From 30b7ad87f4f6f2203521470f8052752671c1fe6a Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 10 Feb 2025 13:49:06 +0000 Subject: [PATCH 1/8] Create Cancer-HaemOnc Test Option FHIR asset to replicate Cancer-HaemOnc Test Option --- ...ndition-AcuteMyeloidLeukaemia-Example.json | 38 ++++++ ...tion-BlastPercentageWGSSample-Example.json | 40 +++++++ ...n-NucleatedCellCountWGSSample-Example.json | 40 +++++++ ...ckSammyNoBoneMarrowTransplant-Example.json | 31 +++++ ...GSTestOrderForm-CancerHaemOnc-Example.json | 109 ++++++++++++++++++ ...Specimen-BoneMarrowAspiration-Example.json | 2 +- ...pecimen-PatrickSammyBloodEDTA-Example.json | 40 +++++++ ...rickSammyBoneMarrowAspiration-Example.json | 45 ++++++++ ...sk-WGSCancerTestOrder-HaemOnc-Example.json | 30 +++++ 9 files changed, 374 insertions(+), 1 deletion(-) create mode 100644 Condition/Condition-AcuteMyeloidLeukaemia-Example.json create mode 100644 Observation/Observation-BlastPercentageWGSSample-Example.json create mode 100644 Observation/Observation-NucleatedCellCountWGSSample-Example.json create mode 100644 Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json create mode 100644 ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json create mode 100644 Specimen/Specimen-PatrickSammyBloodEDTA-Example.json create mode 100644 Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json create mode 100644 Task/Task-WGSCancerTestOrder-HaemOnc-Example.json diff --git a/Condition/Condition-AcuteMyeloidLeukaemia-Example.json b/Condition/Condition-AcuteMyeloidLeukaemia-Example.json new file mode 100644 index 00000000..8c90f875 --- /dev/null +++ b/Condition/Condition-AcuteMyeloidLeukaemia-Example.json @@ -0,0 +1,38 @@ +{ + "resourceType": "Condition", + "id": "Condition-AcuteMyeloidLeukaemia-Example", + "clinicalStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", + "code": "active", + "display": "Active" + } + ] + }, + "verificationStatus": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "provisional", + "display": "Provisional" + } + ] + }, + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1162928000", + "display": "Acute myeloid leukemia (morphologic abnormality)" + } + ] + }, + "subject": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "recordedDate": "2023-09-05" +} \ No newline at end of file diff --git a/Observation/Observation-BlastPercentageWGSSample-Example.json b/Observation/Observation-BlastPercentageWGSSample-Example.json new file mode 100644 index 00000000..ecc9c324 --- /dev/null +++ b/Observation/Observation-BlastPercentageWGSSample-Example.json @@ -0,0 +1,40 @@ +{ + "resourceType": "Observation", + "id": "Observation-BlastPercentageWGSSample-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1015521000000107", + "display": "Percentage blast cells (observable entity)" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", + "value": "RR81235", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + }, + "valueQuantity": { + "value": 25, + "unit": "%", + "system": "http://unitsofmeasure.org", + "code": "%" + }, + "effectiveDateTime": "2023-08-05" +} \ No newline at end of file diff --git a/Observation/Observation-NucleatedCellCountWGSSample-Example.json b/Observation/Observation-NucleatedCellCountWGSSample-Example.json new file mode 100644 index 00000000..b2eaf2cc --- /dev/null +++ b/Observation/Observation-NucleatedCellCountWGSSample-Example.json @@ -0,0 +1,40 @@ +{ + "resourceType": "Observation", + "id": "Observation-NucleatedCellCount-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1022461000000100", + "display": "Nucleated red blood cell count" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "specimen": { + "identifier": { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", + "value": "RR81235", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + }, + "valueQuantity": { + "value": 10, + "unit": "10^12/l", + "system": "http://unitsofmeasure.org", + "code": "10^12/L" + }, + "effectiveDateTime": "2023-09-05" +} \ No newline at end of file diff --git a/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json b/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json new file mode 100644 index 00000000..74494981 --- /dev/null +++ b/Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example.json @@ -0,0 +1,31 @@ +{ + "resourceType": "Observation", + "id": "Observation-PatrickSammyNoBoneMarrowTransplant-Example", + "status": "final", + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "416128008", + "display": "No history of procedure (situation)" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445715009", + "display": "Blood and marrow transplantation (qualifier value)" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "effectiveDateTime": "2023-09-05" +} \ No newline at end of file diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json new file mode 100644 index 00000000..298ca9ba --- /dev/null +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json @@ -0,0 +1,109 @@ +{ + "resourceType": "ServiceRequest", + "id": "ServiceRequest-WGSTestOrderForm-CancerHaemOnc-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" + } + ] + } + ], + "priority": "routine", + "code": { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", + "code": "M89.108", + "display": "Multi Target NGS Panel Small Variant" + }, + { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + } + ] + } + ] + }, + "subject": { + "reference": "Patient/Patient-DemeizaSeo-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449306559" + } + }, + "authoredOn": "2023-09-28", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" + }, + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJZ" + }, + "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" + } + ], + "supportingInfo": [ + { + "reference": "Condition/Condition-AcuteMyeloidLeukaemia-Example" + }, + { + "reference": "Observation/Observation-BlastPercentage-Example" + }, + { + "reference": "Observation/Observation-NucleatedCellCount-Example" + }, + { + "reference": "Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example" + }, + { + "reference": "Consent/Consent-RoDToFollow-Example" + } + ], + "specimen": [ + { + "reference": "Specimen/Specimen-PatrickSammyBloodEDTA-Example" + }, + { + "reference": "Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example" + } + ], + "note": [ + { + "text": "Relevant Family History" + }, + { + "text": "Other Additional Information" + } + ] +} \ No newline at end of file diff --git a/Specimen/Specimen-BoneMarrowAspiration-Example.json b/Specimen/Specimen-BoneMarrowAspiration-Example.json index c5989364..2788bd6d 100644 --- a/Specimen/Specimen-BoneMarrowAspiration-Example.json +++ b/Specimen/Specimen-BoneMarrowAspiration-Example.json @@ -39,7 +39,7 @@ "receivedTime": "2023-08-29T11:00:00Z", "request": [ { - "reference": "ServiceRequest-NonWGSTestOrderForm-HaemOncology-Example" + "reference": "ServiceRequest/ServiceRequest-NonWGSTestOrderForm-HaemOncology-Example" } ] } \ No newline at end of file diff --git a/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json b/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json new file mode 100644 index 00000000..6e57e117 --- /dev/null +++ b/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json @@ -0,0 +1,40 @@ +{ + "resourceType": "Specimen", + "id": "Specimen-PatrickSammyBloodEDTA-Example", + "identifier": [ + { + "system": "https://fhir.add.nhs.uk/Id/specimenId", + "value": "RGT03135A" + } + ], + "status": "unavailable", + "type": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "445295009", + "display": "Blood specimen with EDTA" + } + ] + }, + "subject": { + "reference": "Patient/Patient-MeirLieberman-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "request": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" + } + ], + "collection": { + "collectedDateTime": "2023-09-11T09:00:00Z", + "quantity": { + "system": "http://unitsofmeasure.org", + "code": "mL", + "value": 2.5 + } + } +} \ No newline at end of file diff --git a/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json new file mode 100644 index 00000000..d15ec3af --- /dev/null +++ b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json @@ -0,0 +1,45 @@ +{ + "resourceType": "Specimen", + "id": "Specimen-PatrickSammyBoneMarrowAspiration-Example", + "identifier": [ + { + "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", + "value": "RR81235", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "696B0" + } + } + } + ], + "accessionIdentifier": { + "system": "https://www.leedsth.nhs.uk/path", + "value": "RR8123745", + "assigner": { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RR8" + } + } + }, + "status": "available", + "type": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "396997002", + "display": "Specimen from bone marrow obtained by aspiration" + } + ] + }, + "subject": { + "reference": "Patient/Patient-PatrickSammy-Example" + }, + "receivedTime": "2023-09-11T11:00:00Z", + "request": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" + } + ] +} \ No newline at end of file diff --git a/Task/Task-WGSCancerTestOrder-HaemOnc-Example.json b/Task/Task-WGSCancerTestOrder-HaemOnc-Example.json new file mode 100644 index 00000000..20ade6a8 --- /dev/null +++ b/Task/Task-WGSCancerTestOrder-HaemOnc-Example.json @@ -0,0 +1,30 @@ +{ + "resourceType": "Task", + "id": "Task-WGSCancerTestOrder-HaemOnc-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-CancerHaemOnc-Example" + }, + "for": { + "reference": "Patient/Patient-PatrickSammy-Example", + "identifier": { + "system": "https://fhir.nhs.uk/Id/nhs-number", + "value": "9449307873" + } + }, + "authoredOn": "2023-09-28", + "requester": { + "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" + } +} From 782158051ad199e864f09b5b700a35ae2d4d17aa Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 10 Feb 2025 14:16:20 +0000 Subject: [PATCH 2/8] Update ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json Add new mapping for