VariantFoundIdentifier consider Observation.component:variation-code from http://build.fhir.org/ig/HL7/genomics-reporting/obs-variant.html - MCODE #35

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    • Type: Change Request
    • Resolution: Persuasive with Modification
    • Priority: Medium
    • US Minimal Common Oncology Data Elements (mCODE) (FHIR)
    • STU3
    • Clinical Interoperability Council
    • Profiles
    • GeneticVariantFound
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      Noted. We will change the component VariantFoundIdentifier code from 48003-8 to 81252-9.

      We would however like to keep ClinVar as the binding since it was asked for ASCO. We can change the binding strength however to from extensible to preferred since the description for 81252-9 allows for multiple coding systems. This will allow for adding other variant conventions if they differ among reference labs.

      Proposed Resolution: Persuasive with Mod.

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      Noted. We will change the component VariantFoundIdentifier code from 48003-8 to 81252-9. We would however like to keep ClinVar as the binding since it was asked for ASCO. We can change the binding strength however to from extensible to preferred since the description for 81252-9 allows for multiple coding systems. This will allow for adding other variant conventions if they differ among reference labs. Proposed Resolution: Persuasive with Mod.
    • Richard Esmond/Kurt Allen: 10-0-1
    • Enhancement
    • Non-substantive

      Comment:

      For VariantFoundIdentifier consider Observation.component:variation-code from http://build.fhir.org/ig/HL7/genomics-reporting/obs-variant.html which uses LOINC code 81252-9. This component can be constrained to only pull codes from ClinVar. It is semantically isosemantic and could be used to profile off of the CG IG obs-variant. Suggest using 81252-9 as LOINC code, or again find a way to us the CG IG component and indicate profiling off of both the US CORE observation and off of CG IG obs-variant. The main differences in the LOINC code is the source of specimen 81252-9 is not specific to a tissue, and that the current code use in mcode's variantfoundidentifier is pre-coordinated as coming from DNA. But for an implementor using 81252-9 means that the component in mCODE can be directly captured from CG IG compliant profile instances (which in turn implies EMERGE participants). To promote a common standard for varaintcodeidentifier suggest using 81252-9.

      Summary:

      VariantFoundIdentifier consider Observation.component:variation-code from http://build.fhir.org/ig/HL7/genomics-reporting/obs-variant.html

            Assignee:
            May Terry
            Reporter:
            bheale
            bheale
            Watchers:
            4 Start watching this issue

              Created:
              Updated:
              Resolved: