Uploaded image for project: 'FHIR Specification Feedback'
  1. FHIR Specification Feedback
  2. FHIR-32870

mCODE CancerGeneticVariant missing genomic variant category

    XMLWordPrintableJSON

    Details

    • Type: Change Request
    • Status: Resolved - change required (View Workflow)
    • Priority: Medium
    • Resolution: Persuasive with Modification
    • Specification:
      US Minimal Common Oncology Data Elements (mCODE) (FHIR)
    • Raised in Version:
      1.16.0
    • Work Group:
      Clinical Interoperability Council
    • Related Artifact(s):
      Cancer Genetic Variant
    • Grouping:
    • Resolution Description:
      Hide

      We agree that there is a need to qualify a variant category, but not in Observation.category as initially proposed.

      Instead, we propose to add a new component to CancerGeneticVariant for molecular consequence, whose values are bound to the sequence ontology "structural variant" concept (http://www.sequenceontology.org/browser/current_release/term/SO:0001537).

      This representation aligns with how the HL7 Clinical Genomics Reporting IG represented qualifying variants as fusion, amplification, copy number, etc.

      Show
      We agree that there is a need to qualify a variant category, but not in Observation.category as initially proposed. Instead, we propose to add a new component to CancerGeneticVariant for molecular consequence, whose values are bound to the sequence ontology "structural variant" concept ( http://www.sequenceontology.org/browser/current_release/term/SO:0001537). This representation aligns with how the HL7 Clinical Genomics Reporting IG represented qualifying variants as fusion, amplification, copy number, etc.
    • Resolution Vote:
      Saul Kravitz/Sherita Alai:4-0-0
    • Change Category:
      Correction
    • Change Impact:
      Non-compatible
    • Pre Applied:
      Yes

      Description

      Related to FHIR-32008 (https://jira.hl7.org/browse/FHIR-32008).

      The HL7v2-based messaging spec from Epic contains a variant category which includes terms that further qualify a variant type. For example:

      • Structural
      • Fusion
      • Amplification
        Copy number variation
        Pharmacogenomic Genotype

      Currently, the CancerGeneticVariant Observation.category element has an HL7 observation category code with a preferred binding strength and does not accurately capture the type.

       

        Attachments

          Activity

            People

            Assignee:
            Unassigned Unassigned
            Reporter:
            may_terry May Terry
            Watchers:
            1 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved:
              Vote Date: