Scout user meeting, 24-11-06 9.00

[dnil]

Long due user meeting

A virtual meeting link will be posted and sent to the user mail lists closer to the meeting. You are invited to add discussion points on this issue!

[dnil]

Those of you near by are welcome to K Rum NKS J8-10 Tantal, where we will host the Teams meeting. An invite has been sent to both the Scout email lists. If you didn't receive it, please be in touch with a developer and we will forward it to you - and add you to the appropriate list if you wish.

[dnil]

Discussion topics

Latest important changes

• ACMG classification improvements - feedback?
• Improved cases search form, now supporting advanced queries
• Searchable SV genes (Search SNV & SVs)
• OMICS variants (Fraser, Outrider)
• Major update of igv.js
• Easier to load custom tracks into igv.js - requests or suggestions?
• Removed confusing orpha inheritance from variant page
• Fixed gene panels exporting and importing functionality- all fields get saved, including comments and manual inheritance
• chanjo2 is workable and creates real-time reports - feedback from Lund?
• Gens updates and future development plans
• ?

Free text manual inheritance?

Would it be ok to remove the free text portion of gene panel manual inheritance patterns? We have a controlled vocabulary manual inheritance (drop down menu) as well as an overall Gene comment. Or is this an important feature to some?

Clinical-research upload divide

With large panels with most known disorder genes added per default, the value for avoiding incidental findings is lessened. We are however working on several new pipelines, and would have an opportunity to change it.
The division creates issues when new disease genes are discovered, causing more reruns and potential missed discovery. It does serve keeping the databases smaller, avoiding storing many uninteresting variants, and shortening upload times.

Upcoming LRS features

SNV, SV, STR are given: they work ok for Poorpipe and are well under way for Nallo. ONT STR alternatives? Prio for all the other possibilities? Paraphase, phasing, methylation deviation callers, MEI, ...

Refactoring of ClinVar submissions

• Planned support submission of somatic variants (now disabled)
• Deprecating submissions via files - support only submissions via API

Refactoring of PanelApp green panel

• Thanks @Jakob37 for pointing out the inconsistency between PanelApp API and webservice (the latter used in scout)
• webservice endpoint (175 panels) was built for panels associated to 1000 Genomes (Rare Disease 100K) and is going to be deprecated
• Scout needs to collect panels using the API (451 panels) - which panel type should we include? Signed off or not? Available types:
  • Rare Disease 100K
  • Cancer Germline 100K
  • GMS Rare Disease - NHS Genomic medicine service -
  • GMS Rare Disease Virtual
  • GMS Cancer Germline Virtual
  • Actionable
  • Research
  • External Diagnostic Lab

Ranking

• genmod maintenance
• Default panel, clinical filter rank results
• Implementing rdds results

SV triage workshop?

• Especially BALSAMIC? Also for RD?

Users request

• Additional in silico prediction scores: MAVE, AlphaMissense, UTRannotator, primateAI-3D
• More detailed score returns from predictors (GERP, Phylop, PHAST, ...)
• prediction score - BayesDel

Next User Meeting? Prel March 12th

[SofieCMD]

Another user request, prediction score - BayesDel!

[northwestwitch]

Suggestion: improve filters on SNVs and SVs genes pages.

[dnil]

Thank you for today! Next meeting is scheduled for 250312. See you!