Stream: genomics
Topic: Genomic allele start-end
Liz Amos (Apr 20 2020 at 21:16):
I was trying to gather some of the outstanding TBD codes and noticed something kind of weird. "Genomic allele start end" 81254-5 is in the Variant model http://build.fhir.org/ig/HL7/genomics-reporting/sequencing.html but not in the http://build.fhir.org/ig/HL7/genomics-reporting/variant.html. I now see a component:exact-start-end listed as TBD. Are these related, and if so, does a change need to be requested in LOINC or is this a completely new code?
Patrick Werner (Apr 21 2020 at 15:19):
Hi Liz, we split "Genomic allele start end" with: outer-start-end, inner-start-end, exact-start-end to be more precise
Patrick Werner (Apr 21 2020 at 15:19):
So we would need LOINC terms for all three.
Jamie Jones (Apr 21 2020 at 15:32):
The old terms may be able to be updated into the new ones, right?
Patrick Werner (Apr 21 2020 at 15:33):
these three are all tbd. So there was no existing code? Or i missed it.
Jamie Jones (Apr 21 2020 at 15:34):
The ones in the diagram, (we failed to update it as I recall) there was one way to communicate endpoints before but it didn't explicitly say "exact". And we had inner and outer but they were framed in the context of structural variants only
Patrick Werner (Apr 21 2020 at 15:36):
right!
Patrick Werner (Apr 21 2020 at 15:37):
ah no, we used one of these: https://loinc.org/81297-4/ in the structural variant iirc?
Patrick Werner (Apr 21 2020 at 15:39):
sorry i'm confused (trying to fix haplotype, and listening to the call at the same time)
Jamie Jones (Apr 21 2020 at 15:39):
Yeah, looks like those were created for a different project so we may not be able to change the wording on them. Meaning isn't changing though so it may be fine with the powers that be at LOINC
Patrick Werner (Apr 21 2020 at 15:40):
I agree with @Jamie Jones 81254-5 should become: the exact start end
Patrick Werner (Apr 21 2020 at 15:42):
Jamie Jones said:
Yeah, looks like those were created for a different project so we may not be able to change the wording on them. Meaning isn't changing though so it may be fine with the powers that be at LOINC
You think we should reuse the inner outer LOINC codes? My concern would be having "structural" in it. Which could be a problem, or are we sure that having it doesn't change the concepts?
Kevin Power (Apr 21 2020 at 15:42):
One caveat - This might be less important depending on how we look to do the Variant profile simplification and any changes we do to make the 'identification' of a variant more clear. But, I think adding 'exact' to 81254-5 seems OK to me.
Liz Amos (Apr 21 2020 at 15:43):
I believe they were developed for V2, so we could easily ask (as a work group) that they be updated to reflect. I noticed that the examples in the V2 spec actually use "exact" example values. So, I think it's up to the group to decide if we want to formally request the change in LOINC Name or provide more guidance in the IG.
Liz Amos (Apr 21 2020 at 15:45):
Regardless, it seems to me these LOINC requests keep getting lost. Are there Jira trackers associated with them? It would be nice to "assign" the job of requesting to someone specific.
Kevin Power (Apr 21 2020 at 15:49):
@Liz Amos -- You are correct, we are not very good at managing LOINC requests. We should talk about it. Liz, do you have any recommendations? We could log trackers for the CG side of the equation, but are you talking about managing the discussion with LOINC?
Patrick Werner (Apr 21 2020 at 15:54):
Yes we are messy :-/ sorry Liz. Would it help if we structure all requests/todos into a Google Spreadsheet? We all have access to? A lot of the knowledge/state of our requests is burried in several emails.
Liz Amos (Apr 21 2020 at 16:21):
Thanks, @Kevin Power I am talking about logging trackers . I can help come up with a decision tree for the WG, so basically something like is it A) a new request or B) a change to an existing LOINC code and depending on the answer, we can follow up with additional questions to help facilitate a designated person to enter the request. This way we can have a guide for the group so anyone (that is specified in the Jira tracker) can submit on behalf of the group.
Jamie Jones (Apr 21 2020 at 16:22):
That would be very helpful!
Bret H (Apr 28 2020 at 15:43):
@Rachel Kutner fyi
Last updated: Apr 12 2022 at 19:14 UTC
