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Merged
KazeemHamzat
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Feature-IOPS-3020-WGS-Test-Order-Form-CancerSolidTumour
Feb 12, 2025
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6364815
Create WGS -TestOderForm-Cancer
KazeemHamzat e4e57c5
Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json
KazeemHamzat e6ce8f5
Add a Task Resource
KazeemHamzat 6880b81
Update Task-WGSCancerTestOrder-SolidTumour-Example.json
KazeemHamzat 4dc7c8c
Merge branch 'main' of https://github.com/NHSDigital/NHSDigital-FHIR-…
KazeemHamzat d99f325
Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json
KazeemHamzat 675ed53
Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json
KazeemHamzat b7fff85
Feedback Issues
KazeemHamzat 0ccb691
Update Specimen-SolidTumorDemeizaSeo-Example.json
KazeemHamzat c16af60
Update Specimen-SolidTumorDemeizaSeo-Example.json
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29 changes: 29 additions & 0 deletions
29
BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example.json
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|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| { | ||
| "resourceType": "BodyStructure", | ||
| "id": "BodyStructure-BodySiteLocationAbdomen-Example", | ||
| "morphology": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "369755005", | ||
| "display": "Multiple tumors (qualifier value)" | ||
| } | ||
| ] | ||
| }, | ||
| "location": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "818983003", | ||
| "display": "Structure of abdominopelvic cavity and/or content of abdominopelvic cavity and/or anterior abdominal wall (body structure)" | ||
| } | ||
| ] | ||
| }, | ||
| "patient": { | ||
| "reference": "Patient-DemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/nhs-number", | ||
| "value": "9449306559" | ||
| } | ||
| } | ||
| } |
41 changes: 41 additions & 0 deletions
41
Observation/Observation-PercentageMalignantNuclei-Example.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| { | ||
| "resourceType": "Observation", | ||
| "id": "Observation-PercentageMalignantNuclei-Example", | ||
| "status": "final", | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "1255076007", | ||
| "display": "Percent of cell nuclei positive for proliferation marker protein Ki-67 in primary malignant neoplasm of stomach by immunohistochemistry (observable entity)" | ||
| } | ||
| ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/Patient-DemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/nhs-number", | ||
| "value": "9449306559" | ||
| } | ||
| }, | ||
| "specimen": { | ||
| "reference":"Specimen/Specimen-SolidTumorDemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.add.nhs.uk/Id/specimenId", | ||
| "value": "RA257631", | ||
| "assigner": { | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/ods-organization-code", | ||
| "value": "696B0" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "valueQuantity": { | ||
| "value": 25, | ||
| "unit": "%", | ||
| "system": "http://unitsofmeasure.org", | ||
| "code": "%" | ||
| }, | ||
| "effectiveDateTime": "2023-08-09" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| { | ||
| "resourceType": "Observation", | ||
| "id": "Observation-TumourTypeDemeizaSeo-Example", | ||
| "status": "final", | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "116061001", | ||
| "display": "Solid pseudopapillary carcinoma (morphologic abnormality)" | ||
| } | ||
| ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/Patient-DemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/nhs-number", | ||
| "value": "9449306559" | ||
| } | ||
| }, | ||
| "specimen": { | ||
| "identifier": { | ||
| "system": "https://fhir.add.nhs.uk/Id/specimenId", | ||
| "value": "RA257631" | ||
| } | ||
| }, | ||
| "effectiveDateTime": "2023-09-08T11:00:00Z" | ||
| } |
111 changes: 111 additions & 0 deletions
111
ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| { | ||
| "resourceType": "ServiceRequest", | ||
| "id": "ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example", | ||
| "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" | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| { | ||
| "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-AdditionalContact", | ||
| "valueReference": { | ||
| "reference": "PractitionerRole/PractitionerRole-AnnaLaneKingstonPathology-Example" | ||
| } | ||