category --- ...WGSTestOrderForm-CancerHaemOnc-Example.json | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json index 298ca9ba..0f88c916 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json @@ -43,13 +43,9 @@ "display": "Multi Target NGS Panel Small Variant" }, { - "coding": [ - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "diagnostic", - "display": "Diagnostic" - } - ] + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" } ] }, @@ -60,7 +56,7 @@ "value": "9449306559" } }, - "authoredOn": "2023-09-28", + "authoredOn": "2023-09-08", "requester": { "reference": "PractitionerRole/PractitionerRole-HazelSmithKingstonPathology-Example" }, @@ -83,9 +79,9 @@ { "reference": "Observation/Observation-NucleatedCellCount-Example" }, - { - "reference": "Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example" - }, + { + "reference": "Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example" + }, { "reference": "Consent/Consent-RoDToFollow-Example" } From 5b1435c6c1e2dcf1cbd252db19c40671a7bbf85f Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Mon, 10 Feb 2025 14:42:55 +0000 Subject: [PATCH 3/8] Update ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json New mapping --- ...est-WGSTestOrderForm-CancerHaemOnc-Example.json | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json index 0f88c916..5744e21b 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json @@ -32,6 +32,15 @@ "display": "Cancer - WGS" } ] + }, + { + "coding": [ + { + "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", + "code": "diagnostic", + "display": "Diagnostic" + } + ] } ], "priority": "routine", @@ -41,11 +50,6 @@ "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", "code": "M89.108", "display": "Multi Target NGS Panel Small Variant" - }, - { - "system": "https://fhir.nhs.uk/CodeSystem/reasonfortesting-genomics", - "code": "diagnostic", - "display": "Diagnostic" } ] }, From 6c6ac7ceccc8e95eb5f8be2c8712ed8c62bbb0da Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 12 Feb 2025 09:49:15 +0000 Subject: [PATCH 4/8] Feedback Issues Update values for Specimen.condition,category Create SR for Germline late scenario --- ...WGSTestOrderForm-GermlineLate-Example.json | 111 ++++++++++++++++++ ...pecimen-PatrickSammyBloodEDTA-Example.json | 14 +++ ...rickSammyBoneMarrowAspiration-Example.json | 25 ++++ 3 files changed, 150 insertions(+) create mode 100644 ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json new file mode 100644 index 00000000..01a12493 --- /dev/null +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json @@ -0,0 +1,111 @@ +{ + "resourceType": "ServiceRequest", + "id": "ServiceRequest-WGSTestOrderForm-GermlineLate-Example", + "basedOn": [ + { + "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-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": "M89.108", + "display": "Multi Target NGS Panel Small Variant" + } + ] + }, + "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" + }, + "performer": [ + { + "identifier": { + "system": "https://fhir.nhs.uk/Id/ods-organization-code", + "value": "RJZ" + }, + "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" + } + ], + "supportingInfo": [ + { + "reference": "Condition/Condition-AcuteMyeloidLeukaemia-Example" + }, + { + "reference": "Observation/Observation-BlastPercentage-Example" + }, + { + "reference": "Observation/Observation-NucleatedCellCount-Example" + }, + { + "reference": "Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example" + }, + { + "reference": "Consent/Consent-RoDToFollow-Example" + } + ], + "specimen": [ + { + "reference": "Specimen/Specimen-PatrickSammyBloodEDTA-Example" + } + ], + "note": [ + { + "text": "Relevant Family History" + }, + { + "text": "Other Additional Information" + } + ] +} \ No newline at end of file diff --git a/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json b/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json index 6e57e117..5749eebc 100644 --- a/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json +++ b/Specimen/Specimen-PatrickSammyBloodEDTA-Example.json @@ -1,6 +1,20 @@ { "resourceType": "Specimen", "id": "Specimen-PatrickSammyBloodEDTA-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.add.nhs.uk/Id/specimenId", diff --git a/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json index d15ec3af..1b28ae70 100644 --- a/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json +++ b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json @@ -1,6 +1,20 @@ { "resourceType": "Specimen", "id": "Specimen-PatrickSammyBoneMarrowAspiration-Example", + "extension": [ + { + "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory", + "valueCodeableConcept": { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory", + "code": "liquid-tumour", + "display": "Liquid Tumour" + } + ] + } + } + ], "identifier": [ { "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.24", @@ -37,6 +51,17 @@ "reference": "Patient/Patient-PatrickSammy-Example" }, "receivedTime": "2023-09-11T11:00:00Z", + "condition": [ + { + "coding": [ + { + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", + "code": "fresh-frozen", + "display": "Fresh Frozen" + } + ] + } + ], "request": [ { "reference": "ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example" From 6be8b42b43ee2cc11591a27f8ee0d3ad5e9c58f9 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 12 Feb 2025 09:51:21 +0000 Subject: [PATCH 5/8] Update ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json Remove Specimen-BloodEDTA reference --- .../ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json | 3 --- 1 file changed, 3 deletions(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json index 5744e21b..89aaa544 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json @@ -91,9 +91,6 @@ } ], "specimen": [ - { - "reference": "Specimen/Specimen-PatrickSammyBloodEDTA-Example" - }, { "reference": "Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example" } From c0e922ae85036866e8e6946e05569c6ecc9ec679 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 12 Feb 2025 12:22:33 +0000 Subject: [PATCH 6/8] Update Specimen-PatrickSammyBoneMarrowAspiration-Example.json Specimen.condition to ValueSet-UKcore-SampleState --- .../Specimen-PatrickSammyBoneMarrowAspiration-Example.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json index 1b28ae70..21060e20 100644 --- a/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json +++ b/Specimen/Specimen-PatrickSammyBoneMarrowAspiration-Example.json @@ -55,9 +55,9 @@ { "coding": [ { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", - "code": "fresh-frozen", - "display": "Fresh Frozen" + "system": "http://terminology.hl7.org/CodeSystem/v2-0493", + "code": "FROZ", + "display": "Frozen" } ] } From 9026affc6960804798a826cfb270fdc9016b95dd Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 12 Feb 2025 13:37:13 +0000 Subject: [PATCH 7/8] Update Specimen.condition values Update Specimen.condition values --- Specimen/Specimen-SolidTumor-Example.json | 6 +++--- Specimen/Specimen-TissueResection-Example.json | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Specimen/Specimen-SolidTumor-Example.json b/Specimen/Specimen-SolidTumor-Example.json index 8e28a56c..bea94e09 100644 --- a/Specimen/Specimen-SolidTumor-Example.json +++ b/Specimen/Specimen-SolidTumor-Example.json @@ -48,9 +48,9 @@ { "coding": [ { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", - "code": "fresh-unfixed", - "display": "Fresh Unfixed" + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState", + "code": "fresh", + "display": "Fresh" } ] } diff --git a/Specimen/Specimen-TissueResection-Example.json b/Specimen/Specimen-TissueResection-Example.json index 73325211..413d2498 100644 --- a/Specimen/Specimen-TissueResection-Example.json +++ b/Specimen/Specimen-TissueResection-Example.json @@ -48,9 +48,9 @@ { "coding": [ { - "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState", - "code": "fresh-unfixed", - "display": "Fresh Unfixed" + "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-PrimarySampleState", + "code": "fresh", + "display": "Fresh" } ] } From 89b54bb3dcdab950bdadcc5ce62e8748c99464b0 Mon Sep 17 00:00:00 2001 From: KazeemHamzat Date: Wed, 12 Feb 2025 17:45:38 +0000 Subject: [PATCH 8/8] Feedback Issues Update SR.code values --- ...GSTestOrderForm-CancerHaemOnc-Example.json | 2 +- ...WGSTestOrderForm-GermlineLate-Example.json | 21 ++----------------- 2 files changed, 3 insertions(+), 20 deletions(-) diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json index 89aaa544..c257b7ff 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-CancerHaemOnc-Example.json @@ -49,7 +49,7 @@ { "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", "code": "M89.108", - "display": "Multi Target NGS Panel Small Variant" + "display": "Acute Leukaemia Other" } ] }, diff --git a/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json b/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json index 01a12493..cb62a773 100644 --- a/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json +++ b/ServiceRequest/ServiceRequest-WGSTestOrderForm-GermlineLate-Example.json @@ -53,8 +53,8 @@ "coding": [ { "system": "https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory", - "code": "M89.108", - "display": "Multi Target NGS Panel Small Variant" + "code": "M89.109", + "display": "Acute Leukaemia Other" } ] }, @@ -78,23 +78,6 @@ "display": "KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST" } ], - "supportingInfo": [ - { - "reference": "Condition/Condition-AcuteMyeloidLeukaemia-Example" - }, - { - "reference": "Observation/Observation-BlastPercentage-Example" - }, - { - "reference": "Observation/Observation-NucleatedCellCount-Example" - }, - { - "reference": "Observation/Observation-PatrickSammyNoBoneMarrowTransplant-Example" - }, - { - "reference": "Consent/Consent-RoDToFollow-Example" - } - ], "specimen": [ { "reference": "Specimen/Specimen-PatrickSammyBloodEDTA-Example"