C-G.48: Federated Genomic Variant Discovery & Analysis Using GA4GH Standards
Authors
Keywords
Genetic variation, Federated data analysis Variant representation Data integration Beacon GA4GH
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Genomic data are increasingly distributed across clinical, research and national infrastructures, making interoperability a key challenge for their effective reuse. This is particularly critical for rare disease, cancer and population genomics, where variant interpretation requires integrating both observational data and interpretative knowledge across sources.
GA4GH standards provide a common framework to address these challenges. The Variant Representation Specification (VRS) enables consistent, computable representations of genomic variants across formats and sources, while Categorical VRS (Cat-VRS) extends this to groups of related variants. The Beacon protocol supports federated discovery across distributed datasets without centralising sensitive data, with controlled access and adjustable granularity of query responses. Downstream analyses can be performed within Trusted Research Environments (TREs), where standards such as the Task Execution Service (TES) support federated execution by bringing computation to the data.
This work illustrates how these components can be articulated into a federated analysis pipeline, using a rare disease-oriented scenario as an illustrative example. Starting from a candidate variant, consistent representations enable linking observational occurrences with interpretative evidence from databases and literature, including related variants within the same functional class. Federated discovery through Beacon identifies relevant datasets, while subsequent analyses within TREs enable comparison of phenotypic profiles across cohorts.
The work highlights current efforts and remaining challenges in interoperability, including variant representation harmonisation, integration of heterogeneous data types and alignment between discovery and analysis layers.
Co-authors: Michael Baudis, Valerie Barbie, Tim Beck, Melissa Cline, Friederike Ehrhart, Hindrik Kerstens, Worawich Phornsiricharoenphant, Jordi Rambla, David Salgado, Venkata Satagopam, Sergi Beltran, Emidio Capriotti
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