diff --git a/.gitignore b/.gitignore index 014eff77..8bdb187a 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ IOPS-validation validation-service-fhir-r4 .idea/workspace.xml NHSDigital-DiagnosticReport-Genomics-International.StructureDefinition.json +Ignore diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json new file mode 100644 index 00000000..8d849926 --- /dev/null +++ b/Composition/Composition-EULabGenomicReport-Example.json @@ -0,0 +1,94 @@ +{ + "resourceType": "Composition", + "id": "Composition-EULabGenomicReport-Example", + "meta": { + "profile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/Composition-eu-lab" + ] + }, + "extension": [ + { + "url": "http://hl7.eu/fhir/StructureDefinition/composition-basedOn-order-or-requisition", + "valueReference": { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + } + }, + { + "url": "http://hl7.eu/fhir/StructureDefinition/information-recipient", + "valueReference": { + "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" + } + }, + { + "url": "http://hl7.eu/fhir/laboratory/StructureDefinition/composition-diagnosticReportReference", + "valueReference": { + "reference": "DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example" + } + } + ], + "status": "final", + "type": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51969-4", + "display": "Genetic analysis report" + } + ] + }, + "category": [ + { + "coding": [ + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + }, + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] + } + ], + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "date": "2023-10-16T00:00:00-05:00", + "author": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "title": "Example Genomic Laboratory (Single) Report", + "section": [ + { + "title": "Results", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + } + ] + }, + "entry": [ + { + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" + }, + { + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" + } + ] + } + ] +} \ No newline at end of file diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index c15be63c..0c7ca4b7 100644 --- a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json +++ b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json @@ -4,10 +4,17 @@ "meta": { "profile": [ "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport" + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport", + "http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab" ] }, "extension": [ + { + "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition", + "valueReference": { + "reference": "Composition/Composition-EULabGenomicReport-Example" + } + }, { "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", "valueReference": { @@ -63,13 +70,23 @@ "code": "GE" } ] + }, + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] } ], "code": { "coding": [ { "system": "http://loinc.org", - "code": "51969-4" + "code": "51969-4", + "display": "Genetic analysis report" }, { "system": "http://snomed.info/sct", @@ -91,6 +108,11 @@ } } ], + "specimen": [ + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + } + ], "media": [ { "link": { @@ -115,11 +137,11 @@ ], "result": [ { - "reference": "Observation/Observation-GenomicsVariant-SLC52A2", + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example", "display": "Brown-Vialetto-Van Laere syndrome type 2" }, { - "reference": "Observation/Observation-GenomicImplication-Therapeutic" + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" } ], "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).", diff --git a/NamingSystem/NamingSystem-Genomics-report-number.json b/NamingSystem/NamingSystem-Genomics-report-number.json new file mode 100644 index 00000000..0a1c5332 --- /dev/null +++ b/NamingSystem/NamingSystem-Genomics-report-number.json @@ -0,0 +1,43 @@ +{ + "resourceType": "NamingSystem", + "id": "genomics-report-number", + "name": "GenomicsReportNumber", + "status": "draft", + "kind": "identifier", + "date": "2025-09-08", + "publisher": "NHS England", + "contact": [ + { + "name": "NHS England", + "telecom": [ + { + "system": "email", + "value": "interoperabilityteam@nhs.net", + "use": "work", + "rank": 1 + } + ] + }, + { + "name": "NHS Genomic Medicine Service", + "telecom": [ + { + "system": "email", + "value": "england.genomics@nhs.net", + "use": "work", + "rank": 1 + } + ] + } + ], + "responsible": "NHS Genomic Interop Programme", + "description": "Genomic Medicine Service Unique