Support new format of genepanels
Background
New gene panel builder (AMG-2299) needs adaptations in ELLA. Example of new gene panel format: UtAv.zip
Identify and make necessary changes in all parts of ELLA that uses info from the gene panels. This includes:
- Gene info (popup when clicking a gene name in the top banner): Transcripts, Phenotypes, Inheritance, (BS1/BA1 cutoff?)
- Top bar: Inheritance (left-most item in bottom part)
- Side bar: Inheritance in INH column
- Filtering rules: Inheritance in frequency thresholds
- Gene panel info (modal from button in top bar): Shows list of genes from gene panel, with popups for each gene that currently includes Inheritance, Indications and Transcripts
Implementation
Use latest genepanel format (example). Keep backwards compatible?
The gene info popup (from top banner) should be like this after the changes:
- LINKS: keep as is
- INHERITANCE: keep as is, but using new files
- PHENOTYPES: keep as is (with inheritance), but using new files; see AMG-2705 (curated from OMIM e.g.
Choroideremia (XD)
) - TRANSCRIPTS:
- Default(s): keep as is
- Source: [new; MANE Select / RefSeq Select / Custom; from AMG-2685]
-
HGMD transcript:--> Moved to variant annotation for simplicity, see #2154 (closed)
- BS1/BA1 CUTOFF: Keep if possible, but I'm guessing this is no longer available? Not critical
- GENE COMMENTS: keep as is
If possible, make the gene popup in Gene panel info exactly the same as the Gene info popup, except exclude the GENE COMMENTS section.
Backwards compatibility
We should not require old-style genepanels to be imported, but existing genepanels might need to be migrated. Do the new gene panels contain all the necessary data? Should we remove some columns/data, and if so, how does this affect historical data?
Edited by Morten C. Eike