Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases.
data sharing
data visualization
diagnosis
exome analysis
federated infrastructures
genome analysis
rare diseases
remote data access
standards
Journal
Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676
Informations de publication
Date de publication:
08 Feb 2023
08 Feb 2023
Historique:
received:
29
11
2021
revised:
04
04
2022
accepted:
14
12
2022
entrez:
23
2
2023
pubmed:
24
2
2023
medline:
24
2
2023
Statut:
epublish
Résumé
The Solve-RD project objectives include solving undiagnosed rare diseases (RD) through collaborative research on shared genome-phenome datasets. The RD-Connect Genome-Phenome Analysis Platform (GPAP), for data collation and analysis, and the European Genome-Phenome Archive (EGA), for file storage, are two key components of the Solve-RD infrastructure. Clinical researchers can identify candidate genetic variants within the RD-Connect GPAP and, thanks to the developments presented here as part of joint ELIXIR activities, are able to remotely visualize the corresponding alignments stored at the EGA. The Global Alliance for Genomics and Health (GA4GH) htsget streaming application programming interface (API) is used to retrieve alignment slices, which are rendered by an integrated genome viewer (IGV) instance embedded in the GPAP. As a result, it is no longer necessary for over 11,000 datasets to download large alignment files to visualize them locally. This work highlights the advantages, from both the user and infrastructure perspectives, of implementing interoperability standards for establishing federated genomics data networks.
Identifiants
pubmed: 36819661
doi: 10.1016/j.xgen.2022.100246
pii: S2666-979X(22)00209-9
pmc: PMC9932977
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100246Subventions
Organisme : Medical Research Council
ID : MC_PC_19024
Pays : United Kingdom
Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no conflict of interest.
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