NHS North West Genomics
0.0.8 - ci-build United Kingdom flag

NHS North West Genomics, published by NHS North West Genomics. This guide is not an authorized publication; it is the continuous build for version 0.0.8 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/nw-gmsa/nw-gmsa.github.com/ and changes regularly. See the Directory of published versions

Example Bundle: Bundle - Form Search Results SDC

Bundle SDCSearchResults of type searchset

Entry 1 - fullUrl = http://example.org/fhir/Questionnaire/GenomicTestOrder

Search:Mode = match

Resource Questionnaire:

Profile: Questionnaire

Structure
LinkIDTextCardinalityTypeDescription & Constraintsdoco
.. The aim of this is to support conversion of multiple Genomic Order Forms from several NHS Trusts to HL7 v2 and/or FHIR.Questionnairehttps://fhir.nwgenomics.nhs.uk/Questionnaire/GenomicTestOrder
... PatientPatient0..1groupDefinition: Patient
.... LN/45394-4Patient surname1..1stringDefinition: Patient.name.family
.... LN/45392-8Patient first name1..1stringDefinition: Patient.name.given
.... LN/21112-8Date of birth1..1dateDefinition: Patient.birthDate
.... LN/81954-0Date of death0..1date​Definition: Patient.deceasedDateTime
.... LN/56799-0Address0..1groupDefinition: Patient.address
..... HL7/PID-11-1Address Line0..*string​Definition: Patient.address.line
..... HL7/PID-11-3City0..1string​Definition: Patient.address.city
..... LN/45401-7Postcode0..1stringDefinition: Patient.address.postalCode
.... LN/46098-0Sex registered at birth0..1choiceDefinition: Patient.gender
Value Set: AdministrativeGender
.... LN/32624-9Ethnic Category0..1choice​Definition: Patient.extension:ethnicCategory
Value Set: Ethnicity
.... LN/89061-6NHS Number0..1string​Definition: Patient.identifier:nhsNumber
.... LN/76435-7Hospital Number (Medical Record Number)1..1string​Definition: Patient.identifier:MedicalRecordNumber
.... LN/56797-4Account Number (Episode or Stay Number)0..1string​Definition: ServiceRequest.encounter.identifier.value
..... LN/56797-4-designNotePV1-19 (also known as stay number)0..1display
.... ageAtCollectionAge at collection (ignore for FHIR)0..1decimal
.... LN/89009-5Location0..1stringDefinition: Encounter.location
.... HL7/PD1-3GP Surgery (ODS Code)0..1choice​Definition: Patient.generalPractitioner
... HealthcareProfessionalHealthcare Professional0..1groupDefinition: PractitionerRole
.... LN/18705-4Referring Clinician Name1..1stringDefinition: PractitionerRole.practitioner.display
.... LN/18707-0Referring Clinician Current Speciality1..1choice​Definition: PractitionerRole.specialty.coding.code
Value Set: UK Core Practice Setting Code
.... LN/46608-6Referring Clinician Professional Identifier1..1stringDefinition: PractitionerRole.practitioner.identifier.value
.... LN/89058-2Email0..*stringDefinition: PractitionerRole.telecom.value
.... LN/81230-5Phone0..1stringDefinition: PractitionerRole.telecom.value
.... HL7/ORC-21Referring Organisation ODS Code / Ordering Facility0..1stringDefinition: PractitionerRole.organization.identifier.value
... TestRequestTest Request0..1groupDefinition: ServiceRequest
.... SNM/15220000Test Category0..1choiceDefinition: ServiceRequest.category
Value Set: Order Category
.... HL7/OBR-4-rTest Code (Rare and inherited diseases)1..*choiceDefinition: ServiceRequest.code
Enable When: SNM/15220000 =
Value Set: Genomic Rare and Inherited Disease Test Directory
.... HL7/OBR-4-hTest Code (Haemoglobinopathy)1..*choiceDefinition: ServiceRequest.code
Enable When: SNM/15220000 =
Options: 5 options
.... HL7/OBR-4-cTest Code (Cancer)1..*choiceDefinition: ServiceRequest.code
Enable When: SNM/15220000 =
Value Set: Genomic Cancer Test Directory
.... pedigreeNumberG Number (Pedigree Number) - Order Group Number0..1stringDefinition: ServiceRequest.requisition
.... LN/106194-4Test request ID/Order ID0..1string​Definition: ServiceRequest.identifier:PlacerOrderNumber
.... LN/82768-3Priority0..1choiceDefinition: ServiceRequest.priority
Value Set: Request Priority
.... NOS/GeneticistEmailClinical Geneticist email0..1string​Definition: Observation.valueString
.... NOS/GeneticistDepartmentEmailClinical Geneticist department email0..1string​Definition: Observation.valueString
.... ConsentConsent0..1group
..... LN/19826-7Has consent has been obtained for tests (Y/N)0..1choice​Definition: Observation.valueCodeableConcept
Options: 2 options
..... LN/75520-7Has consent has been obtained for DNA storage (Y/N)0..1choice​Definition: Observation.valueCodeableConcept
Options: 2 options
..... NOS/RODToFollowROD attached or to follow0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
.... PatientClinicalInformationPatient Clinical Information0..1group
..... LN/51967-8CITT code (Specific disease suspected/reason for testing)0..*choiceDefinition: ServiceRequest.reasonCode
Value Set: Genomic Clinical Indication Codes
..... HL7/NTE-1Relevant clinical information and family history0..1stringDefinition: ServiceRequest.note
..... HL7/NTE-2Reason For Variant Re-Interpretation Request0..1stringDefinition: ServiceRequest.note
... SpecimenSpecimen/Biopsy0..1groupDefinition: Specimen
.... HL7/SPMSample collection status0..1choice​Definition: Specimen.status
Value Set: SpecimenStatus
.... LN/80398-1Specimen ID Number0..1stringDefinition: Specimen.identifier
..... LN/80398-1-designNoteORM v2.4 - OBX-3 = LOINC 80398-1 and OBX-2 = CE. OML v2.5.1 SPM-20..1display
.... Specimen/accessionIdentifierLab DNA Number (If Known)0..1stringDefinition: Specimen.accessionIdentifier
.... LN/80398-1-ODSPathology Laboratory Hospital/Trust ID (for Path Lab Sample/Stored DNA)0..1string​Definition: Specimen.accessionIdentifier.assigner.identifier.value
.... LN/33882-2Specimen Collection Date0..1dateTime​Definition: Specimen.collection.collectedDateTime
..... LN/33882-2-designNoteORM v2.4 - OBX-3 = LOINC 33882-2 and OBX-2 = TS . OML v2.5.1 SPM-170..1display
.... LN/66746-9Specimen Type0..1choice​Definition: Specimen.type.coding.code
Value Set: Specimen Type
..... LN/66746-9-designNoteORM v2.4 - OBX-3 = LOINC 66746-9 and OBX-2 = CE. OML v2.5.1 SPM-40..1display
.... SNM/281269004High Infection Risk?0..1choice​Definition: Observation.valueCodeableConcept
Options: 2 options
.... NOS/InfectionRiskDetailsHigh infection Risk Details0..1string​Definition: Observation.valueString
.... LN/74384-9Anticoagulant/preservative?0..1choice​Definition: Observation.valueCodeableConcept
Options: 2 options
.... LN/39111-0Tissue source/organ of origin0..1choiceDefinition: Specimen.collection.bodySite
.... LN/3169-0Specimen Volume/number of slides or scrolls0..1stringDefinition: Specimen.collection.quantity
.... OrderTrackingAudit (Specimen Tracking)0..1groupDefinition: Specimen.collection
..... NOS/SampleReceivedDate and time sample received in lab0..1date​Definition: Specimen.receivedTime
..... NOS/SampleSentDate and time sample sent0..1date​Definition: Observation.valueDateTime
..... NOS/TransportUsedTransport used0..1string​Definition: Observation.valueString
..... LN/97209-1Tracking number0..1string​Definition: Specimen.identifier[ShipmentTrackingNumber]
..... NOS/SampleSentToSample sent to0..1string​Definition: Observation.valueString
..... NOS/SampleSentToNameName of person who sent sample0..1string​Definition: Observation.valueString
... AskAtOrderEntryAsk At Order Entry Questions0..1group
.... SNM/842009Patient is from consanguineous union?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
.... SNM/74996004-pathology-reportConfirm that a pathology report will be provided alongside the sample.0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
.... SNM/118185001Neonatal/Prenatal/Neither?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
..... pregnantPregnant0..1groupEnable When: SNM/118185001 =
...... SNM/370386005Does this test relate to a pregnancy with > 1 fetus?0..1string​Definition: Observation.valueCodeableConcept
Options: 3 options
...... SNM/161714006Patient expected delivery date0..1date​Definition: Observation.valueDateTime
...... SNM/598151000005105Patient gestation0..1integer​Definition: Observation.valueQuantity
.... SNM/17369002Is this test for a pregnancy loss?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
.... SNM/419099009Is this test for a deceased infant?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
... PriorResultsPrior Results0..1group

