FHIR IG analytics| Package | fhir.nwgenomics.nhs.uk |
| Resource Type | Questionnaire |
| Id | Questionnaire-dWGSSubOrder.json |
| FHIR Version | R4 |
| Source | https://build.fhir.org/ig/nw-gmsa/nw-gmsa.github.com/Questionnaire-dWGSSubOrder.html |
| URL | https://fhir.nwgenomics.nhs.uk/Questionnaire/dWGSSubOrder |
| Version | 2.2.0 |
| Status | draft |
| Date | 2026-09-27T08:17:18+00:00 |
| Title | North West Genomics dWGS Sub-Order Manifest |
| Realm | us |
| Authority | hl7 |
| Description | **For analysis purposes only - not an active or planned project.** **CSV manifest description**, not an Ask At Order Entry Questionnaire - this Questionnaire documents the complete digital manifest for a **distributed WGS (dWGS)** sub-contracted order (IHE LTW `LAB-35`), sent by a Requesting Genomic Laboratory (RGL) to North West Genomics acting as Sequencing Genomic Laboratory (SGL): the 37 national digital manifest fields (NHS England `RGL to SGL SOP` Appendix 3) plus 5 local extension fields, with `item.definition` mappings to FHIR where a confirmed mapping exists - see [dWGS](dWGS.html#field-mapping-csv--hl7-v2--fhir). It deliberately carries **every** manifest field, including several also asked by [Genomic Test Order](Questionnaire-GenomicTestOrder.html) (Patient name/DOB/NHS number, Specimen Type, Specimen Collection Date) - because it describes the full CSV structure a Requesting Genomic Laboratory actually sends, not an incremental set of order-entry questions. For the genuinely additional Ask At Order Entry content - the manifest fields **not** already covered by the common core - see [dWGS Ask At Order Entry Questions](Questionnaire-dWGSAskAtOrderEntry.html), which `derivedFrom`/ extends [Genomic Test Order](Questionnaire-GenomicTestOrder.html) in the usual way. |
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Note: links and images are rebased to the (stated) source
Generated Narrative: Questionnaire dWGSSubOrder
Profile: Questionnaire
| LinkID | Text | Cardinality | Type | Description & Constraints |
|---|---|---|---|---|
  | **For analysis purposes only - not an active or planned project.** **CSV manifest description**, not an Ask At Order Entry Questionnaire - this Questionnaire documents the complete digital manifest for a **distributed WGS (dWGS)** sub-contracted order (IHE LTW `LAB-35`), sent by a Requesting Genomic Laboratory (RGL) to North West Genomics acting as Sequencing Genomic Laboratory (SGL): the 37 national digital manifest fields (NHS England `RGL to SGL SOP` Appendix 3) plus 5 local extension fields, with `item.definition` mappings to FHIR where a confirmed mapping exists - see [dWGS](dWGS.html#field-mapping-csv--hl7-v2--fhir). It deliberately carries **every** manifest field, including several also asked by [Genomic Test Order](Questionnaire-GenomicTestOrder.html) (Patient name/DOB/NHS number, Specimen Type, Specimen Collection Date) - because it describes the full CSV structure a Requesting Genomic Laboratory actually sends, not an incremental set of order-entry questions. For the genuinely additional Ask At Order Entry content - the manifest fields **not** already covered by the common core - see [dWGS Ask At Order Entry Questions](Questionnaire-dWGSAskAtOrderEntry.html), which `derivedFrom`/ extends [Genomic Test Order](Questionnaire-GenomicTestOrder.html) in the usual way. | Questionnaire | https://fhir.nwgenomics.nhs.uk/Questionnaire/dWGSSubOrder#2.2.0 | |
  Referral | Referral / Sub-Order | 0..1 | group | Definition: ServiceRequest |
  dWGS/referral_id | Original Order Placer Group Number (Referral ID) | 1..1 | string | Definition: ServiceRequest.requisition |
 dWGS/clinical_indication_test_type_id | Test Code | 0..1 | choice | Definition: ServiceRequest.code Value Set: Genomic Test Codes |
| dWGS/ordering_entity_id | Original Ordering Facility Code | 0..1 | string | Definition: Specimen.identifier.assigner.identifier.value |
  dWGS/ordering_entity_id-designNote | ODS code of the original referring Trust - assigner of the Received Sample Identifier (type=PLAC) below, not the same as the Filler Order Ordering Facility Code. | 0..1 | display | |
