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The RD-connect genome-phenome analysis platform: accelerating diagnosis, research, and gene discovery for rare diseases

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dc.contributor.authorLaurie, Steven
dc.contributor.authorPiscia, davide
dc.contributor.authorMatalonga, Leslie
dc.contributor.authorCorvó, Alberto
dc.contributor.authorFernández-Callejo, Marcos
dc.contributor.authorGarcia-Linares, Carles
dc.contributor.authorHernandez-Ferrer, Carles
dc.contributor.authorLuengo, Cristina
dc.contributor.authorMartínez, Inés
dc.contributor.authorPapakonstantinou, Anastasios
dc.contributor.authorPicó-Amador, Daniel
dc.contributor.authorProtasio, Joan
dc.contributor.authorThompson, Rachel
dc.contributor.authorTonda, Raúl
dc.contributor.authorBayés, Mónica
dc.contributor.authorBullich, Gemma
dc.contributor.authorCamps-Puchadas, Jordi
dc.contributor.authorParamonov, Ida
dc.contributor.authorTrotta, Jean Remí
dc.contributor.authorAlonso Sánchez, Ángel Miguel
dc.contributor.authorAttimonelli, Marcella
dc.contributor.authorBéroud, Christophe
dc.contributor.authorBros-Facer, Virginie
dc.contributor.authorBuske, Orion J.
dc.contributor.authorCañada-Pallarés, Andrés
dc.contributor.authorFernández, José M.
dc.contributor.authorHansson, Mats G.
dc.contributor.authorHorvath, Rita
dc.contributor.authorJacobsen, Julius O. B.
dc.contributor.authorKaliyaperumal, Rajaram
dc.contributor.authorLair-Préterre, Séverine
dc.contributor.authorLicata, Luana
dc.contributor.authorLopes, Pedro
dc.contributor.authorLópez-Martín, Estrella
dc.contributor.authorMascalzoni, Deborah
dc.contributor.authorMonaco, Lucia
dc.contributor.authorPérez-Jurado, Luis A.
dc.contributor.authorPosada-de-la-Paz, Manuel
dc.contributor.authorRambla, Jordi
dc.contributor.authorRath, Ana
dc.contributor.authorRiess, Olaf
dc.contributor.authorRobinson, Peter N.
dc.contributor.authorSalgado, David
dc.contributor.authorSmedley, Damian
dc.contributor.authorSpalding, Dylan
dc.contributor.author't Hoen, Peter A. C.
dc.contributor.authorTöpf, Ana
dc.contributor.authorZaharieva, Irina
dc.contributor.authorGraessner, , Holm
dc.contributor.authorGut, Ivo G.
dc.contributor.authorLochmüller, Hanns
dc.contributor.authorBeltrán, Sergi
dc.contributor.departmentCiencias de la Saludes_ES
dc.contributor.departmentOsasun Zientziakeu
dc.contributor.funderGobierno de Navarra / Nafarroako Gobernuaes
dc.date.accessioned2022-07-19T08:14:55Z
dc.date.available2022-07-19T08:14:55Z
dc.date.issued2022
dc.date.updated2022-06-28T11:39:02Z
dc.description.abstractRare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.en
dc.description.sponsorshipRD-Connect (RD-Connect, an integrated platform connecting registries, biobanks, and clinical bioinformatics) received funding from the Seventh Framework (FP7) Programme of the European Union under grant agreement No 305444. Data were analyzed using the RD-Connect GPAP, which received funding from EU projects Solve-RD, EJP-RD (grant numbers H2020 779257, H2020 825575), Instituto de Salud Carlos III (Grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática, INB), ELIXIR-EXCELERATE (Grant number EU H2020 #676559) and ELIXIR Implementation Studies (Remote real-time visualization of human rare disease genomics data (RD-Connect) stored at the EGA ELIXIR. 2017-2018; ELIXIR IT-2017-INTEGRATION, Rare Disease Infrastructure ELIXIR, 2019-2020 and the Beacon ELIXIR, 2019-2021). The RD-Connect GPAP has leveraged developments funded through project VEIS (001-P-001647 co-financed by the European Regional Development Fund of the European Union in the framework of the Operational Program FEDER of Catalonia 2014-2020 with the support of the Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya) and URD-Cat (PERIS SLT002/16/00174, Departament de Salut, Generalitat de Catalunya). The research leading to these results has received funding from Consequitur (Newton Fund UK/Turkey, MR/N027302/1), BBMRI-LPC (EU FP7 #313010), NeurOmics (EU FP7 #305121), the Economic Development Department of the Navarra Government (Grant number 001114112017), the European Reference Network for Rare Neurological Diseases (Project ID number 739510) and NIH, National Institute of Child Health and Human Development (1R01HD103805-01). We acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Program/Generalitat de Catalunya. We also acknowledge the support of the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and Co-financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program. HL receives support from the Canadian Institutes of Health Research (Foundation Grant FDN-167281), the Canadian Institutes of Health Research and Muscular Dystrophy Canada (Network Catalyst Grant for NMD4C), the Canada Foundation for Innovation (CFI-JELF 38412), and the Canada Research Chairs program (Canada Research Chair in Neuromuscular Genomics and Health, 950-232279).en
dc.format.extent17 p.
