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KazeemHamzatKazeemHamzat
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Feature-IOPS-3020-WGS-Test-Order-Form-CancerSolidTumour (#153)
* Create WGS -TestOderForm-Cancer Create WGS -TestOderForm-Cancer-SolidTumour * Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json update * Add a Task Resource Add a Task Resource * Update Task-WGSCancerTestOrder-SolidTumour-Example.json Update Task Requester reference * Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json Update SR to reflect new mapping of reason-for-testing * Update ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json new mapping * Feedback Issues Update SR.code value * Update Specimen-SolidTumorDemeizaSeo-Example.json Update Specimen.code value * Update Specimen-SolidTumorDemeizaSeo-Example.json Update value for Specimen.condition
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‎BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example.json‎

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{
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"resourceType": "BodyStructure",
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"id": "BodyStructure-BodySiteLocationAbdomen-Example",
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"morphology": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "369755005",
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"display": "Multiple tumors (qualifier value)"
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}
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]
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},
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"location": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "818983003",
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"display": "Structure of abdominopelvic cavity and/or content of abdominopelvic cavity and/or anterior abdominal wall (body structure)"
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}
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]
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},
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"patient": {
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"reference": "Patient-DemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/nhs-number",
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"value": "9449306559"
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}
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}
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}

‎Observation/Observation-PercentageMalignantNuclei-Example.json‎

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{
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"resourceType": "Observation",
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"id": "Observation-PercentageMalignantNuclei-Example",
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"status": "final",
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "1255076007",
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"display": "Percent of cell nuclei positive for proliferation marker protein Ki-67 in primary malignant neoplasm of stomach by immunohistochemistry (observable entity)"
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}
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]
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},
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"subject": {
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"reference": "Patient/Patient-DemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/nhs-number",
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"value": "9449306559"
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}
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},
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"specimen": {
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"reference":"Specimen/Specimen-SolidTumorDemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.add.nhs.uk/Id/specimenId",
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"value": "RA257631",
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"assigner": {
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/ods-organization-code",
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"value": "696B0"
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}
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}
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}
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},
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"valueQuantity": {
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"value": 25,
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"unit": "%",
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"system": "http://unitsofmeasure.org",
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"code": "%"
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},
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"effectiveDateTime": "2023-08-09"
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}

‎Observation/Observation-TumourTypeDemeizaSeo-Example.json‎

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{
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"resourceType": "Observation",
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"id": "Observation-TumourTypeDemeizaSeo-Example",
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"status": "final",
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "116061001",
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"display": "Solid pseudopapillary carcinoma (morphologic abnormality)"
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}
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]
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},
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"subject": {
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"reference": "Patient/Patient-DemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/nhs-number",
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"value": "9449306559"
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}
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},
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"specimen": {
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"identifier": {
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"system": "https://fhir.add.nhs.uk/Id/specimenId",
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"value": "RA257631"
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}
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},
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"effectiveDateTime": "2023-09-08T11:00:00Z"
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}

‎ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example.json‎

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{
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"resourceType": "ServiceRequest",
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"id": "ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example",
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"extension": [
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{
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"url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-Coverage",
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"valueCodeableConcept": {
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"coding": [
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{
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"system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-FundingCategory",
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"code": "nhs-england",
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"display": "NHS England"
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}
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]
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}
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},
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{
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"url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-AdditionalContact",
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"valueReference": {
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"reference": "PractitionerRole/PractitionerRole-AnnaLaneKingstonPathology-Example"
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}
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}
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],
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"status": "active",
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"intent": "order",
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"category": [
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{
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"coding": [
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{
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"system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-GenomeSequencingCategory",
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"code": "cancer-wgs",
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"display": "Cancer - WGS"
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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": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics",
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"code": "diagnostic",
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"display": "Diagnostic"
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}
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]
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}
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],
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"priority": "routine",
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"code": {
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"coding": [
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{
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"system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory",
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"code": "M233.1",
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"display": "WGS Germline and Tumour"
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}
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]
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},
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"subject": {
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"reference": "Patient/Patient-DemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/nhs-number",
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"value": "9449306559"
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}
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},
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"authoredOn": "2023-09-08",
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"requester": {
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"reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example"
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},
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"reasonCode": [
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{
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"coding": [
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{
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"system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics",
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"code": "diagnostic",
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"display": "Diagnostic"
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}
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]
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}
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],
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"performer": [
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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": "RJZ"
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},
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"display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST"
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}
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],
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"supportingInfo": [
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{
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"reference": "Observation/Observation-TumorType-Example"
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},
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{
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"reference": "Observation/Observation-PercentageMalignantNuclei-Example"
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},
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{
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"reference": "Consent/Consent-RoDToFollow-Example"
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}
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],
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"specimen": [
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{
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"reference": "Specimen/Specimen-SolidTumorDemeizaSeo-Example"
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}
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],
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"note": [
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{
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"text": "Relevant Family History"
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},
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{
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"text": "Other Additional Information"
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}
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]
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}

‎Specimen/Specimen-SolidTumorDemeizaSeo-Example.json‎

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{
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"resourceType": "Specimen",
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"id": "Specimen-SolidTumorDemeizaSeo-Example",
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"extension": [
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{
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"url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory",
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"valueCodeableConcept": {
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"coding": [
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{
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"system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory",
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"code": "solid-tumour",
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"display": "Solid Tumour"
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}
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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.add.nhs.uk/Id/specimenId",
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"value": "RA257631"
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}
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],
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"status": "available",
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"type": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "364611000000101",
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"display": "Tissue resection sample"
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}
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]
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},
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"subject": {
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"reference": "Patient/Patient-DemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/nhs-number",
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"value": "9449306559"
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}
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},
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"collection": {
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"collector": {
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/sds-user-id",
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"value": "9999999998"
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},
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"display": "ClinicalScientist-John Taylor"
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},
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"collectedDateTime": "2023-09-09T11:00:00Z",
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"bodySite": {
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"extension": [
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{
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"url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference",
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"valueReference": {
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"reference": "BodyStructure/BodyStructure-BodySiteLocationAbdomen-Example"
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}
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}
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]
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}
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},
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"condition": [
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{
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"coding": [
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{
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"system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState",
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"code": "fresh",
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"display": "Fresh"
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}
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]
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}
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],
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"request": [
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{
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"reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example"
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}
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]
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}

‎Task/Task-WGSCancerTestOrder-SolidTumour-Example.json‎

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{
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"resourceType": "Task",
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"id": "Task-WGSCancerTestOrder-SolidTumor-Example",
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"status": "requested",
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"intent": "order",
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"priority": "routine",
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"code": {
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"coding": [
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{
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"system": "https://fhir.nhs.uk/CodeSystem/task-code-genomics",
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"code": "process-genomic-test-request",
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"display": "Process Genomic Test Request"
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}
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]
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},
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"focus": {
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"reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerSolidTumor-Example"
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},
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"for": {
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"reference": "Patient/Patient-DemeizaSeo-Example",
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"identifier": {
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"system": "https://fhir.nhs.uk/Id/nhs-number",
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"value": "9449306559"
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}
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},
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"authoredOn": "2023-09-09",
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"requester": {
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"reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example"
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}
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}

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