| dWGS/glh_laboratory_id | Filler Order Ordering Facility Code (GLH) | 1..1 | string | Definition: ServiceRequest.requester.identifier.value |
| dWGS/glh_laboratory_id-designNote | A Genomic Laboratory Hub (GLH) ODS code, not the referring Trust's own ODS code - also assigns ServiceRequest.requisition and the Specimen's LIMS identifier (type=FILL). | 0..1 | display | |
| dWGS/retrospective_sample | Retrospective Sample Flag | 0..1 | string | Definition: ServiceRequest.intent |
| dWGS/retrospective_sample-designNote | Values: "New" (ServiceRequest.intent = filler-order) or "Retrospective" (ServiceRequest.intent = reflex-order - NW Genomics is reflexing further testing off a specimen it already holds, not a fresh sub-order). | 0..1 | display | |
 dWGS/clinical_information | Clinical Information | 0..1 | text | Definition: ServiceRequest.note |
| dWGS/approved_by | Approved By | 0..1 | string | |
| Patient | Patient | 0..1 | group | Definition: Patient |
| LN/45392-8 | Patient first name | 1..1 | string | Definition: Patient.name.given |
| LN/45394-4 | Patient surname | 1..1 | string | Definition: Patient.name.family |
 LN/21112-8 | Date of birth | 1..1 | date | Definition: Patient.birthDate |
| LN/89061-6 | NHS Number | 0..1 | string | Definition: Patient.identifier:nhsNumber |
| dWGS/patient_ngis_id | Patient Identifier (NGIS) | 1..1 | string | Definition: Patient.identifier |
 dWGS/patient_ngis_id-designNote | No confirmed identifier system - carried as Patient.identifier.assigner (Genomics England, ODS 8J834, who run NGIS), type=PI (v2-0203 Patient internal identifier). | 0..1 | display | |
| AskAtOrderEntry | Ask At Order Entry Questions | 0..1 | group | |
| NOS/FamilyStructure | Family Structure | 1..1 | string | Definition: Observation.valueCodeableConcept |
| NOS/FamilyStructure-designNote | Values: "Singleton", "Duo" or "Trio" - how many people are being tested together as part of this referral. Text-only (no NW-GMSA-confirmed coding system exists), carried as an Observation referenced from ServiceRequest.supportingInfo. See [dWGS - Singleton, Duo and Trio testing](dWGS.html#singleton-duo-and-trio-testing). | 0..1 | display | |
| NOS/ParticipantType | Participant Type | 1..1 | string | Definition: Observation.valueCodeableConcept |
| NOS/ParticipantType-designNote | Values: "Proband" or "Family Member" - this individual's role within the Family Structure above. Text-only, carried as an Observation referenced from ServiceRequest.supportingInfo. | 0..1 | display | |
| PrimarySpecimen | Primary Specimen (as received by GLH) | 0..1 | group | Definition: Specimen |
 dWGS/primary_sample_received_date | Sample Received Date | 0..1 | dateTime | Definition: Specimen.receivedTime |
| dWGS/primary_sample_id_as_received_by_glh | Received Sample Identifier | 0..1 | string | Definition: Specimen.identifier |
| dWGS/primary_sample_id_as_received_by_glh-designNote | Assigned by the Original Ordering Facility - coded type=PLAC (Placer Identifier). | 0..1 | display | |
| dWGS/primary_sample_id_in_glh_lims | LIMS Sample Identifier | 0..1 | string | Definition: Specimen.identifier |
| dWGS/primary_sample_id_in_glh_lims-designNote | Assigned by the Filler Order Ordering Facility (GLH) - coded type=FILL (Filler Identifier). | 0..1 | display | |
| dWGS/primary_sample_type | Sample Type | 0..1 | string | |
| dWGS/primary_sample_type-designNote | Germline/tumour classifier - low confidence, no clean Specimen field identified; not currently built into any FHIR resource. | 0..1 | display | |
| LN/66746-9 | Sample Material Type | 0..1 | choice | Definition: Specimen.type.coding.code Value Set: Specimen Type |
| dWGS/received_sample_topography | Sample Topography | 0..1 | string | Definition: Specimen.bodySite |
| dWGS/received_sample_topography-designNote | Cancer referrals only. | 0..1 | display | |
| dWGS/received_sample_morphology | Sample Morphology | 0..1 | string | |
 dWGS/received_sample_tumour_content_pct | Tumour Content (%) | 0..1 | decimal | |
