Genome-Phenome Archive (EGA), for file storage, are two key components of the Solve-RD infrastructure. Clinical researchers can identify candidate genetic variants within the RD-Connect GPAP and, thanks to the developments presented here as part of joint ELIXIR activities, are able to remotely visualize the corresponding alignments stored at the EGA. The Global Alliance for Genomics and Health (GA4GH) htsget streaming application programming interface (API) is used to retrieve alignment slices, which are rendered by an integrated genome viewer (IGV) instance embedded in the GPAP. As a result, it is no longer necessary for over 11,000 datasets to download large alignment files to visualize them locally. This work highlights the advantages, from both the user and infrastructure perspectives, of implementing interoperability standards for establishing federated genomics data networks.
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Affiliation(s)
- Alberto Corvò
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- CSC, Espoo, Finland
| | - Alexander Senf
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- AI-Digital, Lincoln, UK
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Daniel Picó-Amador
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Anna Foix Romero
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Emilio Garcia-Rios
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Jorge Izquierdo Ciges
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Anand Mohan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Coline Thomas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Csaba Halmagyi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Mallory Ann Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
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Graessner H, Zurek B, Hoischen A, Beltran S. Solving the unsolved rare diseases in Europe. Eur J Hum Genet 2021; 29:1319-1320. [PMID: 34140650 PMCID: PMC8440595 DOI: 10.1038/s41431-021-00924-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany. .,Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany.
| | - Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
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