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An interconnected data infrastructure to support large-scale rare disease research

Title: An interconnected data infrastructure to support large-scale rare disease research
Authors: Johansson, Lennart F.; Laurie, Steve; Spalding, Dylan; Gibson, Spencer; Ruvolo, David; Thomas, Coline; Piscia, Davide; De Andrade, Fernanda; Been, Gerieke; Bijlsma, Marieke; Brunner, Han; Cimerman, Sandi; Dizjikan, Farid Yavari; Ellwanger, Kornelia; Fernandez, Marcos; Freeberg, Mallory; Van De Geijn, Gert-Jan; Kanninga, Roan; Maddi, Vatsalya; Mehtarizadeh, Mehdi; Neerincx, Pieter; Ossowski, Stephanj; Rath, Ana; Roelofs-Prins, Dieuwke; Stok-Benjamins, Marloes; Van Der Velde, K. Joeri; Veal, Colin; Van Der Vries, Gerben; Wadsley, Marc; Warren, Gregory; Zurek, Birte; Keane, Thomas; Graessner, Holm; Beltran, Sergi; Swertz, Morris A; Brookes, Anthony J.; Riess, Olaf; Haack, Tobias B.; Demidov, German; Sturm, Marc; Schulze-Hentrich, Julia M.; Schüle, Rebecca; Xu, Jishu; Kessler, Christoph; Kellner, Melanie; Synofzik, Matthis; Wilke, Carlo; Traschütz, Andreas; Schöls, Ludger; Hengel, Holger; Lerche, Holger; Kegele, Josua; Heutink, Peter; Scheffer, Hans; Hoogerbrugge, Nicoline; Hoischen, Alexander; Hoen, Peter A. C.; Vissers, Lisenka E. L. M.; Gilissen, Christian; Steyaert, Wouter; Sablauskas, Karolis; De Voer, Richarda M.; Kamsteeg, Erik-Jan; Van De Warrenburg, Bart; Van Os, Nienke; Te Paske, Iris; Janssen, Erik; De Boer, Elke; Steehouwer, Marloes; Yaldiz, Burcu; Kleefstra, Tjitske; Riaz, Umar; Warren, Greg; Shorter, Thomas; Töpf, Ana; Straub, Volker; Bettolo, Chiara Marini; Manera, Jordi Diaz; Hambleton, Sophie; Engelhardt, Karin; Clayton-Smith, Jill; Banka, Siddharth; Alexander, Elizabeth; Jackson, Adam; Faivre, Laurence; Thauvin, Christel; Vitobello, Antonio; Denommé-Pichon, Anne-Sophie; Duffourd, Yannis; Bruel, Ange-Line; Peyron, Christine; Pélissier, Aurore; Gut, Ivo Glynne; Laurie, Steven; Matalonga, Leslie; Papakonstantinou, Anastasios; Bullich, Gemma; Corvo, Alberto; Fernandez-Callejo, Marcos; Hernández, Carles; Picó, Daniel; Paramonov, Ida; Lochmüller, Hanns; Gumus, Gulcin; Bros-Facer, Virginie; Hanauer, Marc; Lagorce, David; Hongnat, Oscar; Chahdil, Maroua; Lebreton, Emeline; Stevanin, Giovanni; Durr, Alexandra; Davoine, Claire-Sophie; Guillot-Noel, Léna; Heinzmann, Anna; Coarelli, Giulia; Bonne, Gisèle; Evangelista, Teresinha; Allamand, Valérie; Nelson, Isabelle; Yaou, Rabah Ben; Metay, Corinne; Eymard, Bruno; Cohen, Enzo; Atalaia, Antonio; Stojkovic, Tanya; Macek, Milan; Turnovec, Marek; Thomasová, Dana; Kremliková, Radka Pourová; Franková, Vera; Havlovicová, Markéta; Lišková, Petra; Dolealová, Pavla; Parkinson, Helen; Robinson, Peter; Danis, Daniel; Robert, Glenn; Costa, Alessia; Patch, Christine; Hanna, Mike; Houlden, Henry; Reilly, Mary; Vandrovcova, Jana; Efthymiou, Stephanie; Morsy, Heba; Cali, Elisa; Magrinelli, Francesca; Sisodiya, Sanjay M.; Rohrer, Jonathan; Muntoni, Francesco; Zaharieva, Irina; Sarkozy, Anna; Timmerman, Vincent; Baets, Jonathan; De Vries, Geert; De Winter, Jonathan; Beijer, Danique; De Jonghe, Peter; Van De Vondel, Liedewei; De Ridder, Willem; Weckhuysen, Sarah; Nigro, Vincenzo; Mutarelli, Margherita; Morleo, Manuela; Pinelli, Michele; Varavallo, Alessandra; Banfi, Sandro; Torella, Annalaura; Musacchia, Francesco; Piluso, Giulio; Ferlini, Alessandra; Selvatici, Rita; Gualandi, Francesca; Bigoni, Stefania; Rossi, Rachele; Neri, Marcella; Aretz, Stefan; Spier, Isabel; Sommer, Anna