| dWGS/received_sample_tumour_content_pct-designNote | Cancer referrals only. | 0..1 | display | |
| dWGS/received_sample_comments | Sample Comments | 0..1 | string | |
| LN/33882-2 | Specimen Collection Date | 0..1 | dateTime | Definition: Specimen.collection.collectedDateTime |
| DispatchedSpecimen | Dispatched Specimen (extracted DNA sent onward) | 0..1 | group | Definition: Specimen |
| dWGS/dispatched_sample_id_in_glh_lims | Dispatched Sample Identifier | 0..1 | string | |
| dWGS/dispatched_sample_lsid | Specimen Barcode | 1..1 | string | Definition: Specimen.container.identifier |
| dWGS/dispatched_sample_lsid-designNote | Carried on Specimen.container.identifier, coded type=ZCID - see NW IdentifierType. | 0..1 | display | |
| dWGS/dispatched_sample_type | Dispatched Sample Type | 0..1 | string | |
| dWGS/dispatched_sample_state | Dispatched Material Type | 0..1 | string | |
| dWGS/dispatched_sample_state-designNote | Not currently built into any FHIR resource - the worked example's single Specimen only carries the primary specimen's Sample Material Type above. | 0..1 | display | |
| dWGS/dispatched_sample_volume_ul | Sample Volume (uL) | 0..1 | decimal | Definition: Specimen.collection.quantity |
| dWGS/dna_extraction_protocol | DNA Extraction Method | 0..1 | string | Definition: Specimen.collection.method |
| dWGS/glh_sample_consignment_number | Consignment Number | 0..1 | string | Definition: Specimen.identifier |
| dWGS/glh_sample_consignment_number-designNote | Carried as a Specimen identifier, coded type=STN (Shipment Tracking Number). | 0..1 | display | |
| LaboratoryQC | Laboratory QC and Logistics | 0..1 | group | |
| dWGS/laboratory_remaining_volume_banked_ul | Remaining Banked Volume (uL) | 0..1 | decimal | |
| dWGS/glh_concentration_ng_ul | DNA Concentration (ng/uL) | 0..1 | decimal | |
| dWGS/glh_od260_280 | DNA Purity (OD260/280) | 0..1 | decimal | |
| dWGS/glh_din_value | DNA Integrity Number | 0..1 | decimal | |
| dWGS/glh_percentage_dna_over_23kb | DNA Fragment Size (% over 23kb) | 0..1 | decimal | |
| dWGS/glh_qc_status | QC Status | 0..1 | string | |
| dWGS/glh_sample_dispatch_date | Dispatch Date | 0..1 | date | |
| dWGS/plating_organisation | Plating Organisation | 0..1 | string | |
| dWGS/gmc_rack_id | Rack Identifier | 0..1 | string | |
| dWGS/gmc_rack_well | Rack Well Position | 0..1 | string | |
| dWGS/gmc_rack_well-designNote | Pattern: [A-H]01-09 or [A-H]10-12. | 0..1 | display | |
| dWGS/prolonged_sample_storage | Sample Storage Method | 0..1 | string | |
| Documentation for this format | ||||
FHIR
FHIRsmith{
"resourceType": "Questionnaire",
"id": "dWGSSubOrder",
"meta": {
"profile": [
"https://fhir.nwgenomics.nhs.uk/StructureDefinition/NWQuestionnaire"
]
},
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/artifact-versionAlgorithm",
"valueCoding": {
"system": "http://hl7.org/fhir/version-algorithm",
"code": "semver"
}
}
],
"url": "https://fhir.nwgenomics.nhs.uk/Questionnaire/dWGSSubOrder",
"version": "2.2.0",
"title": "North West Genomics dWGS Sub-Order Manifest",
"status": "draft",
"date": "2026-09-27T08:17:18+00:00",
"publisher": "NHS North West Genomics",
"contact": [
{
"telecom": [
{
"system": "url",
"value": "https://www.nwgenomics.nhs.uk/contact-us"
}
]
}
],
"description": "**For analysis purposes only - not an active or planned project.**\n\n**CSV manifest description**, not an Ask At Order Entry Questionnaire - this\nQuestionnaire documents the complete digital manifest for a **distributed\nWGS (dWGS)** sub-contracted order (IHE LTW `LAB-35`), sent by a Requesting\nGenomic Laboratory (RGL) to North West Genomics acting as Sequencing\nGenomic Laboratory (SGL): the 37 national digital manifest fields (NHS\nEngland `RGL to SGL SOP` Appendix 3) plus 5 local extension fields, with\n`item.definition` mappings to FHIR where a confirmed mapping exists - see\n[dWGS](dWGS.html#field-mapping-csv--hl7-v2--fhir). It deliberately carries\n**every** manifest field, including several also asked by [Genomic Test\nOrder](Questionnaire-GenomicTestOrder.html) (Patient name/DOB/NHS number,\nSpecimen Type, Specimen Collection Date) - because it describes the full CSV\nstructure a Requesting Genomic Laboratory actually sends, not an incremental\nset of order-entry questions. For the genuinely additional Ask At Order\nEntry content - the manifest fields **not** already covered by the common\ncore - see [dWGS Ask At Order Entry\nQuestions](Questionnaire-dWGSAskAtOrderEntry.html), which `derivedFrom`/\nextends [Genomic Test Order](Questionnaire-GenomicTestOrder.html) in the\nusual way.",
