FHIR Chat · LOINC and reference sequences

Stream: genomics

Topic: LOINC and reference sequences

Andrew Patterson (Mar 23 2018 at 03:35):

Hi, we are needing to report out genomic variants in the short term (July timeframes) - and I totally understand that the CG stuff is all work in progress - so the best I am aiming for is aligning with things where they exist. So one of the fields we need to report out is the human reference sequence that was used. And I've found a useful LOINC code for that and an answer list. But the answer list seems incomplete (it doesn't have GRCh38 for instance, and there are subversions of GRCh37 that are apparently important ). I don't know anything about LOINC processes or timeframes - is it likely we can get answers added to LOINC? Or should I develop my own codesystem?

Andrew Patterson (Mar 23 2018 at 03:36):

https://r.details.loinc.org/LOINC/62374-4.html?sections=Comprehensive
I ask here because this particular LOINC code is listed in the FHIR CG Variant codes

Andrew Patterson (Mar 23 2018 at 03:37):

@Lloyd McKenzie do you know folks in the right places to get this answer list looked at?

Grahame Grieve (Mar 23 2018 at 03:37):

it's possible but tight by LOINC timeframes, I think. see https://loinc.org/submissions/

Andrew Patterson (Mar 23 2018 at 03:39):

Thanks - do we know what process was used internal to LOINC to come up with the list in the first place (or is it essentially ad-hoc when a lab asks for it?)? I'm no genomics expert so there may very well be a good reason for it being the way it is..

Kevin Power (Mar 23 2018 at 13:45):

Since he is not on Zulip, I have sent Clem McDonald an email on this topic and CC'ed you @Andrew Patterson . Clem's work on the V2 LRI sparked some changes in LOINC and I think this is one that he worked on.

Bret H (Mar 29 2018 at 10:53):

Could you post an example of how you are reporting the reference used for the variation? In Sequence Resource there is a place for the reference to be sent using NCBI id. This would be more accurate

Kevin Power (Mar 29 2018 at 14:31):

I think how the PGx example in the current IG shows it:

        "code" : {
          "coding" : [
            {
              "system" : "http://loinc.org",
              "code" : "48013-7",
              "display" : "Genomic reference sequence ID"
            }
          ]
        },
        "valueCodeableConcept" : {
          "coding" : [
            {
              "system" : "http://www.ncbi.nlm.nih.gov/nuccore",
              "code" : "NG_007726.3"
            }
          ]
        }

Last updated: Apr 12 2022 at 19:14 UTC

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FHIR Chat · LOINC and reference sequences · genomics