dc.format.mimetypeapplication/pdfen
dc.identifier.citationLaurie, S.; Piscia, D.; Matalonga, L.; Corvó, A.; Fernández-Callejo, M.; Garcia-Linares, C.; Hernandez-Ferrer, C.; Luengo, C.; Martínez, I.; Papakonstantinou, A.; Picó-Amador, D.; Protasio, J.; Thompson, R.; Tonda, R.; Bayés, M.; Bullich, G.; Camps-Puchadas, J.; Paramonov, I.; Trotta, J. R.; Alonso-Sánchez, A. M.; Attimonelli, M.; Béroud, C.; Bros-Facer, V.; Buske, O. J.; Cañada-Pallarés, A.; Fernández, J. M.; Hansson, M. G.; Horvath, R.; Jacobsen, J. O. B.; Kaliyaperumal, R.; Lair-Préterre, S.; Licata, L.; Lopes, P.; López-Martín, E.; Mascalzoni, D.; Monaco, L.; Pérez-Jurado, L. A.; Posada-de-la-Paz, M.; Rambla, J.; Rath, A.; Riess, O.; Robinson, P. N.; Salgado, D.; Smedley, D.; Spalding, D.; 't Hoen, P. A. C.; Töpf, A.; Zaharieva, I.; Graessner,, H.; Gut, I. G.; Lochmüller, H.; Beltran, S.. (2022). The RD-connect genome-phenome analysis platform: accelerating diagnosis, research, and gene discovery for rare diseases. Human Mutation. 43,6 717-733 .en
dc.identifier.doi10.1002/humu.24353
dc.identifier.issn1059-7794
dc.identifier.urihttps://academica-e.unavarra.es/handle/2454/43348
dc.language.isoengen
dc.publisherWileyen
dc.relation.ispartofHuman Mutation, 2022, 43 (6),717-733en
dc.relation.projectIDinfo:eu-repo/grantAgreement/European Commission/Horizon 2020 Framework Programme/779257en
dc.relation.projectIDinfo:eu-repo/grantAgreement/European Commission/Horizon 2020 Framework Programme/825575en
dc.relation.projectIDinfo:eu-repo/grantAgreement/European Commission/Horizon 2020 Framework Programme/676559en
dc.relation.publisherversionhttps://doi.org/10.1002/humu.24353en
dc.rights© 2022 The Authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial Licenseen
dc.rights.accessRightsAcceso abierto / Sarbide irekiaes
dc.rights.accessRightsinfo:eu-repo/semantics/openAccessen
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectData sharingen
dc.subjectData standardizationen
dc.subjectDiagnosticsen
dc.subjectGenome analysisen
dc.subjectNGSen
dc.subjectPatient matchmakingen
dc.subjectRare diseasesen
dc.titleThe RD-connect genome-phenome analysis platform: accelerating diagnosis, research, and gene discovery for rare diseasesen
dc.typeinfo:eu-repo/semantics/article
dc.type.versionVersión publicada / Argitaratu den bertsioaes
dc.type.versioninfo:eu-repo/semantics/publishedVersionen
dspace.entity.typePublication
relation.isAuthorOfPublication3a1285d1-3d56-4369-b318-c5046f7037bb
relation.isAuthorOfPublication.latestForDiscovery3a1285d1-3d56-4369-b318-c5046f7037bb

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