NHS North West Genomics
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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

Questionnaire: North West Genomics Test Order

Official URL: https://fhir.nwgenomics.nhs.uk/Questionnaire/GenomicTestOrder Version: 0.0.8
Draft as of 2025-10-30 Computable Name:

The aim of this is to support conversion of multiple Genomic Order Forms from several NHS Trusts to HL7 v2 and/or FHIR.

References

Domain Archetype

Genomic Laboratory OrderGenomic Laboratory OrderDiagnostic OrderPatient AdministrationPatientIdentificationNHSNumberIdentificationMedical Record NumberName, date of birth, ethnic category, etc.Case identification / Account NumberHospital Provider Spell IdentifierLaboratory OrderOrder DetailsPlacer Order NumberFiller Order NumberOrdering FacilityOrganisation CodeOrdering PractitionerGene disease assessedClinical IndicationLocal Treatment Category CodeGenomic Test CodeTest Directory CodeSpecimenSpecimen IdAccession NumberShipment Tracking numberSupporting InformationGenomic(Ask At Order Entry Questions)ConsentPregnantConsanguineous union

Genomic Test Order Sections


Diagnostic Order

Name LOINC Value Set / Data Type Cardinality HL7 v2 OML_O21 Message HL7 FHIR ServiceRequest HL7 FHIR Resource (Message + RESTful)
Patient     1..1 PID subject Patient
Case Identification or Episode/Visit/Stay Number 56797-4 HospitalProviderSpellIdentifier 0..1 PV1-19   Encounter.identifier
Placer Order Number   Placer Order Number 1..1 ORC-2 identifier[PlacerOrderNumber]  
Filler Order Number   Filler Order Number 1..1 ORC-3 identifier[FillerOrderNumber]  
Genomic Test Code   Genomic Test Directory 1..1 OBR-4 code  
Order date     1..1 ORC-9 authoredOn  
Ordering Practitioner     1..1 ORC-12 requester[PractitionerRole] PractitionerRole.practitoner
Ordering Facility   England Practitioner Identifier 1..1 ORC-21 requester[PractitionerRole] PractitionerRole.organization
performer   Organisation Code 0..1 implied by destination of message performer Organization
Clinical Indication / CITT code (Suspected Condition)   ​Genomic Condition Codes .. DG1-3 reasonCode  

Specimen

Name LOINC Value Set / Data Type Cardinality HL7 v2 OML_O21 Message HL7 FHIR ServiceRequest HL7 FHIR Resource (Message + RESTful)  
Specimen ID 80398-1   0..* SPM specimen Specimen.identifier[PlacerSpecimenNumber]  
Specimen Accession Number 80398-1   0..* SPM specimen Specimen.accessionIdentifier  
Shipment Tracking Number 97209-1         Specimen.identifier[ShipmentTrackingNumber]  

Note: it is likely that source systems will use ORM_01 and not include specimen details. In this case it is suggested that the specimen details are captured as 'Ask at Order Entry Questions' and so provided as OBX segments.

Supporting Information

Name Code System Value Set / Data Type Cardinality HL7 v2 OML_O21 Message HL7 FHIR Resource (Message + RESTful)  
Patient is from consanguineous union? SNM/842009   0..1 OBX Observation.valueCodeableConcept  
Confirm that a pathology report will be provided alongside the sample. SNM/74996004   0..1   Observation.valueCodeableConcept  
Neonatal/Prenatal/Neither? SNM/118185001   0..1 OBX Observation.valueCodeableConcept  
Pregnant         Observation.valueCodeableConcept  
- Does this test relate to a pregnancy with > 1 fetus? SNM/370386005   0..1 OBX Observation.valueCodeableConcept  
- Patient expected delivery date SNM/161714006   0..1 OBX Observation.valueDateTime  
- Patient gestation SNM/598151000005105   0..1 OBX Observation.valueQuantity  
Is this test for a pregnancy loss? SNM/17369002   0..1 OBX Observation.valueCodeableConcept  
Is this test for a deceased infant? SNM/419099009   0..1 OBX Observation.valueCodeableConcept  

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#0.0.8
... 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")

Notes:

Communication Information Model

Laboratory Order O21 Supporting Information Patient Administration Care Directory Services PatientNHSNumberMedicalRecordNumber «aggregate»ServiceRequest (Test Request)orderPlacerNumberorderFillerNumberorderPlacerGroupNumberaccessionNumbersubject : Patient Specimen (Primary Sample)identifieraccessionNumbersubject : Patient ConditionCode PractitionerRoleorganisation : ODSCodepractitioner: GMP/GMC Numberspecialty: ClinicalSpecialty ServieRequest.identifierOriginal Order Episode Number Observationvalue[x]codesubject : Patient Observation Panelhasmembercodesubject : Patient «aggregate»DocumentReferencePreviousReportsGenomicFamilyStructuretypesubject : Patientcontext.encounter :Visit Number AttachmentcontentTypeurl Binary Encounteridentifier :Episode Numberencounterepisodesubject : Patient PatientNHSNumberMedicalRecordNumbernameaddressbirthDategendertelecom PractitionerprofessionalCodenametelecom OrganizationodsCodenametelecom url hasmember0 specimen /accessionNumber0 subject1 encounter0 reason(Reference/Code)0 basedOn0 supportingInfo0 supportingInfo0 supportingInfo0 requester1 collection.collector0 participant.individual0 subject1 subject1 subject1 subject1 context.encounter1 encounter1

Genomics Test Request Model


Ask at Order Entry questions and prior results

See Domain Archetype and Panels

Communication Model

Placer Order Management [LAB-1]