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.