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

Rare Diseases / genetics Humans Databases, Genetic Phenotype Metadata Computational Biology / methods Genomics / methods
bioinformatics computational biology fair data genetics infrastructure rare disease

Journal

GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872

Informations de publication

Date de publication:
02 Jan 2024
Historique:
received: 07 09 2023
revised: 29 03 2024
accepted: 21 07 2024
medline: 20 9 2024
pubmed: 20 9 2024
entrez: 20 9 2024
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1093/gigascience/giae058 PMID: 39302238
pubmed: 39302238
pii: 7762471
doi: 10.1093/gigascience/giae058
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Horizon 2020 Framework Programme
ID : 779257
Organisme : Instituto de Salud Carlos III
ID : PT13/0001/0044
Organisme : CINECA
ID : H2020 779257

Investigateurs

Olaf Riess (O)
Tobias B Haack (TB)
Holm Graessner (H)
Birte Zurek (B)
Kornelia Ellwanger (K)
Stephan Ossowski (S)
German Demidov (G)
Marc Sturm (M)
Julia M Schulze-Hentrich (JM)
Rebecca Schüle (R)
Jishu Xu (J)
Christoph Kessler (C)
Melanie Kellner (M)
Matthis Synofzik (M)
Carlo Wilke (C)
Andreas Traschütz (A)
Ludger Schöls (L)
Holger Hengel (H)
Holger Lerche (H)
Josua Kegele (J)
Peter Heutink (P)
Han Brunner (H)
Hans Scheffer (H)
Nicoline Hoogerbrugge (N)
Alexander Hoischen (A)
Peter A C 't Hoen (PAC)
Lisenka E L M Vissers (LELM)
Christian Gilissen (C)
Wouter Steyaert (W)
Karolis Sablauskas (K)
Richarda M de Voer (RM)
Erik-Jan Kamsteeg (EJ)
Bart van de Warrenburg (B)
Nienke van Os (N)
Iris Te Paske (I)
Erik Janssen (E)
Elke de Boer (E)
Marloes Steehouwer (M)
Burcu Yaldiz (B)
Tjitske Kleefstra (T)
Anthony J Brookes (AJ)
Colin Veal (C)
Spencer Gibson (S)
Vatsalya Maddi (V)
Mehdi Mehtarizadeh (M)
Umar Riaz (U)
Greg Warren (G)
Farid Yavari Dizjikan (FY)
Thomas Shorter (T)
Ana Töpf (A)
Volker Straub (V)
Chiara Marini Bettolo (CM)
Jordi Diaz Manera (JD)
Sophie Hambleton (S)
Karin Engelhardt (K)
Jill Clayton-Smith (J)
Siddharth Banka (S)
Elizabeth Alexander (E)
Adam Jackson (A)
Laurence Faivre (L)
Christel Thauvin (C)
Antonio Vitobello (A)
Anne-Sophie Denommé-Pichon (AS)
Yannis Duffourd (Y)
Ange-Line Bruel (AL)
Christine Peyron (C)
Aurore Pélissier (A)
Sergi Beltran (S)
Ivo Glynne Gut (IG)
Steven Laurie (S)
Davide Piscia (D)
Leslie Matalonga (L)
Anastasios Papakonstantinou (A)
Gemma Bullich (G)
Alberto Corvo (A)
Marcos Fernandez-Callejo (M)
Carles Hernández (C)
Daniel Picó (D)
Ida Paramonov (I)
Hanns Lochmüller (H)
Gulcin Gumus (G)
Virginie Bros-Facer (V)
Ana Rath (A)
Marc Hanauer (M)
David Lagorce (D)
Oscar Hongnat (O)
Maroua Chahdil (M)
Emeline Lebreton (E)
Giovanni Stevanin (G)
Alexandra Durr (A)
Claire-Sophie Davoine (CS)
Léna Guillot-Noel (L)
Anna Heinzmann (A)
Giulia Coarelli (G)
Gisèle Bonne (G)
Teresinha Evangelista (T)
Valérie Allamand (V)
Isabelle Nelson (I)
Rabah Ben Yaou (RB)
Corinne Metay (C)
Bruno Eymard (B)
Enzo Cohen (E)
Antonio Atalaia (A)
Tanya Stojkovic (T)
Milan Macek (M)
Marek Turnovec (M)
Dana Thomasová (D)
Radka Pourová Kremliková (RP)
Vera Franková (V)
Markéta Havlovicová (M)
Petra Lišková (P)
Pavla Doležalová (P)
Helen Parkinson (H)
Thomas Keane (T)
Mallory Freeberg (M)
Coline Thomas (C)
Dylan Spalding (D)
Peter Robinson (P)
Daniel Danis (D)
Glenn Robert (G)
Alessia Costa (A)
Christine Patch (C)
Mike Hanna (M)
Henry Houlden (H)
Mary Reilly (M)
Jana Vandrovcova (J)
Stephanie Efthymiou (S)
Heba Morsy (H)
Elisa Cali (E)
Francesca Magrinelli (F)
Sanjay M Sisodiya (SM)
