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clingen-data-model / clingen-interpretation

Allele (variant) interpretation model and API for ClinGen
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Strength adjusted evidence codes #191

Closed ronakypatel closed 6 years ago

ronakypatel commented 6 years ago

I have a trouble figuring out, how to incorporate strength adjusted evidence codes in SEPIO-ACMG.

Say for example I want to document PVS1-Strong (Strength downgrade) using interpretation model.

Is this correct?

evidenceLine.evidenceItem.criterion.label => PVS1 evidenceLine.evidenceItem.criterion.defaultStrength => Pathogenic Very Strong evidenceLine.evidenceStrength => Pathogenic Strong

Please correct me if I am wrong.

larrybabb commented 6 years ago

Yes, that is correct.
In reality you don't necessarily have to share the "defaultStrength" at all. I say this because the "defaultStrength" is inherent to the definition of the criterion codes. In other words, it never changes and is part of its fundamental definition. We modeled it because there is no public stable model of these criterion codes and their defaultStrengths, so we simply pass all the criterion information with each .criterion. structure. Ideally, this will be coded and published in a stable available resource someday and tools could look it up separately if needed.