GA4GH Connect Session: Variant Representation Alignment

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Beatrice Amos

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Oct 2, 2025, 3:27:47 PM10/2/25
to Davidcs, Jessica Seegobin, daw...@broadinstitute.org, maxime....@gmail.com, andrei....@scilifelab.uu.se, Mallory Freeberg, Mrinal Thomas, Senkei Umehara, Melissa Cline, mkwo...@yuhs.ac, Hana Snow, drgu...@ugm.ac.id, vivi...@hotmail.com, kta...@ccia.org.au, Klawless, Liane Hughes, Rhaji, Heidi Rehm, Anais Mottaz, kristy....@ugm.ac.id, camille...@scilifelab.uu.se, pda...@bwh.harvard.edu, eleftheri...@scilifelab.uu.se, Xirasasa, Wang, Yunze, Andrew, angela.fue...@scilifelab.uu.se, Puthawala, Daniel, Nicolas BERTIN, GA4GH GKS Steering, GA4GH Variation Representation, GA4GH Variant Annotation, Product - Categorical Variation Representation Specification (Cat-VRS), Arwa Farrukh
Hi everyone,

We're nearly there! GA4GH Connect is happening in Sweden next week! 🎉

I'm so excited to share some prep materials for our session: Variant Representation Alignment: Bridging VRS, VCF, HGVS & SPDI. The session led by Alex Wagner, Melissa Cline and Larry Babb, and supported on the ground by Jessica Seegobin and Arwa Farrukh is happening on:

Date: Thursday, October 9, 2025 
Time: 11:00-12:30 CEST in 
Room: K3+K4 (Floor 3)

If you are joining virtually, please make sure you are registered. Once registered, you will be able to access the Zoom link directly from the Connect page on the event website.
Registration link

📌 Here's your quick access:

This session will be a chance to dig into the challenges of variant interoperability, swap ideas for solutions and opportunities, and hear community perspectives on what's most needed moving forward.
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To help you get the most out of the discussion, we suggest:

1. Quick Background Reading

Take a look at the NHGRI FAIR Data Workshop preprint: Improving the FAIRness and Sustainability of the NHGRI Resources Ecosystem: https://arxiv.org/abs/2508.13498 (PDF: https://arxiv.org/pdf/2508.13498)
Focus especially on page 10/11 (the Variant Identifiers section) for a read into registered, computed, and nomenclature-based identifiers.
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2. Breakout Discussion Questions

We'll be splitting into breakout groups for deeper discussions. Here are some starter questions to think about:
  • What challenges do you face in variant interoperability day-to-day?
  • Which formats/standards do you typically use (VRS, VCF, HGVS, SPDI, ISCN, Star Alleles, GL strings, etc.)?
  • Where do you find limitations or ambiguities?
  • What strengths do you see in the formats you use?
Please join us - absolutely no need to pre-register...but might save you time on the day trying to find that Zoom link!

A big thanks to Jessica and Arwa, who will be supporting this session - they will also help set up the in-room breakouts and make sure our virtual attendees can easily join the Zoom breakout rooms.🙌

If you have any questions, please pop me an email.

Really looking forward to the conversation!😊

Best,
Beatrice


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