GeneticObservation

GeneticObservation is designed as a resource that associates the patient's observed phenotype to the genotype. It is extended from the Observation resource, which contains diagnostic information as well as the social history of a patient. With references to a Sequence resource, reports of a patient’s genotype-phenotype association are documented, making GeneticObservation in clinical decision support.

List of Extension Elements

  • traitAssesed - Target trait being studied
  • variant - HGVS identifier of an variant being associated with the phenotype studied
    • genotype - Reference to a Sequence resource indicating the patient's genotype on a variant
    • interpretation - Interpretation of a variant's effect on the patient's phenotype
    • comment - A comment of the variant's effect

Extension Definition

<Profile xmlns="http://hl7.org/fhir">
    <text>
        <status value="generated"/>
        <div>
            <h1>Sequencing Lab</h1>
            <p>This is an extension to Observation resource, supporting association of phenotype and genotype</p>
        </div>
    </text>
    <status vlaue="draft"/>
    <extensionDefn>
        <code value="traitAssesed"/>
        <display value="Target trait of the observation"/>
        <contextType value="datatype"/>
        <context value="Observation"/>
        <definition>
            <short value="Target of the observation"/>
            <formal value="Ontological representation of the target trait"/>
            <min value="1"/>
            <max value="1"/>
            <type>
                <code value="CodeableConcept"/>
            </type>
        </definition>
    </extensionDefn>
    <extensionDefn id="variant">
        <code value="variant"/>
        <display value="Variant"/>
        <contextType value="resource"/>
        <context value="Observation"/>
        <definition>
            <short value="Variant"/>
            <formal value="HGVS nomencalture of variant being associated with the patient's trait being observed"/>
            <min value="0"/>
            <max value="*"/>
            <type>
                <code value="string"/>
            </type>
        </definition>
    </extensionDefn>
    <extensionDefn>
        <code value="variantGenotype"/>
        <display value="Genotype of the variant"/>
        <contextType value="extension"/>
        <context value="#variant"/>
        <definition>
            <short value="Genotype"/>
            <formal value="Reference to a Sequence resource, indicating the patient's genotype of a particular variant"/>
            <min value="0"/>
            <max value="1"/>
            <type>
                <code value="Resource"/>
            </type>
        </definition>
    </extensionDefn>
    <extensionDefn>
        <code value="variantInterpretation"/>
        <display value="Interpretation of the variant"/>
        <contextType value="extension"/>
        <context value="#variant"/>
        <definition>
            <short value="Interpretation"/>
            <formal value="Interpretation of the a variant's effect on a patient's trait"/>
            <min value="0"/>
            <max value="1"/>
            <type>
                <code value="CodeableConcept"/>
            </type>
        </definition>
    </extensionDefn>
    <extensionDefn>
        <code value="variantComment"/>
        <display value="Comment of the variant's effect of the patient"/>
        <contextType value="extension"/>
        <context value="#variant"/>
        <definition>
            <short value="Comment"/>
            <formal value="Comment of the variant's effect on one of the patient's traits being studied."/>
            <min value="0"/>
            <max value="1"/>
            <type>
                <code value="string"/>
            </type>
        </definition>
    </extensionDefn>
</Profile>