This session will bring together members of the Discovery and Genomic Knowledge Standards Work Streams to examine Beacon’s most challenging and high-value variant representation use cases, including structural variants (SVs), copy number variants (CNVs), complex rearrangements, long-read–derived variation, and other system-level measures of interest.

While Beacon has successfully enabled federated discovery for coordinate-based small variants, these more complex forms of variation expose fundamental difficulties in how variation is represented, queried, and interpreted across Beacon networks.

The goal of this session is to surface and clearly articulate these challenges, establish shared mental models across Beacon implementers and standards developers, and distinguish which problems arise from representational limitations, matching semantics, or protocol-level constraints. By grounding the discussion in concrete Beacon use cases, this session aims to motivate and inform Beacon v3.0 design decisions and future GKS VRS and Cat-VRS development efforts.

This session is intentionally exploratory and problem-focused. Rather than producing finalised designs, it seeks to produce a well-scoped requirements landscape that can guide subsequent technical work, including deeper design sessions on integrating GKS standards into Beacon.