diff --git a/Bundle/Bundle-EULabGenomicReport-Example.json b/Bundle/Bundle-EULabGenomicReport-Example.json new file mode 100644 index 00000000..b2355cb4 --- /dev/null +++ b/Bundle/Bundle-EULabGenomicReport-Example.json @@ -0,0 +1,1073 @@ +{ + "resourceType": "Bundle", + "id": "Bundle-EULabGenomicReport-Example", + "meta": { + "profile": [ + "http://hl7.eu/fhir/laboratory/StructureDefinition/Bundle-eu-lab" + ] + }, + "identifier": { + "system": "https://fhir.nhs.uk/Id/GMSReport", + "value": "c73ece32-b439-40c0-9659-fd51a21deef2" + }, + "type": "document", + "timestamp": "2023-10-16T00:00:00-05:00", + "entry": [ + { + "fullUrl": "http://example.org/fhir/Composition/Composition-EULabGenomicReport-Example", + "resource": { + "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" + } + ] + } + ] + } + }, + { + "fullUrl": "http://example.org/fhir/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example", + "resource": { + "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", + "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": { + "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" + } + ] + }, + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1236877003", + "display": "Genetic pathology" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51969-4", + "display": "Genetic analysis report" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "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", + "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-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).", + "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" + } + ] + } + }, + { + "fullUrl": "http://example.org/fhir/Patient/Patient-PheobeSmitham-Example", + "resource": { + "resourceType": "Patient", + "id": "Patient-PheobeSmitham-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BirthSex", + "valueCodeableConcept": { + "coding": [ + { + "system": 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"fullUrl": "http://example.org/fhir/Specimen/Specimen-PheobeSmitham-Example", + "resource": { + "resourceType": "Specimen", + "id": "Specimen-PheobeSmitham-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", + "code": "germline", + "display": "Germline" + } + ] + } + } + ], + "identifier": [ + { + "system": "https://fhir.leedssth.nhs.uk//Id/specimenId", + "value": "RGD-69050-P-RR12764" + } + ], + "status": "available", + "type": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445295009", + "display": "Blood specimen with EDTA" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307539" + } + }, + "collection": { + "collector": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/sds-user-id", + "value": "9999999998" + }, + "display": "Phletobomist-Lois Lane" + }, + "collectedDateTime": "2023-09-17" + }, + "request": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example" + } + ] + } + }, + { + "fullUrl": "http://example.org/fhir/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "resource": { + "resourceType": "ServiceRequest", + "id": "ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example", + "meta": { + "versionId": "2", + "lastUpdated": "2023-10-09T09:15:00Z" + }, + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory", + "code": "nhs-england", + "display": "NHS England" + } + ] + } + } + ], + "identifier": [ + { + "system": "https://fhir.nhs.uk/Id/GMSOrder", + "value": "RR8F1792" + } + ], + "requisition": { + "assigner": { + "identifier": { + "system": "https://fhir.leedsth.nhs.uk/Id/grouptestId", + "value": "RR8F1792" + } + } + }, + "status": "active", + "intent": "order", + "category": [ + { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", + "code": "rare-disease-wgs", + "display": "Rare Disease - WGS" + } + ] + }, + { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + } + ] + } + ], + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", + "code": "R98.2", + "display": "Likely inborn error of metabolism", + "version": "7" + } + ], + "text": "This is a Trio Testing, comprising 3 family members with their respective specimen`s & Record Of Discussion`s" + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307539" + } + }, + "authoredOn": "2023-09-15T15:00:00Z", + "requester": { + "reference": "PractitionerRole/PractitionerRole-EugeneSmith-Example" + }, + "reasonReference": [ + { + "reference": "Condition/Condition-InbornErrorOfMetabolism-Example" + } + ], + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "supportingInfo": [ + { + "reference": "Observation/Observation-AutisticBehaviour-Example" + }, + { + "reference": "Observation/Observation-DelayedSpeechLanguageDevt-Example" + }, + { + "reference": "Observation/Observation-DiseasePenetrancePheobeSmitham-Example" + }, + { + "reference": "Observation/Observation-IntellectualDisabilityProfound-Example" + }, + { + "reference": "Observation/Observation-NonConsanguinousUnionProband-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + }, + { + "reference": 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Not eligible for R14 or R98. Agreed with testing laboratory at Manchester. Father lives in surrey. Father to have sample taken locally and sent to MFT." + } + ] + } + }, + { + "fullUrl": "http://example.org/fhir/Task/Task-FollowupRecommendationReport-Example", + "resource": { + "resourceType": "Task", + "id": "Task-FollowupRecommendationReport-Example", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/followup-recommendation" + ] + }, + "status": "requested", + "intent": "proposal", + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA14021-2", + "display": "Confirmatory testing recommended" + } + ] + }, + "description": "Testing of Pheobe's parents is recommended (via referral to the clinical genetics service) in order to confirm that both are heterozygous carriers of the missense variant.", + "for": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "reasonReference": { + "reference": "Observation/Observation-GenomicImplication-Therapeutic" + }, + "input": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "NFTH", + "display": "natural father" + } + ] + }, + "valueReference": { + "reference": "Patient/Patient-PheobeSmithamFather-Example" + } + }, + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v3-RoleCode", + "code": "NMTH", + "display": "natural mother" + } + ] + }, + "valueReference": { + "reference": "Patient/Patient-PheobeSmithamMother-Example" + } + } + ] + } + }, + { + "fullUrl": "http://example.org/fhir/DocumentReference/DocumentReference-StructureReporting-Example", + "resource": { + "resourceType": "DocumentReference", + "id": "DocumentReference-StructureReporting-Example", + "status": "current", + "docStatus": "final", + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307539" + } + }, + "date": "2023-10-16T09:45:00Z", + "author": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "description": "Phenotype Report", + "content": [ + { + "attachment": { + "contentType": "application/json", + "url": "drs://drs.genomicsengland.nhs.uk/ga4gh/drs/v1/objects/42375e7d-071c-4eb3-b1c8-cec11e245cf0", + "title": "-Structure Data Capture JSON report" + } + } + ], + "context": { + "related": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmithamFather-Example" + }, + { + "reference": "Specimen/Specimen-PheobeSmithamMother-Example" + } + ] + } + } + } + ] +} \ No newline at end of file diff --git a/Composition/Composition-EULabGenomicReport-Example.json b/Composition/Composition-EULabGenomicReport-Example.json new file mode 100644 index 00000000..46696872 --- /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-GenomicsVariantSLC52A2-Example" + } + ] + } + ] +} \ No newline at end of file diff --git a/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json b/DiagnosticReport/DiagnosticReport-GenomicVariantAssessment-Example.json index d5efe0b4..ed9637d2 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" } ] }, @@ -86,6 +103,11 @@ } } ], + "specimen": [ + { + "reference": "Specimen/Specimen-PheobeSmitham-Example" + } + ], "media": [ { "link": { @@ -110,11 +132,11 @@ ], "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..2d9e4b78 --- /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": "2025-02-10", + "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 7b015a5c..2524e4ea 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/Observation/Observation-NoTransfusionProbandFather-Example.json b/Observation/Observation-NoTransfusionProbandFather-Example.json index 5970c087..1ccd018e 100644 --- a/Observation/Observation-NoTransfusionProbandFather-Example.json +++ b/Observation/Observation-NoTransfusionProbandFather-Example.json @@ -27,5 +27,5 @@ "value": "9449307636" } }, - "effectiveDateTime": "2023-09-15T15:00:00Z", + "effectiveDateTime": "2023-09-15T15:00:00Z" } \ No newline at end of file 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..2c9a6baf 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example.json @@ -19,6 +19,12 @@ } } ], + "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 5f2bc664..61e265b3 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,11 +1,11 @@ { - "updated": "2025-05-08T09:07:12.7767319+01:00", + "updated": "2025-09-05T16:14:34.8200964+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.eu.laboratory": "0.1.0-ballot" }, "missing": {} } diff --git a/package.json b/package.json index e679bd07..63ed107b 100644 --- a/package.json +++ b/package.json @@ -7,9 +7,11 @@ ], "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "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.genomics-reporting": "3.0.0-ballot", + "hl7.fhir.uv.ips": "1.1.0", + "hl7.fhir.eu.laboratory": "0.1.0-ballot" } }