REDCap form changes - variant type

[roseanna-hamilton]

I've added a dropdown field into the REDCap variant form with two options - SNV and CNV

[stefpiatek]

Replying to related comment here:

Yeah That's a tricky one, I think that CNVs should be modelled separately in FHIR because a lot of the SNV/small variant details don't really apply to CNVs, and if we're storing data in a structured format then just storing all of the CNV text doesn't quite make sense.

It looks like this https://loinc.org/81297-4/ is set up for structural variants (e.g. CNVs) and this is set up for complex variants https://loinc.org/81251-1/ (e.g. SNVs or small variants) so maybe using those is worthwhile?

[stefpiatek]

For now not implementing, could add in this type information into a variant report, or create a specific profile for simple variants and structural variants