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.

DiagnosticReport-GenomicVariantAssessment-Example

Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning structured reports back to a requester.
(NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For more information about this sample structured report, see, Duo/Trio scenario-wireframe. Additional guidance on Structured Reports is available on the HL7 Genomic Reporting Implementation Guide.

DiagnosticReport

id : DiagnosticReport-GenomicVariantAssessment-Example

meta

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

profile : https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport

extension

url : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action

value

reference : Task/Task-FollowupRecommendationReport-Example

display : Confirmatory testing recommended

extension

url : http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

value

type : citation

display : Johnson et al 2012 (PMID22740598)

extension

url : http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

value

type : citation

display : Foley et al 2014 (PMID22740598)

extension

url : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note

value

extension

url : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code

value

coding

system : http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs

code : test-disclaimer

text : Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868).

basedOn

reference : ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example

status : final

category

coding

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

code : GE

code

coding

system : http://loinc.org

code : 51969-4

subject

reference : Patient/Patient-PheobeSmitham-Example

effective : 2023-10-16T00:00:00-05:00

issued : 2023-09-16T00:00:00-05:00

performer

identifier

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

value : R0A

media

link

type : DocumentReference

display : Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition.

extension

url : http://hl7.org/fhir/StructureDefinition/data-absent-reason

value : unsupported

extension

url : http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link

value

reference : DocumentReference/DocumentReference-StructureReporting-Example

result

reference : Observation/Observation-GenomicsVariant-SLC52A2

display : Brown-Vialetto-Van Laere syndrome type 2

result

reference : Observation/Observation-GenomicImplication-Therapeutic

conclusion : Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).

conclusionCode

coding

system : http://loinc.org

code : LA6576-8

display : Positive

coding

system : http://snomed.info/sct

code : 699866005

display : Brown-Vialetto-Van Laere syndrome

presentedForm

contentType : application/pdf

language : en-GB

url : https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1

size : 43272

title : Genomic Report for Pheobe Smitham

creation : 2023-10-16

{
    "resourceType": "DiagnosticReport",
    "id": "DiagnosticReport-GenomicVariantAssessment-Example",
    "meta": {
        "profile":  [
            "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report",
            "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport"
        ]
    },
    "extension":  [
        {
            "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action",
            "valueReference": {
                "reference": "Task/Task-FollowupRecommendationReport-Example",
                "display": "Confirmatory testing recommended"
            }
        },
        {
            "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact",
            "valueRelatedArtifact": {
                "type": "citation",
                "display": "Johnson et al 2012 (PMID22740598)"
            }
        },
        {
            "url": "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact",
            "valueRelatedArtifact": {
                "type": "citation",
                "display": "Foley et al 2014 (PMID22740598)"
            }
        },
        {
            "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note",
            "valueAnnotation": {
                "extension":  [
                    {
                        "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code",
                        "valueCodeableConcept": {
                            "coding":  [
                                {
                                    "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs",
                                    "code": "test-disclaimer"
                                }
                            ]
                        }
                    }
                ],
                "text": "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)."
            }
        }
    ],
    "basedOn":  [
        {
            "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example"
        }
    ],
    "status": "final",
    "category":  [
        {
            "coding":  [
                {
                    "system": "http://terminology.hl7.org/CodeSystem/v2-0074",
                    "code": "GE"
                }
            ]
        }
    ],
    "code": {
        "coding":  [
            {
                "system": "http://loinc.org",
                "code": "51969-4"
            }
        ]
    },
    "subject": {
        "reference": "Patient/Patient-PheobeSmitham-Example"
    },
    "effectiveDateTime": "10/16/2023 05:00:00",
    "issued": "09/16/2023 05:00:00",
    "performer":  [
        {
            "identifier": {
                "system": "https://fhir.nhs.uk/Id/ods-organization-code",
                "value": "R0A"
            }
        }
    ],
    "media":  [
        {
            "link": {
                "type": "DocumentReference",
                "display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition.",
                "extension":  [
                    {
                        "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
                        "valueCode": "unsupported"
                    }
                ]
            },
            "extension":  [
                {
                    "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link",
                    "valueReference": {
                        "reference": "DocumentReference/DocumentReference-StructureReporting-Example"
                    }
                }
            ]
        }
    ],
    "result":  [
        {
            "reference": "Observation/Observation-GenomicsVariant-SLC52A2",
            "display": "Brown-Vialetto-Van Laere syndrome type 2"
        },
        {
            "reference": "Observation/Observation-GenomicImplication-Therapeutic"
        }
    ],
    "conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).",
    "conclusionCode":  [
        {
            "coding":  [
                {
                    "system": "http://loinc.org",
                    "code": "LA6576-8",
                    "display": "Positive"
                },
                {
                    "system": "http://snomed.info/sct",
                    "code": "699866005",
                    "display": "Brown-Vialetto-Van Laere syndrome"
                }
            ]
        }
    ],
    "presentedForm":  [
        {
            "contentType": "application/pdf",
            "language": "en-GB",
            "url": "https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1",
            "size": 43272,
            "title": "Genomic Report for Pheobe Smitham",
            "creation": "2023-10-16"
        }
    ]
}

