Federated Variant-Level Matching (VLM) Project

There are practical barriers to gaining access to genotype and phenotype information from diverse sources in a timely manner to inform routine rare variant interpretation. Access to this data would allow the clinical and research communities to achieve more accurate and timely diagnosis and intervention. Nascent efforts in the area of “variant matching” — querying for data on a single variant or class of variants — are beginning but need dedicated focus to overcome significant barriers to implementation. This GA4GH Implementation Forum (GIF) project is focused on addressing those barriers to support a large federated network of genomic databases. This network enables the query of variant-level genotypes and allows users to gain access to individual-level phenotypic features upon obtaining a genotype match. This work engages and builds upon the Beacon Network utilizing the Beacon v2.0 API (Rambla et al, 2022), but also explicitly engages the rare disease community, building off of successful efforts of the Matchmaker Exchange and efforts to expand from genes to variants (Boycott et al, 2022; Rodrigues et al, 2022). 

Best practices are being developed to help guide the community in launching nodes on the network. Privacy and consent practices are based on prior efforts to define allowable submissions to ClinVar and the Matchmaker Exchange (Dyke et al, 2017; Azzariti et al 2018; Wright et al, 2019). The platform is working towards the use of the GA4GH Passports standard to allow authentication of access across nodes (Voisin et al, 2021). Many groups are working to connect to the network.

To participate in VLM project activities, monthly videoconference calls are held among implementers on the last Thursday of the month at 8:00–9:00 EDT (12:00–13:00 UTC).

We also make use of the monthly Matchmaker Exchange (MME) videoconference calls for additional topics that span both gene-level and variant-level matching. The MME call takes place on the 3rd Wednesday of the month at 11:00–12:00 EDT (15:00–16:00 UTC).

To join these monthly calls please contact vlm@ga4gh.org.