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Ghose R, Aranguren-Ibáñez Á, Arecco N, Balboa D, Bataller M, Beltran S, Benisty H, Bénard A, Bernardo E, Carbonell Sala S, Casals E, Ciampi L, Condemi L, Corvó A, Cosín-Tomás M, Cuenca-Ardura M, Duran Serrano JM, Espejo Díaz MI, Fernandez Callejo M, Gañez-Zapater A, Garcia-Castellanos R, Garrido R, Henkin G, Hermoso Pulido T, Hernandez-Alias X, Herrero Vicente J, Ingham M, Lim WM, Llonch S, Marmesat Bertoli E, Miguel-Escalada I, Montero-Blay A, Navarrete Hernández C, Neguembor MV, Ní Chárthaigh RA, Pardo-Lorente N, Pascual-Reguant L, Pérez-Lluch S, Perza R, Pesaresi M, Picó Amador D, Pifarré P, Piscia D, Plana-Carmona M, Ponomarenko J, Radusky L, Rivero E, Rogalska M, Torcal Garcia G, Wojnacki J. From research to rapid response: mass COVID-19 testing by volunteers at the Centre for Genomic Regulation. F1000Res 2021; 9:1336. [PMID: 34745570 PMCID: PMC8564741 DOI: 10.12688/f1000research.27497.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to contribute to mass testing, which has been a critical measure to contain the infection in several countries. Through this article, we share our experiences and learnings as a group of volunteers at the Centre for Genomic Regulation (CRG) in Barcelona, Spain. As members of the ORFEU project, an initiative by the Government of Catalonia to achieve mass testing of people at risk and contain the epidemic in Spain, we share our motivations, challenges and the key lessons learnt, which we feel will help better prepare the global society to address similar situations in the future.
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Affiliation(s)
- Ritobrata Ghose
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, 08005, Spain
| | - Álvaro Aranguren-Ibáñez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Niccolò Arecco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Diego Balboa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Marc Bataller
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Angèle Bénard
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Edgar Bernardo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sílvia Carbonell Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Eloi Casals
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Livia Condemi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Alberto Corvó
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Marta Cosín-Tomás
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,ISGlobal, Barcelona, 08036, Spain.,CIBER de Epidemiología y Salud Pública, Barcelona, 08023, Spain
| | - Mirabai Cuenca-Ardura
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Juan Manuel Duran Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - María Isabel Espejo Díaz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Marcos Fernandez Callejo
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Antoni Gañez-Zapater
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Raquel Garcia-Castellanos
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Romina Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Gil Henkin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Jorge Herrero Vicente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Matthew Ingham
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Wei Ming Lim
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sílvia Llonch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Elena Marmesat Bertoli
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Irene Miguel-Escalada
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Cristina Navarrete Hernández
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Róisín-Ana Ní Chárthaigh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Natalia Pardo-Lorente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Reyes Perza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Martina Pesaresi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Daniel Picó Amador
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Paula Pifarré
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ezequiel Rivero
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Malgorzata Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Guillem Torcal Garcia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - José Wojnacki
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
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Matalonga L, Hernández-Ferrer C, Piscia D, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S. Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. Eur J Hum Genet 2021; 29:1337-1347. [PMID: 34075210 PMCID: PMC8440686 DOI: 10.1038/s41431-021-00852-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/18/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022] Open
Abstract
Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics.
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Affiliation(s)
- Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Hernández-Ferrer
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - 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
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Daniel Picó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Garcia-Linares
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Anastasios Papakonstantinou
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Alberto Corvó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ricky Joshi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Hector Diez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - 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
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- European Reference Network for Rare Neurological Diseases, Tübingen, Germany
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 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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Matalonga L, Hernández-Ferrer C, Piscia D, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S. Correction to: Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. Eur J Hum Genet 2021; 29:1466-1469. [PMID: 34393220 DOI: 10.1038/s41431-021-00934-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Hernández-Ferrer
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | | | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - 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
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | | | | | | | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Daniel Picó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Garcia-Linares
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Anastasios Papakonstantinou
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Alberto Corvó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ricky Joshi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Hector Diez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - 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
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,European Reference Network for Rare Neurological Diseases, Tübingen, Germany
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 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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