Stream: genomics
Topic: Hemizygotes as Complex Variants
Rachel Kutner (May 05 2020 at 23:25):
In the HL7v2 specification, there is a section for Complex Variants. This section has a concept, Complex Variant Type (https://loinc.org/81263-6/) with an Answer List (https://loinc.org/LL3999-1/) containing Hemizygous.
Allelic State already allows marking a variant of another type as "Hemizygous" zygosity - Why is Hemizygous also a type of Complex Variant? What are the examples for when a Hemizygous variant would need to be represented as a grouping of individual variants?
Additionally: Do these concepts (Complex Variant, Complex Variant Type) have corollaries in the FHIR IG? Can someone point me to documentation on how they would be represented there?
Kevin Power (May 05 2020 at 23:32):
In FHIR IG, we boiled down to just a single Variant profile. You will find a component for 'complex-var-type' and it has the same LOINC code/answer list as you referenced above.
Kevin Power (May 05 2020 at 23:55):
And not to skip your other question - we do have some overlap between some value sets like that I am afraid. TBH - we haven't spent a ton of time on complex variant examples and validation, so it doesn't surprise me that we have some things to make better.
Rachel Kutner (May 06 2020 at 20:10):
Sorry if I'm repeating myself, I'm just still a bit unclear on the decision to include hemizygous in the Complex Variant Type terms. Do we have documentation regarding the decision to include that as a Complex Variant Type? I'm not sure I understand when it would be represented this way.
Kevin Power (May 06 2020 at 20:25):
I think that is really a LOINC question. The LOINC code (https://loinc.org/81263-6/ ) is still in Trial status, and it says the source for the answer list was "Source: Genetic Home Reference, National Library of Medicine"
@Liz Amos anything else you might say or weigh in with?
Liz Amos (May 06 2020 at 22:06):
So, I got some info from Clem - the complex variant is a string of nucleotides that doesn't have an opposite string, the best example being a male chromosome or a pair with a deleted string. However, this may not be important or useful now, especially in the context of FHIR. (FYI - I relayed this from a phone call so I probably got some details wrong!) Happy to follow up in other methods of communication.
Bret H (May 10 2020 at 13:46):
@Rachel Kutner hemizygous is noted in the alleic-state component of variant in the FHIR IG . http://hl7.org/fhir/uv/genomics-reporting/variant-definitions.html#Observation.component:allelic-state
Last updated: Apr 12 2022 at 19:14 UTC