"jurisdiction": [
{
"coding": [
{
"system": "urn:iso:std:iso:3166",
"code": "GB",
"display": "United Kingdom of Great Britain and Northern Ireland"
}
]
}
],
"item": [
{
"linkId": "Referral",
"definition": "http://hl7.org/fhir/StructureDefinition/ServiceRequest#ServiceRequest",
"text": "Referral / Sub-Order",
"type": "group",
"item": [
{
"linkId": "dWGS/referral_id",
"definition": "http://hl7.org/fhir/StructureDefinition/ServiceRequest#ServiceRequest.requisition",
"text": "Original Order Placer Group Number (Referral ID)",
"type": "string",
"required": true
},
{
"linkId": "dWGS/clinical_indication_test_type_id",
"definition": "http://hl7.org/fhir/StructureDefinition/ServiceRequest#ServiceRequest.code",
"text": "Test Code",
"type": "choice",
"required": false,
"answerValueSet": "https://fhir.nwgenomics.nhs.uk/ValueSet/GenomicTestCodes"
},
{
"linkId": "dWGS/ordering_entity_id",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.identifier.assigner.identifier.value",
"text": "Original Ordering Facility Code",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/ordering_entity_id-designNote",
"text": "ODS code of the original referring Trust - assigner of the Received Sample Identifier (type=PLAC) below, not the same as the Filler Order Ordering Facility Code.",
"type": "display"
}
]
},
{
"linkId": "dWGS/glh_laboratory_id",
"definition": "http://hl7.org/fhir/StructureDefinition/ServiceRequest#ServiceRequest.requester.identifier.value",
"text": "Filler Order Ordering Facility Code (GLH)",
"type": "string",
"required": true,
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/glh_laboratory_id-designNote",
"text": "A Genomic Laboratory Hub (GLH) ODS code, not the referring Trust's own ODS code - also assigns ServiceRequest.requisition and the Specimen's LIMS identifier (type=FILL).",
"type": "display"
}
]
},
{
"linkId": "dWGS/retrospective_sample",
"definition": "http://hl7.org/fhir/StructureDefinition/ServiceRequest#ServiceRequest.intent",
"text": "Retrospective Sample Flag",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/retrospective_sample-designNote",
"text": "Values: \"New\" (ServiceRequest.intent = filler-order) or \"Retrospective\"\n(ServiceRequest.intent = reflex-order - NW Genomics is reflexing further testing\noff a specimen it already holds, not a fresh sub-order).",
"type": "display"
}
]
},
{
"linkId": "dWGS/clinical_information",
"definition": "http://hl7.org/fhir/StructureDefinition/ServiceRequest#ServiceRequest.note",
"text": "Clinical Information",
"type": "text"
},
{
"linkId": "dWGS/approved_by",
"text": "Approved By",
"type": "string"
}
]
},
{
"linkId": "Patient",
"definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient",
"text": "Patient",
"type": "group",
"item": [
{
"linkId": "LN/45392-8",
"definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.name.given",
"code": [
{
"system": "http://loinc.org",
"code": "45392-8"
}
],
"text": "Patient first name",
"type": "string",
"required": true
},
{
"linkId": "LN/45394-4",
"definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.name.family",
"code": [
{
"system": "http://loinc.org",
"code": "45394-4"
}
],
"text": "Patient surname",
"type": "string",
"required": true
},
{
"linkId": "LN/21112-8",
"definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.birthDate",
"code": [
{
"system": "http://loinc.org",
"code": "21112-8"
}
],
"text": "Date of birth",
"type": "date",
"required": true
},
{
"linkId": "LN/89061-6",
"definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.identifier:nhsNumber",
"code": [
{
"system": "http://loinc.org",
"code": "89061-6"
}
],
"text": "NHS Number",
"type": "string"
},
{
"linkId": "dWGS/patient_ngis_id",
"definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.identifier",
"text": "Patient Identifier (NGIS)",
"type": "string",
"required": true,
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/patient_ngis_id-designNote",
"text": "No confirmed identifier system - carried as Patient.identifier.assigner (Genomics England, ODS 8J834, who run NGIS), type=PI (v2-0203 Patient internal identifier).",
"type": "display"
}
]
}
]
},
{
"linkId": "AskAtOrderEntry",
"text": "Ask At Order Entry Questions",
"type": "group",
"item": [
{
"linkId": "NOS/FamilyStructure",
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueCodeableConcept",
"code": [
{
"system": "https://fhir.nwgenomics.nhs.uk/CodeSystem/NWGMSA",
"code": "FamilyStructure"
}
],
"text": "Family Structure",
"type": "string",
"required": true,
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "NOS/FamilyStructure-designNote",
"text": "Values: \"Singleton\", \"Duo\" or \"Trio\" - how many people are being tested together\nas part of this referral. Text-only (no NW-GMSA-confirmed coding system exists),\ncarried as an Observation referenced from ServiceRequest.supportingInfo. See\n[dWGS - Singleton, Duo and Trio testing](dWGS.html#singleton-duo-and-trio-testing).",
"type": "display"
}
]
},
{
"linkId": "NOS/ParticipantType",
"definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.valueCodeableConcept",
"code": [
{
"system": "https://fhir.nwgenomics.nhs.uk/CodeSystem/NWGMSA",
"code": "ParticipantType"
}
],
"text": "Participant Type",
"type": "string",
"required": true,
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "NOS/ParticipantType-designNote",
"text": "Values: \"Proband\" or \"Family Member\" - this individual's role within the Family\nStructure above. Text-only, carried as an Observation referenced from\nServiceRequest.supportingInfo.",
"type": "display"
}
]
}
]
},
{
"linkId": "PrimarySpecimen",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen",
"text": "Primary Specimen (as received by GLH)",
"type": "group",
"item": [
{
"linkId": "dWGS/primary_sample_received_date",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.receivedTime",
"text": "Sample Received Date",
"type": "dateTime"
},
{
"linkId": "dWGS/primary_sample_id_as_received_by_glh",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.identifier",
"text": "Received Sample Identifier",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/primary_sample_id_as_received_by_glh-designNote",
"text": "Assigned by the Original Ordering Facility - coded type=PLAC (Placer Identifier).",
"type": "display"
}
]
},
{
"linkId": "dWGS/primary_sample_id_in_glh_lims",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.identifier",
"text": "LIMS Sample Identifier",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/primary_sample_id_in_glh_lims-designNote",
"text": "Assigned by the Filler Order Ordering Facility (GLH) - coded type=FILL (Filler Identifier).",
"type": "display"
}
]
},
{
"linkId": "dWGS/primary_sample_type",
"text": "Sample Type",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/primary_sample_type-designNote",
"text": "Germline/tumour classifier - low confidence, no clean Specimen field identified; not currently built into any FHIR resource.",
"type": "display"
}
]
},
{
"linkId": "LN/66746-9",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.type.coding.code",
"code": [
{
"system": "http://loinc.org",
"code": "66746-9",
"display": "Specimen Type"
},
{
"system": "http://snomed.info/sct",
"code": "123038009",
"display": "Specimen"
}
],
"text": "Sample Material Type",
"type": "choice",
"answerValueSet": "https://fhir.nwgenomics.nhs.uk/ValueSet/specimen-type"
},
{
"linkId": "dWGS/received_sample_topography",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.bodySite",
"text": "Sample Topography",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/received_sample_topography-designNote",
"text": "Cancer referrals only.",
"type": "display"
}
]
},
{
"linkId": "dWGS/received_sample_morphology",
"text": "Sample Morphology",
"type": "string"
},
{
