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

• DOI: 10.1016/j.xgen.2022.100246
• Publication Date: 2023-01-11T15:54:18Z
• Authors: Alberto Corvò; Leslie Matalonga; Dylan Spalding; Alexander Senf; Steven Laurie; Daniel Picó-Amador; Marcos Fernandez-...; Ida Paramonov; Anna Foix Romero; Emilio Garcia-Rios; Jorge Izquierdo C...; Anand Mohan; Coline Thomas; Andres Felipe Sil...; Csaba Halmagyi; Mallory Ann Freeberg; Ana Töpf; Rita Horvath; Gary Saunders; Ivo Gut; Thomas Keane; Davide Piscia; Sergi Beltran
• Keywords: Phenome

The Solve-RD project objectives include solving undiagnosed rare diseases (RD) through collaborative research on shared genome-phenome datasets. RD-Connect Genome-Phenome Analysis Platform (GPAP), for data collation and analysis, the European Archive (EGA), file storage, are two key components of infrastructure. Clinical researchers can identify candidate genetic variants within GPAP and, thanks to developments presented here as part joint ELIXIR activities, able remotely visualize corresponding alignments stored at EGA. Global Alliance Genomics Health (GA4GH) htsget streaming application programming interface (API) is used retrieve alignment slices, which rendered by an integrated genome viewer (IGV) instance embedded in GPAP. As a result, it no longer necessary over 11,000 datasets download large files them locally. This work highlights advantages, from both user infrastructure perspectives, implementing interoperability standards establishing federated genomics networks.