Report Number", + "usage": "Assigned by central GMS system on receipt of a test report", + "uniqueId": [ + { + "type": "uri", + "value": "https://fhir.nhs.uk/Id/GMSReport", + "preferred": true + } + ] +} \ No newline at end of file diff --git a/Observation/Observation-GenomicTherapeuticImplication-Example.json b/Observation/Observation-GenomicTherapeuticImplication-Example.json index 8d292591..cf035818 100644 --- a/Observation/Observation-GenomicTherapeuticImplication-Example.json +++ b/Observation/Observation-GenomicTherapeuticImplication-Example.json @@ -3,7 +3,8 @@ "id": "Observation-GenomicTherapeuticImplication-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, "status": "final", @@ -47,7 +48,7 @@ ], "derivedFrom": [ { - "reference": "Observation/Oservation-GenomicsVariant-SLC52A2" + "reference": "Observation/Observation-GenomicsVariantSLC52A2-Example" } ], "component": [ @@ -85,8 +86,8 @@ "coding": [ { "system": "http://snomed.info/sct", - "code": "777436008", - "display": "Riboflavin" + "code": "438481000124108", + "display": "Riboflavin supplement" } ] } diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json index 8aa93f7a..8100a059 100644 --- a/Observation/Observation-GenomicsVariantSLC52A2-Example.json +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -3,7 +3,8 @@ "id": "Observation-GenomicsVariantSLC52A2-Example", "meta": { "profile": [ - "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab" ] }, "status": "final", diff --git a/Patient/Patient-PheobeSmitham-Example.json b/Patient/Patient-PheobeSmitham-Example.json index d00bb016..008c2c62 100644 --- a/Patient/Patient-PheobeSmitham-Example.json +++ b/Patient/Patient-PheobeSmitham-Example.json @@ -1,6 +1,12 @@ { "resourceType": "Patient", "id": "Patient-PheobeSmitham-Example", + "meta": { + "profile": [ + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient", + "http://hl7.eu/fhir/laboratory/StructureDefinition/Patient-eu-lab" + ] + }, "extension": [ { "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex", diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json index b01a400c..78c5ad88 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json @@ -3,7 +3,11 @@ "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", "meta": { "versionId": "2", - "lastUpdated": "2023-10-09T09:15:00Z" + "lastUpdated": "2023-10-09T09:15:00Z", + "profile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/ServiceRequest-eu-lab", + "https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest" + ] }, "extension": [ { @@ -19,6 +23,12 @@ } } ], + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/GMSOrder", + "value": "RR8F1792" + } + ], "requisition": { "assigner": { "identifier": { diff --git a/Task/Task-FollowupRecommendationReport-Example.json b/Task/Task-FollowupRecommendationReport-Example.json index 0a93f4b8..cf0ddec9 100644 --- a/Task/Task-FollowupRecommendationReport-Example.json +++ b/Task/Task-FollowupRecommendationReport-Example.json @@ -22,7 +22,7 @@ "reference": "Patient/Patient-PheobeSmitham-Example" }, "reasonReference": { - "reference": "Observation/Observation-GenomicImplication-Therapeutic" + "reference": "Observation/Observation-GenomicTherapeuticImplication-Example" }, "input": [ { diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 445b05cd..22f7c41b 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,15 @@ { - "updated": "2025-09-05T15:50:23.3766758+01:00", + "updated": "2025-09-05T16:30:58.9974559+01:00", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", + "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.r5.core": "5.0.0", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", "hl7.terminology.r4": "5.3.0", "hl7.fhir.uv.extensions.r4": "1.0.0", + "hl7.fhir.uv.ips": "1.1.0", + "fhir.dicom": "2022.4.20221006", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.0.0-comment", "hl7.fhir.r4b.core": "4.3.0", "us.nlm.vsac": "0.9.0", diff --git a/package.json b/package.json index 9f273180..f056a1d5 100644 --- a/package.json +++ b/package.json @@ -3,11 +3,12 @@ "description": "FHIR Genomics Implementation Guide", "author": "nhsdigital", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.18-pre-release", + "fhir.r4.ukcore.stu3.currentbuild": "0.24.0-pre-release", "hl7.fhir.r4.core": "4.0.1", "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", + "hl7.fhir.uv.ips": "1.1.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot", "ihe.iti.pcf": "1.0.0-comment" - }, "fhirVersions": [ "4.0.1"