Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
Primary Sample
Purpose
For samples directly obtained from a patient. To track samples, direct storage, handling and testing decisions including ensuring volumes received match what was sent. Further detail which may support testing and interpretation. To enable patient to opt out of having a sample/biopsy stored.
Notes
Mapped to Specimen. Extensions lifted from mCODE are currently under review. Observation codes linked to samples are pending addition to SNOMED-CT
Additional observation code fields from MDS v1.04 mappings are still under review
Mapping
Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description |
---|---|---|---|
Primary Sample - Destination organization ODS code | Not in scope for FHIR R4, could use Specimen.note or record this information against Task, e.g. inferred through the Task.owner who is intended to receive the specimen (TBC, if required a request to backport Specimen.container.location will be made to support capture of this information) | SAC-15 | Destination for primary sample. |
Primary Sample - Id (many) | Specimen.identifier.value | SPM-2 | Id of sample provided linked to the previously stated assigning authority. Occurs multiple times. |
Primary Sample - Id assigning authority ODS code (many) | Specimen.identifier.assigner | SPM-2.1.2 | Authority who assigned the sample id (e.g. histopathology, SHIMDS, etc). Occurs multiple times. |
Primary Sample - Received date | Specimen.receivedTime | SPM-18 | Date at which a specimen was received at a laboratory. |
Primary Sample - Sample storage details | Not in scope for FHIR R4, could use Specimen.note or record this information against Task.input (TBC, if required a request to backport Specimen.container.location will be made to support capture of this information) | SAC-15 | Where a primary sample is in storage or where it needs to be stored. |
Primary Sample - Volume | Specimen.collection.quantity | SPM-12 | Volume of provided sample. |
Primary Sample - Test Request Id | Specimen.request | ORC-2, included within the same OML message | The id of the associated genomic test being requested. |
Primary Sample - Patient NHS number | Patient.identifier:system = https://fhir.nhs.uk/Id/nhs-number | PID-3 where PID-3.5=2.16.840.1.113883.2.1.3.2.4.18.23, within same OML message | Patient NHS number. |
Primary Sample - Patient Local identifier | Patient.identifier:system != https://fhir.nhs.uk/Id/nhs-number (local NamingSystem can be used, assigner determined through assigner field) | PID-3 where PID-3.5 = 2.16.840.1.113883.2.1.3.2.4.18.24, within same OML message | Patient identification code other than NHS number. |
Primary Sample - Obtained date | Specimen.collection.collectedDateTime | SPM-17 | The time at which the sample/biopsy was obtained from the patient. |
Primary Sample - Primary Sample | Specimen.type | SPM-4 | Tissue of origin. |
Primary Sample - Primary Sample State | Specimen.condition | SPM-24 | How has the specimen been preserved/fixed. Note: The ValueSet for this field is pending review to align with MDSv1.04 |
Primary Sample - Necrosis | Observation.code( code=6574001 (TBC), specimen=Specimen ) | OBX segment with appropriate code | % necrotic cells in specimen volume. |
Primary Sample - Nucleated cell count | Observation.code( code=1022461000000100, specimen=Specimen ) | OBX segment with appropriate code | Nucleated cell count in the specimen/biopsy (Solid Tumour and Haem-Onc). |
Primary Sample - Tumour nuclear content | Observation.code( code=444901007 (TBC), specimen=Specimen ) | OBX segment with appropriate code | Neoplastic cell content in the specimen/biopsy (Solid Tumour) - sourced at local lab. (%) |
Primary Sample - Tumour cellularity | Observation.code( code=TBC, specimen=Specimen ) | OBX segment with appropriate code | The proportion which is tumour nuclei. |
Primary Sample - Solid tumour morphology | BodyStructure.morphology( patient=Patient ), referenced from Specimen.collection.bodysite.extension:bodySiteReference if in reference to a specimen, or referenced from a Condition if in relation to the patient's condition (pending profiling of bodySiteReference backport to R4 Condition) | Additional SPM-4/5 qualifiers | The histology and likely course of development of a tumour. |
Primary Sample - Solid tumour topography | BodyStructure.location(patient=Patient), referenced from Specimen.collection.bodysite.extension:bodySiteReference if in reference to a specimen, or referenced from a Condition if in relation to the patient's condition (pending profiling of bodySiteReference backport to R4 Condition) | SPM-8 | The tumour sample site. eg from colon, stomach etc. |
Primary Sample - Biopsy site | Specimen.collection.bodySite | SPM-8/SPM-9 | Site of biopsy. |
Primary Sample - Skin/Bone affected status | Observation.valueBoolean ( code=22201000087104, specimen=Specimen ), assume unaffected if not provided | OBX segment with appropriate code | If the skin or bone provided is unaffected or affected. |
Primary Sample - Maternal cell contamination (MCC) | Observation.valueBoolean( code=726741007, specimen=Specimen ), assume no MCC if not provided | OBX segment with appropriate code | Confirmation if MCC has been excluded from sample. |
Primary Sample - Option for all products of conception | Additional Specimen.collection.extension:specimen-specialHandling with appropriate code/text | SPM-15 | Future management for products of conception. |
Primary Sample - Blasts % | Observation.code( code=1022601000000101, specimen=Specimen ) | OBX segment with appropriate code | Blast count in the specimen/biopsy (Haemonc) - sourced at local SIHMDS. |
Primary Sample - High infection risk reason | Specimen.collection.extension:specimen-specialHandling.valueCoding.code | SPM-16.2 | The high contamination risk reason for a sample/biopsy. |