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

ID Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
PS-2 Primary Sample - Local identifier Specimen.identifier.value SPM-2 Local ids applied to a sample
PS-3 Primary Sample - ODS code of organisation which assigned local id Specimen.identifier.assigner SPM-2.1.2 ODS code of the organisation which assigned the local sample id.
PS-10 Primary Sample - Obtained date Specimen.collection.collectedDateTime SPM-17 Date at which a specimen/biopsy was obtained from patient.
PS-11 Primary Sample - Primary Sample Specimen.type SPM-4 The primary sample material.
PS-12 Primary Sample - Primary Sample State Specimen.condition SPM-24 The state of the primary sample.
PS-25 Primary Sample - Preservative/Container Specimen.container.additiveCodeableConcept SPM-6 (TBC) How the primary sample is preserved.
PS-30 Primary Sample - Block identifier Specimen.parent.identifier SPM-3 Sample block identifier.
PS-31 Primary Sample - Fixative type Specimen.processing.additive SPM-6 Sample fixative type.
PS-32 Primary Sample - Hours to fixation Difference between Specimen.collection.collectedDateTime and Specimen.processing.timeDateTime N/A, though SPM-6.9 could be used (TBC) Sample hours to fixation.
PS-33 Primary Sample - Hours in fixative Specimen.processing.timePeriod N/A, though SPM-6.9 could be used (TBC) Sample hours in fixative.
PS-34 Primary Sample - Tumour enrichment method Additional Specimen.processing elements N/A Not part of the HL7v2 spec Method used for tumour enrichment.
PS-13 Primary Sample - Necrosis Observation.code( code=405921002 (TBC), focus=Specimen ) OBX segment with appropriate code % necrotic (dead) cells in primary sample.
PS-14 Primary Sample - Nucleated cell count Observation.code( code=1022461000000100, focus=Specimen ) OBX segment with appropriate code Nucleated (with nucleous) cell (non tumour and tumour) count in the primary sample (Solid Tumour and Haem-Onc).
PS-15 Primary Sample - Tumour nuclear content in whole section Observation.code( code=371510003 (TBC), focus=Specimen ) OBX segment with appropriate code Neoplastic (tumour) cell content in the primary sample whole section(Solid Tumour) - sourced at local lab. (%)
PS-26 Primary Sample - Tumour nuclear content in marked area Observation.code( code=(TBC), focus=Specimen ) OBX segment with appropriate code Neoplastic (tumour) cell content in the primary sample marked area(Solid Tumour) - sourced at local lab. (%)
PS-17 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.
PS-18 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.
PS-29 Primary Sample - Is biopsy Specimen.collection.method(code=129314006) SPM-7 with appropriate SNOMED CT/LOINC code for Biopsy Digital confirmation that the sample is a biopsy.
PS-19 Primary Sample - Biopsy site Specimen.collection.bodySite SPM-8/SPM-9 Site where the primary sample was taken from.
PS-21 Primary Sample - Observed maternal cell contamination (MCC) Observation.valueBoolean( code=726741007, focus=Specimen ), assume no observed MCC if not provided OBX segment with appropriate code An observed outcome which may indicate MCC
PS-27 Primary Sample - Test confirmed maternal cell contamination (MCC) Observation.valueQuantity( code=726741007, focus=Specimen ) OBX segment with appropriate code Analytically confirmed MCC levels
PS-22 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.
PS-23 Primary Sample - Blasts % Observation.code( code=1015521000000107, focus=Specimen ) OBX segment with appropriate code Blast (immature blood cells) count in the primary sample (Haemonc) - sourced at local SIHMDS.
PS-24 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.
PS-28 Primary Sample - Patient life status at the time of collection Inferred though Specimen.collection.collectedDateTime after Patient.deceasedDateTime Inferred through SPM-17 later than PID-30 If the patient was alive or deceased at the point of collecting a sample.
PS-35 Primary Sample - Solid tumour type Specific Condition.code e.g. child concepts of 128462008 for metastatic tumours (potentially linked from mCODE extension on BodyStructure) DG1-3 The origin or context of a tumour sample.