Jonathan Rohrer (J)
Francesco Muntoni (F)
Irina Zaharieva (I)
Anna Sarkozy (A)
Vincent Timmerman (V)
Jonathan Baets (J)
Geert de Vries (G)
Jonathan De Winter (J)
Danique Beijer (D)
Peter de Jonghe (P)
Liedewei Van de Vondel (L)
Willem De Ridder (W)
Sarah Weckhuysen (S)
Vincenzo Nigro (V)
Margherita Mutarelli (M)
Manuela Morleo (M)
Michele Pinelli (M)
Alessandra Varavallo (A)
Sandro Banfi (S)
Annalaura Torella (A)
Francesco Musacchia (F)
Giulio Piluso (G)
Alessandra Ferlini (A)
Rita Selvatici (R)
Francesca Gualandi (F)
Stefania Bigoni (S)
Rachele Rossi (R)
Marcella Neri (M)
Stefan Aretz (S)
Isabel Spier (I)
Anna Katharina Sommer (AK)
Sophia Peters (S)
Carla Oliveira (C)
Jose Garcia-Pelaez (J)
Rita Barbosa-Matos (R)
Celina São José (CS)
Marta Ferreira (M)
Irene Gullo (I)
Susana Fernandes (S)
Luzia Garrido (L)
Pedro Ferreira (P)
Fátima Carneiro (F)
Morris A Swertz (MA)
Lennart Johansson (L)
Joeri K van der Velde (JK)
Gerben van der Vries (G)
Pieter B Neerincx (PB)
David Ruvolo (D)
Kristin M Abbott (KM)
Wilhemina S Kerstjens Frederikse (WSK)
Eveline Zonneveld-Huijssoon (E)
Dieuwke Roelofs-Prins (D)
Marielle van Gijn (M)
Sebastian Köhler (S)
Alison Metcalfe (A)
Alain Verloes (A)
Séverine Drunat (S)
Delphine Heron (D)
Cyril Mignot (C)
Boris Keren (B)
Jean-Madeleine de Sainte Agathe (JM)
Caroline Rooryck (C)
Didier Lacombe (D)
Aurelien Trimouille (A)
Manuel Posada De la Paz (MP)
Eva Bermejo Sánchez (EB)
Estrella López Martín (EL)
Beatriz Martínez Delgado (BM)
F Javier Alonso García de la Rosa (FJAG)
Andrea Ciolfi (A)
Bruno Dallapiccola (B)
Simone Pizzi (S)
Francesca Clementina Radio (FC)
Marco Tartaglia (M)
Alessandra Renieri (A)
Simone Furini (S)
Chiara Fallerini (C)
Elisa Benetti (E)
Peter Balicza (P)
Maria Judit Molnar (MJ)
Ales Maver (A)
Borut Peterlin (B)
Alexander Münchau (A)
Katja Lohmann (K)
Rebecca Herzog (R)
Martje Pauly (M)
Alfons Macaya (A)
Ana Cazurro-Gutiérrez (A)
Belén Pérez-Dueñas (B)
Francina Munell (F)
Clara Franco Jarava (CF)
Laura Batlle Masó (LB)
Anna Marcé-Grau (A)
Roger Colobran (R)
Andrés Nascimento Osorio (AN)
Daniel Natera de Benito (DN)
Hanns Lochmüller (H)
Rachel Thompson (R)
Kiran Polavarapu (K)
Bodo Grimbacher (B)
David Beeson (D)
Judith Cossins (J)
Peter Hackman (P)
Mridul Johari (M)
Marco Savarese (M)
Bjarne Udd (B)
Rita Horvath (R)
Patrick F Chinnery (PF)
Thiloka Ratnaike (T)
Fei Gao (F)
Katherine Schon (K)
Gabriel Capella (G)
Laura Valle (L)
Elke Holinski-Feder (E)
Andreas Laner (A)
Verena Steinke-Lange (V)
Evelin Schröck (E)
Andreas Rump (A)
Ayşe Nazlı Başak (AN)
Dimitri Hemelsoet (D)
Bart Dermaut (B)
Nika Schuermans (N)
Bruce Poppe (B)
Hannah Verdin (H)
Davide Mei (D)
Annalisa Vetro (A)
Simona Balestrini (S)
Renzo Guerrini (R)
Kristl Claeys (K)
Gijs W E Santen (GWE)
Emilia K Bijlsma (EK)
Mariette J V Hoffer (MJV)
Claudia A L Ruivenkamp (CAL)
Kaan Boztug (K)
Matthias Haimel (M)
Isabelle Maystadt (I)
Isabell Cordts (I)
Marcus Deschauer (M)
Ioannis Zaganas (I)
Evgenia Kokosali (E)
Mathioudakis Lambros (M)
Athanasios Evangeliou (A)
Martha Spilioti (M)
Elisabeth Kapaki (E)
Mara Bourbouli (M)
Pasquale Striano (P)
Federico Zara (F)
Antonella Riva (A)
Michele Iacomino (M)
Paolo Uva (P)
Marcello Scala (M)
Paolo Scudieri (P)
Maria-Roberta Cilio (MR)
Evelina Carpancea (E)
Chantal Depondt (C)
Damien Lederer (D)
Yves Sznajer (Y)
Sarah Duerinckx (S)
Sandrine Mary (S)
Christel Depienne (C)
Andreas Roos (A)
Patrick May (P)

Informations de copyright

© The Author(s) 2024. Published by Oxford University Press GigaScience.

