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  1. FHIR Specification Feedback
  2. FHIR-16173

Clarify usage of Genotype/Haplotype/SequenceConfiguration or remove for now

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    • Icon: Change Request Change Request
    • Resolution: Persuasive with Modification
    • Icon: Medium Medium
    • Genomics Reporting (FHIR)
    • STU3
    • Clinical Genomics
    • STU
    • documentation [deprecated]
    • 1.2.3
    • Hide

      "Sequence Configuration"

      Rename to "Sequence Phase Relationship"

      —

      • "Sequence Phase Relationship".focus: *

      Change cardinality to 0..* - Supports more than two 'in-cis' findings - with appropriate cautions about indicating multiple 'in-trans' findings

      Make Sequence a valid target - Support HLA and potentially other use cases

      —

      • "Sequence Phase Relationship".method: *

      Use same LOINC as allelic phase basis

      *Required Pattern: *{"coding":[

      {"system":"[http://loinc.org]","code":"82309-6"}

      ]}

      *Binding: * LOINC Answer List LL4050-2 (preferred)

      —

      • Haplotype.method: *

      Use same LOINC as allelic phase basis

      *Required Pattern: *{"coding":[

      {"system":"[http://loinc.org]","code":"82309-6"}

      ]}

      *Binding: * LOINC Answer List LL4050-2 (preferred)

      —

      • DescribedVariant profile: *

      Remove "allelic phase" component - {"coding":[

      {"system":"[http://loinc.org]","code":"82120-7"}

      ]}

      Remove "allelic phase basis" component - {"coding":[

      {"system":"[http://loinc.org]","code":"82309-6"}

      ]}

      Show
      " Sequence Configuration " Rename to "Sequence Phase Relationship" — "Sequence Phase Relationship".focus: * Change cardinality to 0.. * - Supports more than two 'in-cis' findings - with appropriate cautions about indicating multiple 'in-trans' findings Make Sequence a valid target - Support HLA and potentially other use cases — "Sequence Phase Relationship".method: * Use same LOINC as allelic phase basis *Required Pattern: *{"coding":[ {"system":"[http://loinc.org]","code":"82309-6"} ]} *Binding: * LOINC Answer List LL4050-2 (preferred) — Haplotype.method: * Use same LOINC as allelic phase basis *Required Pattern: *{"coding":[ {"system":"[http://loinc.org]","code":"82309-6"} ]} *Binding: * LOINC Answer List LL4050-2 ( p referred) — DescribedVariant profile: * Remove "allelic phase" component - {"coding":[ {"system":"[http://loinc.org]","code":"82120-7"} ]} Remove "allelic phase basis" component - {"coding":[ {"system":"[http://loinc.org]","code":"82309-6"} ]}
    • Lloyd/Bob Dolin: 18-0-0
    • Clarification
    • Non-compatible

    Description

      The Genotype/Haplotype/Sequence Configuration profiles involve groupings for various purposes. I do not believe our documentation for these is clear enough to ensure consistent usage. As an example - Sequence Configuration has basically no documentation in the IG.

      While these concepts are important, I am concerned that we do not have enough consensus to represent in our first draft of this IG. We need to either remove them for now or spend time creating additional documentation in order to be very clear how each should be used. As a starting point, does everyone feel that the usage of Genotype/Haplotype in the PGx example is correct? http://hl7.org/fhir/uv/genomics-reporting/pharmacogenomics.html#examples

      It is also used in HLA examples. http://hl7.org/fhir/uv/genomics-reporting/transplants.html

      I am concerned that Genotype/Haplotype are not being used consistently even in our own initial examples.

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            Unassigned Unassigned
            cerkyp Kevin Power
            Kevin Power
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              Updated:
              Resolved: