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  1. FHIR Specification Feedback
  2. FHIR-32870

mCODE CancerGeneticVariant missing genomic variant category

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    • Icon: Change Request Change Request
    • Resolution: Persuasive with Modification
    • Icon: Medium Medium
    • US Minimal Common Oncology Data Elements (mCODE) (FHIR)
    • 1.16.0 [deprecated]
    • Clinical Interoperability Council
    • Cancer Genetic Variant [deprecated]
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      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.

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      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.
    • Saul Kravitz/Sherita Alai:4-0-0
    • Correction
    • Non-compatible
    • 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.

       

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            may_terry May Terry
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