doco Documentation for this format

Options Sets

Answer options for HL7/OBR-4-h

  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R361.1 ("Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R361.2 ("Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R372.1 ("Newborn screening for sickle cell disease in a transfused baby")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R93.1 ("Sickle cell, thalassaemia and other haemoglobinopathies")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R93.2 ("Sickle cell, thalassaemia and other haemoglobinopathies")

Answer options for LN/19826-7

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")

Answer options for LN/75520-7

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")

Answer options for NOS/RODToFollow

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")
  • http://loinc.org#LA4489-6 ("Unknown")

Answer options for SNM/281269004

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")

Answer options for LN/74384-9

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")

Answer options for SNM/842009

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")
  • http://loinc.org#LA4489-6 ("Unknown")

Answer options for SNM/74996004-pathology-report

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")
  • http://loinc.org#LA4489-6 ("Unknown")

Answer options for SNM/118185001

  • http://snomed.info/sct#77386006 ("Pregnancy")
  • http://snomed.info/sct#255407002 ("Neonatal")
  • http://loinc.org#LA32-8 ("No")

Answer options for SNM/370386005

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")
  • http://loinc.org#LA4489-6 ("Unknown")

Answer options for SNM/17369002

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")
  • http://loinc.org#LA4489-6 ("Unknown")

Answer options for SNM/419099009

  • http://loinc.org#LA33-6 ("Yes")
  • http://loinc.org#LA32-8 ("No")
  • http://loinc.org#LA4489-6 ("Unknown")