Investigate PanelApp as a source of complex variation

[apriltuesday]

From Ellie: OT Platform currently uses PanelApp gene-disease associations but not the STRs (curated in house by Genomis England) or CNVs (sourced from ClinGen haplosufficiency assessments) which could provide additional complex variation to EVA but it is probably worth comparing whether these are already covered by ClinVar.

[tcezard]

PanelApp contains variants associated with loosely defined phenotype and a panel that link the variant to a family of diseases.
Two Challenges:

• How to associate loosely defined phenotypes with EFO ontology through Zooma and manual curation.
• Ensure that the variants from PanelApp are represented in the same way as the one in Clinvar to identify fuplicate

I suggests that the next steps are:

• Retrieve data from region and str and investigate how Zooma perfoms on Phenotypes fields
• Check that the CNV can be represented in the same coordinate system as clinvar