FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

Observation-GenomicsVariantSLC52A2-Example

Example of an observation representing a Genomic variant.

Observation

id : Observation-GenomicsVariantSLC52A2-Example

meta

profile : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant

status : final

basedOn

reference : ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example

category

coding

system : http://terminology.hl7.org/CodeSystem/observation-category

code : laboratory

category

coding

system : http://terminology.hl7.org/CodeSystem/v2-0074

code : GE

code

coding

system : http://loinc.org

code : 69548-6

subject

reference : Patient/Patient-PheobeSmitham-Example

effective : 2023-09-16

performer

identifier

system : https://fhir.nhs.uk/Id/ods-organization-code

value : R0A

value

coding

system : http://loinc.org

code : LA9633-4

display : Present

method

coding

system : http://loinc.org

code : LA26398-0

display : Sequencing

specimen

reference : Specimen/Specimen-PheobeSmitham-Example

component

code

coding

system : http://loinc.org

code : 48004-6

value

coding

system : http://varnomen.hgvs.org

code : NM_024531.4:c.9163>A p.(Gly306Arg)

component

code

coding

system : http://loinc.org

code : 81290-9

value

coding

system : http://varnomen.hgvs.org

code : Chr8:g.1455840683>A

component

code

coding

system : http://loinc.org

code : 81252-9

value

coding

system : http://www.sequenceontology.org

code : SO:0001583

display : missense_variant

component

code

coding

system : http://loinc.org

code : 48018-6

value

coding

system : http://www.genenames.org/

code : HGNC:30224

display : SLC52A2

component

code

coding

system : http://loinc.org

code : 53034-5

value

coding

system : http://loinc.org

code : LA6705-3

display : homozygous

component

code

coding

system : http://loinc.org

code : 94186-4

value

coding

system : http://loinc.org

code : LA4489-6

display : Unknown

component

code

coding

system : http://loinc.org

code : 48002-0

value

coding

system : http://loinc.org

code : LA6683-2

display : Germline

{
    "resourceType": "Observation",
    "id": "Observation-GenomicsVariantSLC52A2-Example",
    "meta": {
        "profile":  [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
        ]
    },
    "status": "final",
    "basedOn":  [
        {
            "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example"
        }
    ],
    "category":  [
        {
            "coding":  [
                {
                    "system": "http://terminology.hl7.org/CodeSystem/observation-category",
                    "code": "laboratory"
                }
            ]
        },
        {
            "coding":  [
                {
                    "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
                    "code": "GE"
                }
            ]
        }
    ],
    "code": {
        "coding":  [
            {
                "system": "http://loinc.org",
                "code": "69548-6"
            }
        ]
    },
    "subject": {
        "reference": "Patient/Patient-PheobeSmitham-Example"
    },
    "effectiveDateTime": "2023-09-16",
    "performer":  [
        {
            "identifier": {
                "system": "https://fhir.nhs.uk/Id/ods-organization-code",
                "value": "R0A"
            }
        }
    ],
    "valueCodeableConcept": {
        "coding":  [
            {
                "system": "http://loinc.org",
                "code": "LA9633-4",
                "display": "Present"
            }
        ]
    },
    "method": {
        "coding":  [
            {
                "system": "http://loinc.org",
                "code": "LA26398-0",
                "display": "Sequencing"
            }
        ]
    },
    "specimen": {
        "reference": "Specimen/Specimen-PheobeSmitham-Example"
    },
    "component":  [
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "48004-6"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://varnomen.hgvs.org",
                        "code": "NM_024531.4:c.9163>A p.(Gly306Arg)"
                    }
                ]
            }
        },
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "81290-9"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://varnomen.hgvs.org",
                        "code": "Chr8:g.1455840683>A"
                    }
                ]
            }
        },
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "81252-9"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://www.sequenceontology.org",
                        "code": "SO:0001583",
                        "display": "missense_variant"
                    }
                ]
            }
        },
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "48018-6"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://www.genenames.org/",
                        "code": "HGNC:30224",
                        "display": "SLC52A2"
                    }
                ]
            }
        },
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "53034-5"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "LA6705-3",
                        "display": "homozygous"
                    }
                ]
            }
        },
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "94186-4"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "LA4489-6",
                        "display": "Unknown"
                    }
                ]
            }
        },
        {
            "code": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "48002-0"
                    }
                ]
            },
            "valueCodeableConcept": {
                "coding":  [
                    {
                        "system": "http://loinc.org",
                        "code": "LA6683-2",
                        "display": "Germline"
                    }
                ]
            }
        }
    ]
}

<Observation xmlns="http://hl7.org/fhir">
    <id value="Observation-GenomicsVariantSLC52A2-Example" />
    <meta>
        <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" />
    </meta>
    <basedOn>
        <reference value="ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" />
    </basedOn>
    <status value="final" />
    <category>
        <coding>
            <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
            <code value="laboratory" />
        </coding>
    </category>
    <category>
        <coding>
            <system value="http://terminology.hl7.org/CodeSystem/v2-0074" />
            <code value="GE" />
        </coding>
    </category>
    <code>
        <coding>
            <system value="http://loinc.org" />
            <code value="69548-6" />
        </coding>
    </code>
    <subject>
        <reference value="Patient/Patient-PheobeSmitham-Example" />
    </subject>
    <effectiveDateTime value="2023-09-16" />
    <performer>
        <identifier>
            <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
            <value value="R0A" />
        </identifier>
    </performer>
    <valueCodeableConcept>
        <coding>
            <system value="http://loinc.org" />
            <code value="LA9633-4" />
            <display value="Present" />
        </coding>
    </valueCodeableConcept>
    <method>
        <coding>
            <system value="http://loinc.org" />
            <code value="LA26398-0" />
            <display value="Sequencing" />
        </coding>
    </method>
    <specimen>
        <reference value="Specimen/Specimen-PheobeSmitham-Example" />
    </specimen>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="48004-6" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://varnomen.hgvs.org" />
                <code value="NM_024531.4:c.9163&gt;A p.(Gly306Arg)" />
            </coding>
        </valueCodeableConcept>
    </component>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="81290-9" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://varnomen.hgvs.org" />
                <code value="Chr8:g.1455840683&gt;A" />
            </coding>
        </valueCodeableConcept>
    </component>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="81252-9" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://www.sequenceontology.org" />
                <code value="SO:0001583" />
                <display value="missense_variant" />
            </coding>
        </valueCodeableConcept>
    </component>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="48018-6" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://www.genenames.org/" />
                <code value="HGNC:30224" />
                <display value="SLC52A2" />
            </coding>
        </valueCodeableConcept>
    </component>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="53034-5" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://loinc.org" />
                <code value="LA6705-3" />
                <display value="homozygous" />
            </coding>
        </valueCodeableConcept>
    </component>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="94186-4" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://loinc.org" />
                <code value="LA4489-6" />
                <display value="Unknown" />
            </coding>
        </valueCodeableConcept>
    </component>
    <component>
        <code>
            <coding>
                <system value="http://loinc.org" />
                <code value="48002-0" />
            </coding>
        </code>
        <valueCodeableConcept>
            <coding>
                <system value="http://loinc.org" />
                <code value="LA6683-2" />
                <display value="Germline" />
            </coding>
        </valueCodeableConcept>
    </component>
</Observation>

Notice

Observation-GenomicsVariantSLC52A2-Example

Propose a change to Observation-GenomicsVariantSLC52A2-Example