HGVS data element LOINC code(s) see CG WG IG. - MCODE #36

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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
    • Hide

      Upon review of the most recent CI Build of the ObsVariant profile (http://build.fhir.org/ig/HL7/genomics-reporting/obs-variant.html), we will split the VariantFoundHGVSName component code all 3 HGVS components found in obsVariant.

      Moreover, we will align with the component value to value[x] with a binding to the hgvs value set http://hl7.org/fhir/genomics-reporting/ValueSet/hgvs (once the latest CG IG is published).

      As noted in GF#32899, We will work more actively with the CGWG to find better alignment with the Genomics Reporting IG for the next release, however the result might not be a direct derivation of the CG profiles. Rather, we will work towards a design which allows mCODE generated FHIR instances to validate against the CG profiles with minimal changes.

      Proposed resolution: Persuasive with Mod

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      Upon review of the most recent CI Build of the ObsVariant profile ( http://build.fhir.org/ig/HL7/genomics-reporting/obs-variant.html ), we will split the VariantFoundHGVSName component code all 3 HGVS components found in obsVariant. Moreover, we will align with the component value to value [x]  with a binding to the hgvs value set  http://hl7.org/fhir/genomics-reporting/ValueSet/hgvs  (once the latest CG IG is published). As noted in GF#32899, We will work more actively with the CGWG to find better alignment with the Genomics Reporting IG for the next release, however the result might not be a direct derivation of the CG profiles. Rather, we will work towards a design which allows mCODE generated FHIR instances to validate against the CG profiles with minimal changes. Proposed resolution: Persuasive with Mod
    • Richard Esmond/Kurt Allen: 10-0-1
    • Correction
    • Compatible, substantive

      Comment:

      VariantFoundHGVSName compare to several components in CG IG obs-variant http://build.fhir.org/ig/HL7/genomics-reporting/obs-variant.html see "The components dna-chg:48004-6 and dna-chg-type:48019-4 are used to deliver the Human Genome Variation Society (HGVS) nomenclature for the observed DNA marker and codify the type of change observed. If the described variant is structural, genomic-dna-chg:81290-9 is used instead of dna-chg:48004-6. " Might choose one or incorporate all 3. Further, the LOINC code 82154-6 is meant for Structural variants (where there has been chromosomal rearrangements), the existence of this code was to support an element that no longer exists. Sorry for the confusion.

      Summary:

      HGVS data element LOINC code(s) see CG WG IG.

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

              Created:
              Updated:
              Resolved: