Your browser doesn't support javascript.
loading
An interconnected data infrastructure to support large-scale rare disease research.
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, Stephan; 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.
Affiliation
  • Johansson LF; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Laurie S; Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
  • Spalding D; Universitat de Barcelona (UB), Gran Via de les Corts Catalanes, 585, L'Eixample, 08007, Barcelona, Spain.
  • Gibson S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
  • Ruvolo D; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
  • Thomas C; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Piscia D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
  • de Andrade F; Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
  • Been G; Universitat de Barcelona (UB), Gran Via de les Corts Catalanes, 585, L'Eixample, 08007, Barcelona, Spain.
  • Bijlsma M; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Brunner H; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Cimerman S; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Dizjikan FY; Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, The Netherlands.
  • Ellwanger K; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O.Box 9103, Nijmegen, 6500 HD, The Netherlands.
  • Fernandez M; Department of Clinical Genetics, Maastricht University Medical Centre, P. Debyelaan 25, Maastricht, 6229 HX, The Netherlands.
  • Freeberg M; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • van de Geijn GJ; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
  • Kanninga R; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstraße 7, Tübingen 72076, Germany.
  • Maddi V; Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028, Barcelona, Spain.
  • Mehtarizadeh M; Universitat de Barcelona (UB), Gran Via de les Corts Catalanes, 585, L'Eixample, 08007, Barcelona, Spain.
  • Neerincx P; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CV10 1SD, UK.
  • Ossowski S; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Rath A; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Roelofs-Prins D; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
  • Stok-Benjamins M; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
  • 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.
  • Veal C; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstraße 7, Tübingen 72076, Germany.
  • van der Vries G; Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany.
  • Wadsley M; INSERM, US-14 Orphanet, 96 rue Didot, Paris 75014, France.
  • Warren G; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Zurek B; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Keane T; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Graessner H; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
  • Beltran S; Department of Genetics, University of Groningen, University Medical Center Groningen, HPC CB50, P.O. Box 30001, Groningen, 9700 RB, The Netherlands.
  • Swertz MA; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
  • Brookes AJ; Department of Genetics, Genomics and Cancer Sciences, University of Leicester, University Road, Leicester, Leicester, LE1 7RH, UK.
Gigascience ; 132024 Jan 02.
Article in En | MEDLINE | ID: mdl-39302238
ABSTRACT
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.
Subject(s)
Key words
Fulltext
Add to My VHL
Print
XML
PubMed Links
Search on Google

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Rare Diseases Limits: Humans Language: En Journal: Gigascience Year: 2024 Document type: Article Affiliation country: Netherlands Country of publication: United States
Fulltext
Add to My VHL
Print
XML
PubMed Links
Search on Google

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Rare Diseases Limits: Humans Language: En Journal: Gigascience Year: 2024 Document type: Article Affiliation country: Netherlands Country of publication: United States