Auteurs

Lennart F Johansson (LF)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0002-4914-3737

Steve Laurie (S)

Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
Universitat de Barcelona (UB), Gran Via de les Corts Catalanes, 585, L'Eixample, 08007, Barcelona, Spain.
ORCID: 0000-0003-3913-5829

Dylan Spalding (D)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
ORCID: 0000-0002-4285-2493

Spencer Gibson (S)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
ORCID: 0000-0003-0768-1542

David Ruvolo (D)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0002-5745-5298

Coline Thomas (C)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
ORCID: 0000-0003-2253-1171

Davide Piscia (D)

Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
Universitat de Barcelona (UB), Gran Via de les Corts Catalanes, 585, L'Eixample, 08007, Barcelona, Spain.
ORCID: 0000-0002-0468-0408

Fernanda de Andrade (F)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0003-4689-6319

Gerieke Been (G)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0009-0002-6667-5951

Marieke Bijlsma (M)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.

Han Brunner (H)

Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, The Netherlands.
Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O.Box 9103, Nijmegen, 6500 HD, The Netherlands.
Department of Clinical Genetics, Maastricht University Medical Centre, P. Debyelaan 25, Maastricht, 6229 HX, The Netherlands.
ORCID: 0000-0001-9274-8865

Sandi Cimerman (S)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0009-0009-9918-2185

Farid Yavari Dizjikan (FY)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.

Kornelia Ellwanger (K)

Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstraße 7, Tübingen 72076, Germany.
ORCID: 0000-0003-4845-5795

Marcos Fernandez (M)

Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
Universitat de Barcelona (UB), Gran Via de les Corts Catalanes, 585, L'Eixample, 08007, Barcelona, Spain.
ORCID: 0000-0002-9968-3766

Mallory Freeberg (M)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
ORCID: 0000-0003-2949-3921

Gert-Jan van de Geijn (GJ)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0001-6161-0476

Roan Kanninga (R)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.

Vatsalya Maddi (V)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
ORCID: 0000-0002-6188-7384

Mehdi Mehtarizadeh (M)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.

Pieter Neerincx (P)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0002-9800-8638

Stephan Ossowski (S)

Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstraße 7, Tübingen 72076, Germany.
Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany.
ORCID: 0000-0002-7416-9568

Ana Rath (A)

INSERM, US-14 Orphanet, 96 rue Didot, Paris 75014, France.
ORCID: 0000-0003-4308-6337

Dieuwke Roelofs-Prins (D)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.

Marloes Stok-Benjamins (M)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0001-8534-378X

K Joeri van der Velde (KJ)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0002-0934-8375

Colin Veal (C)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
ORCID: 0000-0002-9840-2512

Gerben van der Vries (G)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0009-0000-1422-1435

Marc Wadsley (M)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
ORCID: 0000-0002-7014-2595

Gregory Warren (G)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.

Birte Zurek (B)

Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstraße 7, Tübingen 72076, Germany.
ORCID: 0000-0002-8200-7542

Thomas Keane (T)

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
ORCID: 0000-0001-7532-6898

Holm Graessner (H)

Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstraße 7, Tübingen 72076, Germany.
Centre for Rare Diseases, University of Tübingen, Geschäftsstelle Eisenbahnstraße 63, Tübingen 72072, Germany.
ORCID: 0000-0001-9803-7183

Sergi Beltran (S)

Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Diagonal, 643, 08028, Barcelona, Spain.
ORCID: 0000-0002-2810-3445

Morris A Swertz (MA)

Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
ORCID: 0000-0002-0979-3401

Anthony J Brookes (AJ)

Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
ORCID: 0000-0001-8686-0017

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Classifications MeSH

questionsmedicales.fr › États, signes et symptômes pathologiques › Processus pathologiques › Caractéristiques de la maladie › Maladies rares › An interconnected data infrastructure to...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › An interconnected data infrastructure to...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › An interconnected data infrastructure to...
questionsmedicales.fr › Phénomènes génétiques › Phénotype › An interconnected data infrastructure to...
questionsmedicales.fr › Sciences de l'information › Gestion de l'information › Métadonnées › An interconnected data infrastructure to...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › An interconnected data infrastructure to...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › An interconnected data infrastructure to...