diff --git a/ServiceRequest/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json b/Bundle/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json similarity index 100% rename from ServiceRequest/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json rename to Bundle/Bundle-NonWGSTestOrderFormUpdated-FetalScenario-Example.json diff --git a/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json new file mode 100644 index 00000000..4f223b87 --- /dev/null +++ b/DiagnosticReport/DiagnosticReport-GenomicReport-VariantAssessment.json @@ -0,0 +1,124 @@ +{ + "resourceType": "DiagnosticReport", + "id": "DiagnosticReport-GenomicReport-VariantAssessment", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report" + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action", + "valueReference": { + "reference": "Task/Task-GenomicReport-FollowupRecommendation", + "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": "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" + } + } + ], + "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" + } + ] +} \ No newline at end of file diff --git a/DocumentReference/DocumentReference-StructureDataCapture-Example.json b/DocumentReference/DocumentReference-StructureDataCapture-Example.json new file mode 100644 index 00000000..a59c61b9 --- /dev/null +++ b/DocumentReference/DocumentReference-StructureDataCapture-Example.json @@ -0,0 +1,48 @@ +{ + "resourceType": "DocumentReference", + "id": "DocumentReference-StructureDataCapture-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/Observation/Observation-GenomicImplication-Therapeutic.json b/Observation/Observation-GenomicImplication-Therapeutic.json new file mode 100644 index 00000000..fcea1fb4 --- /dev/null +++ b/Observation/Observation-GenomicImplication-Therapeutic.json @@ -0,0 +1,98 @@ +{ + "resourceType": "Observation", + "id": "Observation-GenomicImplication-Therapeutic", + "meta": { + "profile": [ + "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication" + ] + }, + "status": "final", + "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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PheobeSmitham-Example" + }, + "effectiveDateTime": "2023-09-16", + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "R0A" + } + } + ], + "derivedFrom": [ + { + "reference": "Observation/Oservation-GenomicsVariant-SLC52A2" + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", + "code": "therapeutic-implication", + "display": "Therapeutic Implication" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA9661-5", + "display": "Presumed responsive" + } + ] + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "51963-7", + "display": "Medication assessed" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "777436008", + "display": "Riboflavin" + } + ] + } + } + ], + "note" : [{ + "text" : "High dose riboflavin supplementation has been reported to ameliorate the progression of this disorder (Foley et al 2014 PMID22740598)" + }] +} \ No newline at end of file diff --git a/Observation/Observation-GenomicsVariantSLC52A2-Example.json b/Observation/Observation-GenomicsVariantSLC52A2-Example.json new file mode 100644 index 00000000..a5a6a2dc --- /dev/null +++ b/Observation/Observation-GenomicsVariantSLC52A2-Example.json @@ -0,0 +1,207 @@ +{ + "resourceType": "Observation", + "id": "Observation-GenomicsVariantSLC52A2", + "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" + } + ] + } + } + ] +} \ No newline at end of file diff --git a/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json index d1a55273..af54b540 100644 --- a/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json +++ b/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json @@ -50,7 +50,7 @@ "targetProfile": [ "https://fhir.hl7.org.uk/StructureDefinition/UKCore-AllergyIntolerance", "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference", + "http://hl7.org/fhir/StructureDefinition/DocumentReference", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Condition-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Observation-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-DiagnosticReport-Genomics" diff --git a/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json index 9053ca40..359188e2 100644 --- a/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json +++ b/StructureDefinition/NHSDigital-Procedure-Genomics.StructureDefinition.json @@ -141,7 +141,7 @@ { "code": "Reference", "targetProfile": [ - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference", + "http://hl7.org/fhir/StructureDefinition/DocumentReference", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Condition-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-DiagnosticReport-Genomics", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Observation-Genomics", @@ -158,7 +158,7 @@ "code": "Reference", "targetProfile": [ "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Composition", - "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference", + "http://hl7.org/fhir/StructureDefinition/DocumentReference", "https://fhir.nhs.uk/StructureDefinition/NHSDigital-DiagnosticReport-Genomics" ], "aggregation": [ diff --git a/Task/Task-GenomicReport-FollowupRecommendation.json b/Task/Task-GenomicReport-FollowupRecommendation.json new file mode 100644 index 00000000..602a2f1e --- /dev/null +++ b/Task/Task-GenomicReport-FollowupRecommendation.json @@ -0,0 +1,57 @@ +{ + "resourceType": "Task", + "id": "Task-GenomicReport-FollowupRecommendation", + "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" + } + } + ] +} \ No newline at end of file diff --git a/fhirpkg.lock.json b/fhirpkg.lock.json index 03fa2328..cf246c4a 100644 --- a/fhirpkg.lock.json +++ b/fhirpkg.lock.json @@ -1,8 +1,13 @@ { - "updated": "2023-09-18T12:13:04.1481382+01:00", + "updated": "2024-05-16T10:18:19.8963748+01:00", "dependencies": { - "fhir.r4.ukcore.stu3.currentbuild": "0.0.13-pre-release", - "hl7.fhir.r4.core": "4.0.1" + "fhir.r4.ukcore.stu3.currentbuild": "0.0.17-pre-release", + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot", + "hl7.terminology.r4": "5.3.0", + "hl7.fhir.uv.extensions.r4": "1.0.0" }, "missing": {} } + + diff --git a/options.json b/options.json new file mode 100644 index 00000000..15f98d2b --- /dev/null +++ b/options.json @@ -0,0 +1,6 @@ +{ + "strict-validation": false, + "ignore-folders": [], + "ignore-files": [], + "error-if-metaProfile-present": false +} diff --git a/package.json b/package.json index 0adb71d4..b88c24e4 100644 --- a/package.json +++ b/package.json @@ -8,6 +8,9 @@ "jurisdiction": "urn:iso:std:iso:3166:-2:GB-ENG", "dependencies": { "fhir.r4.ukcore.stu3.currentbuild": "0.0.17-pre-release", - "hl7.fhir.r4.core": "4.0.1" + "hl7.fhir.r4.core": "4.0.1", + "hl7.fhir.uv.genomics-reporting": "3.0.0-ballot" } } + +