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Merge pull request #157 from NHSDigital/Issue-2663
HL7 EU Lab Structured Report Alignment
2 parents 695697f + 2270935 commit 027f435

11 files changed

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‎.gitignore‎

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validation-service-fhir-r4
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.idea/workspace.xml
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NHSDigital-DiagnosticReport-Genomics-International.StructureDefinition.json
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‎Composition/Composition-EULabGenomicReport-Example.json‎

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{
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"resourceType": "Composition",
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"id": "Composition-EULabGenomicReport-Example",
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"meta": {
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"profile": [
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"http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab"
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]
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},
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"extension": [
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{
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"url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition",
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"valueReference": {
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"reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example"
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}
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},
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{
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"url": "http://hl7.eu/fhir/StructureDefinition/information-recipient",
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"valueReference": {
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"reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example"
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}
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},
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{
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"url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference",
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"valueReference": {
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"reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example"
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}
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}
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],
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"status": "final",
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"type": {
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"coding": [
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{
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"system": "http://loinc.org",
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"code": "51969-4",
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"display": "Genetic analysis report"
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}
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]
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},
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"category": [
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{
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"coding": [
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{
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"system": "http://loinc.org",
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"code": "26436-6",
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"display": "Laboratory studies (set)"
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}
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]
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},
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{
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "1236877003",
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"display": "Genetic pathology"
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}
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]
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}
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],
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"subject": {
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"reference": "Patient/Patient-PheobeSmitham-Example"
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},
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"date": "2023-10-16T00:00:00-05:00",
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"author": [
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{
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/ods-organization-code",
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"value": "R0A"
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}
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}
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],
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"title": "Example Genomic Laboratory (Single) Report",
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"section": [
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{
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"title": "Results",
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"code": {
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"coding": [
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{
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"system": "http://loinc.org",
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"code": "26436-6",
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"display": "Laboratory studies (set)"
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}
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]
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},
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"entry": [
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{
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"reference": "Observation/Observation-GenomicTherapeuticImplication-Example"
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},
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{
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"reference": "Observation/Observation-GenomicsVariantSLC52A2-Example"
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}
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]
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}
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]
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}

‎DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json‎

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"meta": {
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"profile": [
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"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report",
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"https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport"
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"https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport",
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"http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab"
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]
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},
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"extension": [
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{
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"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition",
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"valueReference": {
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"reference": "Composition/Composition-EULabGenomicReport-Example"
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}
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},
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{
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"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action",
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"valueReference": {
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"code": "GE"
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}
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]
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},
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{
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "1236877003",
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"display": "Genetic pathology"
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}
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]
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}
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],
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"code": {
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"coding": [
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{
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"system": "http://loinc.org",
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"code": "51969-4"
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"code": "51969-4",
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"display": "Genetic analysis report"
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},
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{
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"system": "http://snomed.info/sct",
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}
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}
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],
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"specimen": [
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{
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"reference": "Specimen/Specimen-PheobeSmitham-Example"
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}
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],
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"media": [
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{
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"link": {
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],
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"result": [
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{
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"reference": "Observation/Observation-GenomicsVariant-SLC52A2",
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"reference": "Observation/Observation-GenomicsVariantSLC52A2-Example",
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"display": "Brown-Vialetto-Van Laere syndrome type 2"
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},
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{
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"reference": "Observation/Observation-GenomicImplication-Therapeutic"
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"reference": "Observation/Observation-GenomicTherapeuticImplication-Example"
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}
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],
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"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).",

‎NamingSystem/NamingSystem-Genomics-report-number.json‎

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{
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"resourceType": "NamingSystem",
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"id": "genomics-report-number",
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"name": "GenomicsReportNumber",
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"status": "draft",
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"kind": "identifier",
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"date": "2025-09-08",
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"publisher": "NHS England",
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"contact": [
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{
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"name": "NHS England",
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"telecom": [
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{
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"system": "email",
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"value": "interoperabilityteam@nhs.net",
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"use": "work",
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"rank": 1
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}
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]
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},
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{
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"name": "NHS Genomic Medicine Service",
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"telecom": [
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{
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"system": "email",
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"value": "england.genomics@nhs.net",
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"use": "work",
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"rank": 1
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}
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]
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}
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],
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"responsible": "NHS Genomic Interop Programme",
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"description": "Genomic Medicine Service Unique Report Number",
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"usage": "Assigned by central GMS system on receipt of a test report",
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"uniqueId": [
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{
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"type": "uri",
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"value": "https://fhir.nhs.uk/Id/GMSReport",
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"preferred": true
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}
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]
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}

‎Observation/Observation-GenomicTherapeuticImplication-Example.json‎

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"id": "Observation-GenomicTherapeuticImplication-Example",
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"meta": {
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"profile": [
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"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
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"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication",
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"http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab"
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]
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},
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"status": "final",
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],
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"derivedFrom": [
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{
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"reference": "Observation/Oservation-GenomicsVariant-SLC52A2"
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"reference": "Observation/Observation-GenomicsVariantSLC52A2-Example"
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}
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],
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"component": [
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "777436008",
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"display": "Riboflavin"
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"code": "438481000124108",
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"display": "Riboflavin supplement"
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}
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]
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}

‎Observation/Observation-GenomicsVariantSLC52A2-Example.json‎

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"id": "Observation-GenomicsVariantSLC52A2-Example",
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"meta": {
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"profile": [
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"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
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"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant",
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"http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab"
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]
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},
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"status": "final",

‎Patient/Patient-PheobeSmitham-Example.json‎

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{
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"resourceType": "Patient",
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"id": "Patient-PheobeSmitham-Example",
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"meta": {
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"profile": [
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"https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient",
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"http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab"
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]
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},
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"extension": [
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{
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"url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex",

‎ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json‎

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"id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example",
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"meta": {
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"versionId": "2",
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"lastUpdated": "2023-10-09T09:15:00Z"
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"lastUpdated": "2023-10-09T09:15:00Z",
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"profile": [
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"http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab",
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"https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest"
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]
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},
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"extension": [
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{
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}
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}
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],
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"identifier": [
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{
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"system": "https://fhir.nhs.uk/Id/GMSOrder",
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"value": "RR8F1792"
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}
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],
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"requisition": {
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"assigner": {
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"identifier": {

‎Task/Task-FollowupRecommendationReport-Example.json‎

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"reference": "Patient/Patient-PheobeSmitham-Example"
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},
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"reasonReference": {
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"reference": "Observation/Observation-GenomicImplication-Therapeutic"
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"reference": "Observation/Observation-GenomicTherapeuticImplication-Example"
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},
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"input": [
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{

‎fhirpkg.lock.json‎

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{
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"updated": "2025-09-05T15:50:23.3766758+01:00",
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"updated": "2025-09-05T16:30:58.9974559+01:00",
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"dependencies": {
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"fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release",
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"fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release",
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"hl7.fhir.r4.core": "4.0.1",
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"hl7.fhir.r5.core": "5.0.0",
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"hl7.fhir.uv.genomics-reporting": "3.0.0-ballot",
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"hl7.terminology.r4": "5.3.0",
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"hl7.fhir.uv.extensions.r4": "1.0.0",
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"hl7.fhir.uv.ips": "1.1.0",
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"fhir.dicom": "2022.4.20221006",
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"hl7.fhir.eu.laboratory": "0.1.0-ballot",
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"ihe.iti.pcf": "1.0.0-comment",
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"hl7.fhir.r4b.core": "4.3.0",
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"us.nlm.vsac": "0.9.0",

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