"linkId": "dWGS/received_sample_tumour_content_pct",
"text": "Tumour Content (%)",
"type": "decimal",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/received_sample_tumour_content_pct-designNote",
"text": "Cancer referrals only.",
"type": "display"
}
]
},
{
"linkId": "dWGS/received_sample_comments",
"text": "Sample Comments",
"type": "string"
},
{
"linkId": "LN/33882-2",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.collection.collectedDateTime",
"code": [
{
"system": "http://loinc.org",
"code": "33882-2",
"display": "Collection date of Specimen"
}
],
"text": "Specimen Collection Date",
"type": "dateTime"
}
]
},
{
"linkId": "DispatchedSpecimen",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen",
"text": "Dispatched Specimen (extracted DNA sent onward)",
"type": "group",
"item": [
{
"linkId": "dWGS/dispatched_sample_id_in_glh_lims",
"text": "Dispatched Sample Identifier",
"type": "string"
},
{
"linkId": "dWGS/dispatched_sample_lsid",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.container.identifier",
"text": "Specimen Barcode",
"type": "string",
"required": true,
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/dispatched_sample_lsid-designNote",
"text": "Carried on Specimen.container.identifier, coded type=ZCID - see NW IdentifierType.",
"type": "display"
}
]
},
{
"linkId": "dWGS/dispatched_sample_type",
"text": "Dispatched Sample Type",
"type": "string"
},
{
"linkId": "dWGS/dispatched_sample_state",
"text": "Dispatched Material Type",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/dispatched_sample_state-designNote",
"text": "Not currently built into any FHIR resource - the worked example's single Specimen only carries the primary specimen's Sample Material Type above.",
"type": "display"
}
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-unit",
"valueCoding": {
"system": "http://unitsofmeasure.org",
"code": "uL",
"display": "uL"
}
}
],
"linkId": "dWGS/dispatched_sample_volume_ul",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.collection.quantity",
"text": "Sample Volume (uL)",
"type": "decimal"
},
{
"linkId": "dWGS/dna_extraction_protocol",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.collection.method",
"text": "DNA Extraction Method",
"type": "string"
},
{
"linkId": "dWGS/glh_sample_consignment_number",
"definition": "http://hl7.org/fhir/StructureDefinition/Specimen#Specimen.identifier",
"text": "Consignment Number",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/glh_sample_consignment_number-designNote",
"text": "Carried as a Specimen identifier, coded type=STN (Shipment Tracking Number).",
"type": "display"
}
]
}
]
},
{
"linkId": "LaboratoryQC",
"text": "Laboratory QC and Logistics",
"type": "group",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-unit",
"valueCoding": {
"system": "http://unitsofmeasure.org",
"code": "uL",
"display": "uL"
}
}
],
"linkId": "dWGS/laboratory_remaining_volume_banked_ul",
"text": "Remaining Banked Volume (uL)",
"type": "decimal"
},
{
"linkId": "dWGS/glh_concentration_ng_ul",
"text": "DNA Concentration (ng/uL)",
"type": "decimal"
},
{
"linkId": "dWGS/glh_od260_280",
"text": "DNA Purity (OD260/280)",
"type": "decimal"
},
{
"linkId": "dWGS/glh_din_value",
"text": "DNA Integrity Number",
"type": "decimal"
},
{
"linkId": "dWGS/glh_percentage_dna_over_23kb",
"text": "DNA Fragment Size (% over 23kb)",
"type": "decimal"
},
{
"linkId": "dWGS/glh_qc_status",
"text": "QC Status",
"type": "string"
},
{
"linkId": "dWGS/glh_sample_dispatch_date",
"text": "Dispatch Date",
"type": "date"
},
{
"linkId": "dWGS/plating_organisation",
"text": "Plating Organisation",
"type": "string"
},
{
"linkId": "dWGS/gmc_rack_id",
"text": "Rack Identifier",
"type": "string"
},
{
"linkId": "dWGS/gmc_rack_well",
"text": "Rack Well Position",
"type": "string",
"item": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/questionnaire-item-control",
"code": "help"
}
]
}
}
],
"linkId": "dWGS/gmc_rack_well-designNote",
"text": "Pattern: [A-H]01-09 or [A-H]10-12.",
"type": "display"
}
]
},
{
"linkId": "dWGS/prolonged_sample_storage",
"text": "Sample Storage Method",
"type": "string"
}
]
}
]
}