rileyhgrant
commented
1 year ago Heya @gtiao!
Thanks for filing this issue. This is something that the browser team should have bandwidth for. At the very least, in the relative future we could work with their team to make mockups and iterate on ideas before forming a more concrete plan. I'd guess at that point they can confidently say they're working with gnomAD to reporters this month?
Whether or not full implementation / release can happen ahead of a few things on the horizon (v2 RMC, v4 release) I'm not as sure.
What's the best way for me / the team to communicate with them?
Elinor Karlsson and Kerstin Lindblad-Toh are coming out with a big Science paper package at the end of April describing their recent work developing base-pair-resolution constraint by doing comparative genomics across 240 placental mammals. They have constraint not only in coding but also in non-coding regions and believe this will be a useful score for interpretation of human genetic variation.
They got in touch with Heidi who suggested I talk to them about exploring a visualization in gnomAD that would display base-level constraint. I showed them the RMC demo browser and they were interested in having a demo space provided to them, as well as a spec on how to format their scores, so that they can run a small design pilot with the team to see whether we can design a visualization that would be useful for users.
They will likely need two visualization schematics: one for coding variants, and one for noncoding variants, as the dynamic range of scores for coding regions (which are overall much more constrained than noncoding regions) is different (and the third position in each codon is always less constrained than the first two). For this reason being able to mock up and iterate through designs with the browser team would be helpful for exploring whether this is a feature we'd want to release.
There is no particular timeline for this pilot/feature request, although obviously they would be delighted to be able to say to reporters in April that they are working with gnomAD on releasing this to the public (assuming we're far enough along on the pilot to be able to say that displaying the scores will be useful).