Katharina; Peters, Sophia; Oliveira, Carla; Garcia-Pelaez, Jose; Barbosa-Matos, Rita; José, Celina São; Ferreira, Marta; Gullo, Irene; Fernandes, Susana; Garrido, Luzia; Ferreira, Pedro; Carneiro, Fátima; Van Der Velde, Joeri K.; Abbott, Kristin M.; Frederikse, Wilhemina S. Kerstjens; Zonneveld-Huijssoon, Eveline; Van Gijn, Marielle; Köhler, Sebastian; Metcalfe, Alison; Verloes, Alain; Drunat, Séverine; Heron, Delphine; Mignot, Cyril; Keren, Boris; De Sainte Agathe, Jean-Madeleine; Rooryck, Caroline; Lacombe, Didier; Trimouille, Aurelien; De La Paz, Manuel Posada; Sánchez, Eva Bermejo; Martín, EstrellaLópez; Delgado, Beatriz Martínez; De La Rosa, F. Javier Alonso García; Ciolfi, Andrea; Dallapiccola, Bruno; Pizzi, Simone; Radio, Francesca Clementina; Tartaglia, Marco; Renieri, Alessandra; Furini, Simone; Fallerini, Chiara; Benetti, Elisa; Balicza, Peter; Molnar, Maria Judit; Maver, Ales; Peterlin, Borut; Münchau, Alexander; Lohmann, Katja; Herzog, Rebecca; Pauly, Martje; Macaya, Alfons; Cazurro-Gutiérrez, Ana; Pérez-Dueñas, Belén; Munell, Francina; Jarava, Clara Franco; Masó, Laura Batlle; Marcé-Grau, Anna; Colobran, Roger; Osorio, Andrés Nascimento; De Benito, Daniel Natera; Thompson, Rachel; Polavarapu, Kiran; Grimbacher, Bodo; Beeson, David; Cossins, Judith; Hackman, Peter; Johari, Mridul; Savarese, Marco; Udd, Bjarne; Horvath, Rita; Chinnery, Patrick F.; Ratnaike, Thiloka; Gao, Fei; Schon, Katherine; Capella, Gabriel; Valle, Laura; Holinski-Feder, Elke; Laner, Andreas; Steinke-Lange, Verena; Schröck, Evelin; Rump, Andreas; Başak, Ayşe Nazll; Hemelsoet, Dimitri; Dermaut, Bart; Schuermans, Nika; Poppe, Bruce; Verdin, Hannah; Mei, Davide; Vetro, Annalisa; Balestrini, Simona; Guerrini, Renzo; Claeys, Kristl; Santen, Gijs W. E.; Bijlsma, Emilia K.; Hoffer, Mariette J. V.; Ruivenkamp, Claudia A. L.; Boztug, Kaan; Haimel, Matthias; Maystadt, Isabelle; Cordts, Isabell; Deschauer, Marcus; Zaganas, Ioannis; Kokosali, Evgenia; Lambros, Mathioudakis; Evangeliou, Athanasios; Spilioti, Martha; Kapaki, Elisabeth; Bourbouli, Mara; Striano, Pasquale; Zara, Federico; Riva, Antonella; Iacomino, Michele; Uva, Paolo; Scala, Marcello; Scudieri, Paolo; Cilio, Maria-Roberta; Carpancea, Evelina; Depondt, Chantal; Lederer, Damien; Sznajer, Yves; Duerinckx, Sarah; Mary, Sandrine; Depienne, Christel; Roos, Andreas; May, Patrick
Contributors: Johansson, Lennart F.; Laurie, Steve; Spalding, Dylan; Gibson, Spencer; Ruvolo, David; Thomas, Coline; Piscia, Davide; De Andrade, Fernanda; Been, Gerieke; Bijlsma, Marieke; Brunner, Han; Cimerman, Sandi; Dizjikan, Farid Yavari; Ellwanger, Kornelia; Fernandez, Marco; Freeberg, Mallory; Van De Geijn, Gert-Jan; Kanninga, Roan; Maddi, Vatsalya; Mehtarizadeh, Mehdi; Neerincx, Pieter; Ossowski, Stephanj; Rath, Ana; Roelofs-Prins, Dieuwke; Stok-Benjamins, Marloe; Van Der Velde, K. Joeri; Veal, Colin; Van Der Vries, Gerben; Wadsley, Marc; Warren, Gregory; Zurek, Birte; Keane, Thoma; Graessner, Holm; Beltran, Sergi; Swertz, Morris A; Brookes, Anthony J.; Riess, Olaf; Haack, Tobias B.; Demidov, German; Sturm, Marc; Schulze-Hentrich, Julia