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Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Corvò, Alberto 
Matalonga, Leslie 
Spalding, Dylan 
Senf, Alexander 
Laurie, Steven 

Abstract

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.

Description

Keywords

data sharing, data visualization, diagnosis, exome analysis, federated infrastructures, genome analysis, rare diseases, remote data access, standards

Journal Title

Cell Genom

Conference Name

Journal ISSN

2666-979X
2666-979X

Volume Title

3

Publisher

Elsevier BV