North West Genomic Medicine Service Alliance
0.0.1 - ci-build United Kingdom flag

DRAFT Implementation Guide

This is for collaboration and discussion purposes and is subject to change.

North West Genomic Medicine Service Alliance - Local Development build (v0.0.1) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Questionnaire: North West Genomics Test Order Future

Official URL: https://nw-gmsa.github.io/Questionnaire/GenomicTestOrderFuture Version: 0.0.1
Draft as of 2025-06-19 Computable Name:

THIS IS FOR ANALYSIS, and is not to be used for implementation at present.

The aim of this is to support conversion of multiple Genomic Order Forms HL7 v2 and FHIR.

Structure
LinkIDTextCardinalityTypeDescription & Constraintsdoco
.. THIS IS FOR ANALYSIS, and is not to be used for implementation at present. The aim of this is to support conversion of multiple Genomic Order Forms HL7 v2 and FHIR.Questionnairehttps://nw-gmsa.github.io/Questionnaire/GenomicTestOrderFuture#0.0.1
... 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 collection0..1decimal
.... locationLocation0..1string
.... 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..1stringDefinition: PractitionerRole.telecom.value
.... LN/81230-5Phone0..1stringDefinition: PractitionerRole.telecom.value
.... HL7/ORC-21Referring Organisation ODS Code0..1stringDefinition: PractitionerRole.organization.identifier.value
... TestRequestTest Request0..1groupDefinition: ServiceRequest
.... SNM/15220000Test Category0..1choiceDefinition: ServiceRequest.category
Value Set: Order Category
Options: 5 options
.... 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
.... 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
..... consent-3ROD attached or to follow0..1choiceOptions: 3 options
.... PatientClinicalInformationPatient Clinical Information0..1group
..... LN/51967-8CITT code (Specific disease suspected/reason for testing)0..*choiceDefinition: ServiceRequest.reasonCode
Value Set: Genomic Condition Code
..... HL7/NTERelevant clinical information and family history0..1stringDefinition: ServiceRequest.note
... SpecimenSpecimen/Biopsy0..1groupDefinition: Specimen
.... LN/80398-1Specimen ID Number / Lab DNA Number (If Known)0..1string​Definition: Specimen.identifier.value
..... LN/80398-1-designNoteORM v2.4 - OBX-3 = LOINC 80398-1 and OBX-2 = CE. OML v2.5.1 SPM-20..1display
.... LN/80398-1-ODSPathology Laboratory Hospital/Trust ID0..1string​Definition: Specimen.identifier.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
.... 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/xxxx1Date and time sample received in lab0..1date​Definition: Specimen.receivedTime
..... NOS/xxxx2Date and time sample sent0..1date
..... NOS/xxxx3Transport used0..1string
..... LN/97209-1Tracking number0..1string
..... NOS/xxxx5Sample sent to0..1string
..... NOS/xxxx6Name of person who sent sample0..1string
... 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/385675009Reason for variant re-interpretation request0..1string​Definition: Observation.valueCodeableConcept
.... SNM/119297000Specimen Source (Blood Restrictions)0..1string​Definition: Observation.valueCodeableConcept
.... SNM/782964007Clinical Indication0..1string​Definition: Observation.valueCodeableConcept
Value Set: http://snomed.info/sct/900000000000207008?fhir_vs=ecl/<782964007
.... SNM/78989007Please enter the trisomy screening risk (including the chromosome of interest if appropriate).0..1string​Definition: Observation.valueCodeableConcept
.... SNM/782902008Transplant?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
..... SNM/5447007Transplant Type0..1choiceEnable When: SNM/782902008 =
Value Set: http://snomed.info/sct/900000000000207008?fhir_vs=ecl/<737294004
.... LN/21908-9Advanced Lung Cancer Stage0..1choiceValue Set: http://snomed.info/sct/900000000000207008?fhir_vs=ecl/<1222594003
.... SNM/74996004Extra Testing Form Completed?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
..... SNM/74996004-designNotePlease Note That An Additional Test Order Form 'Whole Genome Sequencing Rare Disease Order Form (Link at Top of Form)' is Required To Activate Testing. If This is Not Received, The DNA Will Be Extracted and Stored0..1display
.... SNM/77386006Does this test relate to an ongoing pregnancy?0..1choice​Definition: Observation.valueCodeableConcept
Options: 3 options
..... pregnantPregnant0..1groupEnable When: SNM/77386006 =
...... 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/169222003What were the Abnormal Scan Findings0..1string​Definition: Observation.valueQuantity
... PriorResultsPrior Results0..1group
.... HaemoglobinopathyTestResultsHaemoglobinopathy Testing Prior Results0..1groupEnable When: SNM/15220000 =
..... LN/58410-2CBC panel - Blood by Automated count0..1reference
...... LN/58410-2-designNoteSee Questionnaire [CBC panel - Blood by Automated count](https://nw-gmsa.github.io/R4/Questionnaire-58410-2.html)0..1display
.... RareAndInheritedDiseasesGeneticTestingRare and Inherited Disease Prior Results0..1groupEnable When: SNM/15220000 =
.... CancerGeneticTestingCancer Testing Prior Results0..1groupEnable When: SNM/15220000 =
..... UnknownResultsPanelUnknown Results Panel0..1group
...... SNM/250537006Neoplastic Cell Content Level0..1quantity​Definition: Observation.valueQuantity
...... NOS/230031Neoplastic Cell Content Level %0..1quantity​Definition: Observation.valueQuantity
..... SNM/252416005Macrodissection Requirements0..1string
..... NOS/230033Blast Cell Count0..1quantity​Definition: Observation.valueQuantity

doco Documentation for this format

Options Sets

Answer options for SNM/15220000

  • https://nw-gmsa.github.io/CodeSystem/nwgmsa#RareAndInheritedDiseasesGeneticTesting ("Rare and inherited diseases Genetic Testing (procedure)")
  • http://snomed.info/sct#1186936003 ("Storage of specimen (procedure)")
  • https://nw-gmsa.github.io/CodeSystem/nwgmsa#PreNatalGeneticTesting ("Pre Natal Genetic Testing (procedure)")
  • https://nw-gmsa.github.io/CodeSystem/nwgmsa#HaemoglobinopathyGeneticTesting ("Haemoglobinopathy Genetic Testing (procedure)")
  • https://nw-gmsa.github.io/CodeSystem/nwgmsa#CancerGeneticTesting ("Cancer Genetic Testing (procedure)")

Answer options for HL7/OBR-4-h

  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R361.1 ("R361.1 Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R361.2 ("R361.2 Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R372.1 ("R372.1 Newborn screening for sickle cell disease in a transfused baby")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R93.1 ("R93.1 Sickle cell, thalassaemia and other haemoglobinopathies")
  • https://fhir.nhs.uk/CodeSystem/England-GenomicTestDirectory#R93.2 ("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 consent-3

  • 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/782902008

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

Answer options for SNM/74996004

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

Answer options for SNM/77386006

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

Answer options for SNM/370386005

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