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Lookup NU author(s): Dr Ana TopfORCiD
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND).
© 2023 The AuthorsThe 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.
Author(s): Corvo A, Matalonga L, Spalding D, Senf A, Laurie S, Pico-Amador D, Fernandez-Callejo M, Paramonov I, Romero AF, Garcia-Rios E, Ciges JI, Mohan A, Thomas C, Silva Valencia AF, Halmagyi C, Freeberg MA, Topf A, Horvath R, Saunders G, Gut I, Keane T, Piscia D, Beltran S
Publication type: Article
Publication status: Published
Journal: Cell Genomics
Year: 2023
Volume: 3
Issue: 2
Print publication date: 08/02/2023
Online publication date: 11/01/2023
Acceptance date: 14/12/2022
Date deposited: 23/02/2023
ISSN (electronic): 2666-979X
Publisher: Cell Press
URL: https://doi.org/10.1016/j.xgen.2022.100246
DOI: 10.1016/j.xgen.2022.100246
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