Molecular diagnosis & Molecular diagnosis other

[hinri]

is this in conjunction with clinical findings and risk factors or just (any) genetic findings?

[joerivandervelde]

Excellent point - you could imagine also reporting known pathogenic variants in healthy individuals due to disease low penetrance. However here does not feel like to right place to do it. So indeed, this field is supposed to be in conjunction with the clinical diagnosis for this patient. Clinical diagnosis may be established without a genetic diagnosis, of course. The description fields must reflect this clearly.

[joerivandervelde]

Suggest to split in 'gene' and 'variant' part so we can have a codebook lookup for the genes, as well as parsable variant data (if sticking to a format like 12:4568721C>A)

[joerivandervelde]

could be different from Clinical Diagnosis for various reasons, this is not a bad thing

[joerivandervelde]

of course, allow for multiple genetic diagnoses

[gurnoor1990]

How to add list of variants, (could it be a text description), cross-reference ?

[gurnoor1990]

Shall we separate Genetic diagnosis (Genes) and Genetic diagnosis (Variants)?

[jambelien]

Good point Gurnoor. If we need the entire list of variants I think cross referencing will be best, most pragmatic right? if it is a certain (small) subset, you might absorb them in the FAIRgenomes ontology?

[joerivandervelde]

Suggesting: make this field into Gene-Variant notation only. So:

Clinical Diagnosis -> Select one or multiple (rare) disorders from codebook, often they are already linked to a gene.

Genetic Diagnosis -> Specify causal variant(s) for the above disorders, or perhaps they are new findings. Format HGVS, for example:

AGT:c.803T>C 9:g.22125503G>C ENST00000003084:c.1431_1433delTTC

[joerivandervelde]

use comma-separated HGVS notation of DNA variants causal for disease. Alternatively, you may express other pathogenic molecular mechanisms here.

[joerivandervelde]

for clinical genetics: also need classification, esp. for a new variant (VUS, LP, P, ..)

[gurnoor1990]

Split it into 2 fields, consult pathologist and genecist

[gurnoor1990]

Molecular diagnosis (free text) <- renamed to -> Molecular diagnosis other