| } | ||
| ], | ||
| "status": "active", | ||
| "intent": "order", | ||
| "category": [ | ||
| { | ||
| "coding": [ | ||
| { | ||
| "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory", | ||
| "code": "cancer-wgs", | ||
| "display": "Cancer - 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": "M233.1", | ||
| "display": "WGS Germline and Tumour" | ||
| } | ||
| ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/Patient-DemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/nhs-number", | ||
| "value": "9449306559" | ||
| } | ||
| }, | ||
| "authoredOn": "2023-09-08", | ||
| "requester": { | ||
| "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" | ||
| }, | ||
| "reasonCode": [ | ||
| { | ||
| "coding": [ | ||
| { | ||
| "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", | ||
| "code": "diagnostic", | ||
| "display": "Diagnostic" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "performer": [ | ||
| { | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/ods-organization-code", | ||
| "value": "RJZ" | ||
| }, | ||
| "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" | ||
| } | ||
| ], | ||
| "supportingInfo": [ | ||
| { | ||
| "reference": "Observation/Observation-TumorType-Example" | ||
| }, | ||
| { | ||
| "reference": "Observation/Observation-PercentageMalignantNuclei-Example" | ||
| }, | ||
| { | ||
| "reference": "Consent/Consent-RoDToFollow-Example" | ||
| } | ||
| ], | ||
| "specimen": [ | ||
| { | ||
| "reference": "Specimen/Specimen-SolidTumorDemeizaSeo-Example" | ||
| } | ||
| ], | ||
| "note": [ | ||
| { | ||
| "text": "Relevant Family History" | ||
| }, | ||
| { | ||
| "text": "Other Additional Information" | ||
| } | ||
| ] | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| { | ||
| "resourceType": "Specimen", | ||
| "id": "Specimen-SolidTumorDemeizaSeo-Example", | ||
| "extension": [ | ||
| { | ||
| "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", | ||
| "valueCodeableConcept": { | ||
| "coding": [ | ||
| { | ||
| "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", | ||
| "code": "solid-tumour", | ||
| "display": "Solid Tumour" | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| ], | ||
| "identifier": [ | ||
| { | ||
| "system": "https://fhir.add.nhs.uk/Id/specimenId", | ||
| "value": "RA257631" | ||
| } | ||
| ], | ||
| "status": "available", | ||
| "type": { | ||
| "coding": [ | ||
| { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "364611000000101", | ||
| "display": "Tissue resection sample" | ||
| } | ||
| ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/Patient-DemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/nhs-number", | ||
| "value": "9449306559" | ||
| } | ||
| }, | ||
| "collection": { | ||
| "collector": { | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/sds-user-id", | ||
| "value": "9999999998" | ||
| }, | ||
| "display": "ClinicalScientist-John Taylor" | ||
| }, | ||
| "collectedDateTime": "2023-09-09T11:00:00Z", | ||
| "bodySite": { | ||
| "extension": [ | ||
| { | ||
| "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference", | ||
| "valueReference": { | ||
| "reference": "BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "condition": [ | ||
| { | ||
| "coding": [ | ||
| { | ||
| "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState", | ||
| "code": "fresh", | ||
| "display": "Fresh" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "request": [ | ||
| { | ||
| "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| { | ||
| "resourceType": "Task", | ||
| "id": "Task-WGSCancerTestOrder-SolidTumor-Example", | ||
| "status": "requested", | ||
| "intent": "order", | ||
| "priority": "routine", | ||
| "code": { | ||
| "coding": [ | ||
| { | ||
| "system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics", | ||
| "code": "process-genomic-test-request", | ||
| "display": "Process Genomic Test Request" | ||
| } | ||
| ] | ||
| }, | ||
| "focus": { | ||
| "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example" | ||
| }, | ||
| "for": { | ||
| "reference": "Patient/Patient-DemeizaSeo-Example", | ||
| "identifier": { | ||
| "system": "https://fhir.nhs.uk/Id/nhs-number", | ||
| "value": "9449306559" | ||
| } | ||
| }, | ||
| "authoredOn": "2023-09-09", | ||
| "requester": { | ||
| "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" | ||
| } | ||
| } |
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