<DiagnosticReport xmlns="http://hl7.org/fhir">
    <id value="DiagnosticReport-GenomicVariantAssessment-Example" />
    <meta>
        <profile value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" />
        <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" />
    </meta>
    <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action">
        <valueReference>
            <reference value="Task/Task-FollowupRecommendationReport-Example" />
            <display value="Confirmatory testing recommended" />
        </valueReference>
    </extension>
    <extension url="http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact">
        <valueRelatedArtifact>
            <type value="citation" />
            <display value="Johnson et al 2012 (PMID22740598)" />
        </valueRelatedArtifact>
    </extension>
    <extension url="http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact">
        <valueRelatedArtifact>
            <type value="citation" />
            <display value="Foley et al 2014 (PMID22740598)" />
        </valueRelatedArtifact>
    </extension>
    <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note">
        <valueAnnotation>
            <extension url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code">
                <valueCodeableConcept>
                    <coding>
                        <system value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs" />
                        <code value="test-disclaimer" />
                    </coding>
                </valueCodeableConcept>
            </extension>
            <text value="Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." />
        </valueAnnotation>
    </extension>
    <basedOn>
        <reference value="ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" />
    </basedOn>
    <status value="final" />
    <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="51969-4" />
        </coding>
    </code>
    <subject>
        <reference value="Patient/Patient-PheobeSmitham-Example" />
    </subject>
    <effectiveDateTime value="2023-10-16T00:00:00-05:00" />
    <issued value="2023-09-16T00:00:00-05:00" />
    <performer>
        <identifier>
            <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
            <value value="R0A" />
        </identifier>
    </performer>
    <result>
        <reference value="Observation/Observation-GenomicsVariant-SLC52A2" />
        <display value="Brown-Vialetto-Van Laere syndrome type 2" />
    </result>
    <result>
        <reference value="Observation/Observation-GenomicImplication-Therapeutic" />
    </result>
    <media>
        <extension url="http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link">
            <valueReference>
                <reference value="DocumentReference/DocumentReference-StructureReporting-Example" />
            </valueReference>
        </extension>
        <link>
            <extension url="http://hl7.org/fhir/StructureDefinition/data-absent-reason">
                <valueCode value="unsupported" />
            </extension>
            <type value="DocumentReference" />
            <display value="Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition." />
        </link>
    </media>
    <conclusion value="Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707)." />
    <conclusionCode>
        <coding>
            <system value="http://loinc.org" />
            <code value="LA6576-8" />
            <display value="Positive" />
        </coding>
        <coding>
            <system value="http://snomed.info/sct" />
            <code value="699866005" />
            <display value="Brown-Vialetto-Van Laere syndrome" />
        </coding>
    </conclusionCode>
    <presentedForm>
        <contentType value="application/pdf" />
        <language value="en-GB" />
        <url value="https://cts5j3.axshare.com/?id=mhxwul&amp;p=final_report_issued_test_complete&amp;g=1" />
        <size value="43272" />
        <title value="Genomic Report for Pheobe Smitham" />
        <creation value="2023-10-16" />
    </presentedForm>
</DiagnosticReport>

Notice

DiagnosticReport-GenomicVariantAssessment-Example

Propose a change to DiagnosticReport-GenomicVariantAssessment-Example