PR Release

[rileyhgrant]

GeniE is already public and has users, there is currently PR planned to make this app more known to users on Wednesday, May 29th.

This is issue serves as a punchlist of all the things that need to be accomplished ahead of May 29th.

GeniE is having PR discussing in on Tuesday Jun 04, 2024

---

Large features

• [x] #220 | Integrate gnomAD v4.1
• [x] #98 | Allow adding Structural Variants
• [ ] | Add Analytics to track stats
• [x] #196 | Add Dashboard
  • [x] email hover overs -- truncate at a certain number of characters and add ...
  • [x] use OrphaNet prevalences
  • [x] standardize calculation format
  • [x] add inheritance types
  • [x] change backend to accept changes
  • [x] #233
  • [x] Make dashboard publicly available, not just to Staff. Replace "public lists" with "Dashboard"
  • [x] #236 | Add pagination and searchability to DashboardList page
  • [x] Reformat OrphaNet urls to link to the Gene
  • [x] Add add'l tests
• [x] #212 | Populate dashboard with pre-calculated lists, provide file for download
• [x] #231 | Add flags to dashboard calculation logic
• [ ] #211 | ClinVar auto-monthly
• [x] | v2 SV support
• [x] | edit v2 pipeline, reload v2 data with homozygote_count
• [ ] | add tests to validate the current variant adding behavior (if add malformed, 400, if add SV on v2, malformed, etc)
• [x] | add proper structural variant type in ../types.ts

Smaller features

• [x] #172 | Add additional genetic prevalence formula
• [x] #161 | Add flags (TODO: split this into 3 tickets, one per flag)
  • [x] #219 | Low_AN
  • [x] #171 | High_AF
  • [x] #237 | # Homozygotes
• [x] #213 | Optionally remove homozygotes from calcs (dashboard too?)
• [x] #173 | Remove HC LoF that have B/LB in ClinVar, also high revel scores but B/LB
• [x] | Make AF column fit in default view
• [x] | Allow naming of supporting documents (also maybe more than 1 supporting doc?)
• [x] | Allow adding of SVs in v4 custom lists
• [ ] | Hide submitting for representative to only if its already public? or if its representative, think about this, make more intuitive

Copy edits

• [x] | edit wording of homozygote tooltip: "<#> homozygous individual(s) in gnomAD"
• [x] | edit wording of homozygote toggle: "include gnomAD homozygotes in calculations"
• [x] | edit wording of Dashboard Lists -> Dashboard, both in url and header of page
• [x] | edit wording of submitting for representivity -> apply to be included on dashboard
• [x] | edit wording for "not representative" to "This variant list is not currently represented on the GeniE Dashboard"
• [x] Header "representivity" should change, maybe just "Dashboard"
• [x] #166 | Update website text
• [x] #162 | Add hover over text
• [x] #230 | Update help text

Bugfixes

• [ ] #228 | Don't include conflicting ClinVar where non are path/likely path
• [ ] #227 | Check if component hooks get called on page scroll events

Time Sensitive

• [x] Generate full dashboard_models / dashboard_downloads files
• [x] https://github.com/broadinstitute/gnomad-blog/pull/157 | Stage blog - release on day

[sambaxter]

Under "Add Dashboard to GeniE #196 | Add Dashboard" I just want to make sure we update the gene list to be all the gene's on mutaz's list - it looks like right now this ticket is only listed for the download file.

[rileyhgrant]

Under "Add Dashboard to GeniE #196 | Add Dashboard" I just want to make sure we update the gene list to be all the gene's on mutaz's list - it looks like right now this ticket is only listed for the download file.

Hiya Sam, yep it will be, that's the last larger ticket on my docket re: GeniE, I need to run the pipeline to generate the whole list of dashboard models / the download list and then use those in production.

[sambaxter]

Under "Add Dashboard to GeniE #196 | Add Dashboard" I just want to make sure we update the gene list to be all the gene's on mutaz's list - it looks like right now this ticket is only listed for the download file.

Hiya Sam, yep it will be, that's the last larger ticket on my docket re: GeniE, I need to run the pipeline to generate the whole list of dashboard models / the download list and then use those in production.

Awesome! Just wanted to make sure