Stream: genomics / eMerge Pilot
Topic: Inherited Disease Pathogenicity - risk factor not available
Mullai Murugan (Mar 17 2019 at 17:55):
The valueCodeableConcept element in the InheritedDiseasePathogenicity profile requires binding with the LOINC LL4043-6 answer list. In addition to the values to in the answer list, we also utilize "risk factor" from the Clinvar Clinical Significance list. Can we discuss options - should the LOINC answer list be expanded, can the binding be changed, or required changed to extensible/preferred (possibly not optimal)?
Tracker #20549
Kevin Power (Mar 18 2019 at 13:24):
I think it makes sense to have a different profile to represent "Genetic Risk Factor". It would allow a different value set, and possibly other values to be captured as components?
Bret H (Mar 19 2019 at 15:40):
@Mullai Murugan have you looked at the condition resource?
Mullai Murugan (Dec 10 2019 at 23:40):
@Bret H @Kevin Power with ACMG considering updating its guidelines to include risk factor, we would prefer to include this option to the valueCodeableConcept in InheritedDiseasePathogenicity.
Kevin Power (Dec 10 2019 at 23:48):
What do the “answers” to a risk factor look like?
Mullai Murugan (Dec 11 2019 at 00:46):
clinvar definition https://www.ncbi.nlm.nih.gov/clinvar/docs/properties/
Here is what we are currently including - e.g. result:
A heterozygous c.3920T>A (p.Ile1307Lys) risk factor variant in the APC (NM_000038.5) gene was detected....This variant is classified as as a risk allele with an increased risk for colorectal
neoplasia in the Ashkenazi Jewish population. However the risk in non Jewish populations has not been determined.
Jamie Jones (Dec 11 2019 at 01:11):
This sounds like a great component for a diagnostic implication
Kevin Power (Dec 11 2019 at 01:20):
We have a spot for the “associated cancer” already I guess. Is the new component someway to quantify the risk? Do we also need the “population “? Or is this just text?
Mullai Murugan (Dec 12 2019 at 00:02):
I apologize but I am not sure I am following - why would this require a component? The code in InhDisPath is "Genetic Variation Clinical Significance", wouldn't "Risk Factor" just be a value similar to Pathogenic or Likely Pathogenic?
Jamie Jones (Dec 12 2019 at 00:45):
This is definitely a component aiding a diagnosis, we'll have to look more at risk factor
Jamie Jones (Dec 12 2019 at 00:47):
We're actively considering moving the components and profiles around slightly so I'll consider this use case, thanks for pointing out the update.
Jamie Jones (Dec 12 2019 at 02:27):
Can anyone explain why the list has "multiple gene", "spans multiple genes", and also "in overlapping genes" as separate entries?
Jamie Jones (Dec 12 2019 at 02:33):
Ok, I looked up overlapping genes and that's something different that's pretty cool. Don't see any distinction between multiple gene and spans multiple genes though.
Bret H (Dec 16 2019 at 14:33):
@Jamie Jones @Kevin Power Mullai is asking about extending the existing value set with the concept 'risk factor'
Last updated: Apr 12 2022 at 19:14 UTC