M.; Schüle, Rebecca; Xu, Jishu; Kessler, Christoph; Kellner, Melanie; Synofzik, Matthi; Wilke, Carlo; Traschütz, Andrea; Schöls, Ludger; Hengel, Holger; Lerche, Holger; Kegele, Josua; Heutink, Peter; Scheffer, Han; Hoogerbrugge, Nicoline; Hoischen, Alexander; Hoen, Peter A. C.; Vissers, Lisenka E. L. M.; Gilissen, Christian; Steyaert, Wouter; Sablauskas, Karoli; De Voer, Richarda M.; Kamsteeg, Erik-Jan; Van De Warrenburg, Bart; Van Os, Nienke; Te Paske, Iri; Janssen, Erik; De Boer, Elke; Steehouwer, Marloe; Yaldiz, Burcu; Kleefstra, Tjitske; Riaz, Umar; Warren, Greg; Shorter, Thoma; Töpf, Ana; Straub, Volker; Bettolo, Chiara Marini; Manera, Jordi Diaz; Hambleton, Sophie; Engelhardt, Karin; Clayton-Smith, Jill; Banka, Siddharth; Alexander, Elizabeth; Jackson, Adam; Faivre, Laurence; Thauvin, Christel; Vitobello, Antonio; Denommé-Pichon, Anne-Sophie; Duffourd, Yanni; Bruel, Ange-Line; Peyron, Christine; Pélissier, Aurore; Gut, Ivo Glynne; Laurie, Steven; Matalonga, Leslie; Papakonstantinou, Anastasio; Bullich, Gemma; Corvo, Alberto; Fernandez-Callejo, Marco; Hernández, Carle
Publication Year: 2024
Collection: Università degli Studi di Siena: USiena air
Subject Terms: bioinformatic; computational biology; fair data; genetic; infrastructure; rare disease
Description: The Solve-RD project brings together clinicians, scientists, and patient representatives from 51 institutes spanning 15 countries to collaborate on genetically diagnosing ("solving") rare diseases (RDs). The project aims to significantly increase the diagnostic success rate by co-analyzing data from thousands of RD cases, including phenotypes, pedigrees, exome/genome sequencing, and multiomics data. Here we report on the data infrastructure devised and created to support this co-analysis. This infrastructure enables users to store, find, connect, and analyze data and metadata in a collaborative manner. Pseudonymized phenotypic and raw experimental data are submitted to the RD-Connect Genome-Phenome Analysis Platform and processed through standardized pipelines. Resulting files and novel produced omics data are sent to the European Genome-Phenome Archive, which adds unique file identifiers and provides long-term storage and controlled access services. MOLGENIS "RD3" and Café Variome "Discovery Nexus" connect data and metadata and offer discovery services, and secure cloud-based "Sandboxes" support multiparty data analysis. This successfully deployed and useful infrastructure design provides a blueprint for other projects that need to analyze large amounts of heterogeneous data.
Document Type: article in journal/newspaper
File Description: ELETTRONICO
Language: English
Relation: info:eu-repo/semantics/altIdentifier/pmid/39302238; info:eu-repo/semantics/altIdentifier/wos/WOS:001350076800001; volume:13; numberofpages:14; journal:GIGASCIENCE; https://hdl.handle.net/11365/1277024; https://pmc.ncbi.nlm.nih.gov/articles/PMC11413801/
DOI: 10.1093/gigascience/giae058
DOI: 10.1093/gigascience/giae058/7762471?login=true
Availability: https://hdl.handle.net/11365/1277024; https://doi.org/10.1093/gigascience/giae058; https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giae058/7762471?login=true; https://pmc.ncbi.nlm.nih.gov/articles/PMC11413801/
Rights: info:eu-repo/semantics/openAccess ; license:Creative commons ; license uri:http://creativecommons.org/licenses/by/4.0/
Accession Number: edsbas.C17C1220
Database: BASE