Artikel
RD-Connect: data sharing and analysis for rare disease research within the integrated platform and through GA4GH Beacon and Matchmaker Exchange
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Autoren
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Andreas Roos
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre, Newcastle upon Tyne, United Kingdom
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Sergi Beltran
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
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Davide Piscia
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
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Steven Laurie
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
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Joan Protasio
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
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Andres Cañada
- Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
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José María Fernández
- Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
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Rajaram Kaliyaperumal
- Leiden University Medical Center, Leiden, Netherlands
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Séverine Lair
- Interactive Biosoftware, Rouen, France
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Pedro Sernadela
- University of Aveiro, Aveiro, Portugal
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Marta Girdea
- Hospital for Sick Children and University of Toronto, Toronto, Canada
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Rachel Thompson
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre, Newcastle upon Tyne, United Kingdom
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Hanns Lochmuller
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre, Newcastle upon Tyne, United Kingdom
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Marco Roos
- Leiden University Medical Center, Leiden, Netherlands
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Peter A.C. 't Hoen
- Leiden University Medical Center, Leiden, Netherlands
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Alfonso Valencia
- Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
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David Salgado
- Aix-Marseille Université, Marseille, France
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Christophe Béroud
- Aix-Marseille Université, Marseille, France
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Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
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RD-Connect Consortium
- Institute of Genetic Medicine, John Walton Muscular Dystrophy Research Centre, Newcastle upon Tyne, United Kingdom
| Veröffentlicht: | 14. September 2016 |
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Gliederung
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Introduction: RD-Connect is a platform for rare disease research bringing together multiple omics data types (genomics, proteomics, transcriptomics) with biosample and clinical information at an individual-patient, family or whole-cohort level.
Objectives: The RD-Connect platform aims to provide both a centralized data repository and a user-friendly online analysis system to facilitate rare disease omics research.
Patients & Methods: Whole-genome, exome or gene panel data from patients with rare diseases and family members are deposited at the European Genome-phenome Archive for long-term storage, then processed by RD-Connect's standardised analysis and annotation pipeline to make data from different sequencing providers comparable. Clinical information is recorded in PhenoTips, simplifying clinical data entry using the Human Phenotype Ontology. Results are available to authorised users through the highly configurable platform (platform.rd-connect.eu) which enables filtering and prioritization of variants using common genomic location, effect, pathogenicity and population frequency annotations, enabling users to do their primary genomic analysis of their own patients online and compare with other submitted cohorts.
Results: As well as analysis of the researcher’s own cohort, the platform enables data sharing at various levels. At the most basic (“does this variant exist in this cohort?”) is the Global Alliance Beacon (beacon-network.org). At the next – finding patients in different databases with matching phenotype and candidate variant in the same gene – it is further developing Matchmaker Exchange (www.matchmakerexchange.org), allowing users of different systems to exchange data to find confirmatory cases. Finally, since patients have been consented for data sharing, authorized users can access datasets from other centres for further study. Although open to any rare disease, the platform is enriched for neuromuscular and neurodegenerative phenotypes, including ~1000 NMD/NDD datasets from NeurOmics (rd-neuromics.eu) and ~2000 other neurogenetic and neuromuscular cases being integrated in the coming months.
Conclusion: RD-Connect is a valuable tool for omics data sharing and analysis that is free and open for contributions: contactplatform@rd-connect.eu.
