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-038 Primary Sample - ODS code of organisation which collected sample Specimen.collection.collector.identifier.assigner Likely SPM-2.1.2 Though there is no direct mapping for collector org within the SPM segment The reason an organisation has been involved with the sample such as they took the sample.
PS-002 Primary Sample - Local identifier Specimen.identifier.value SPM-2 Local ids applied to a sample
PS-003 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-010 Primary Sample - Obtained date Specimen.collection.collectedDateTime SPM-17 Date at which a specimen/biopsy was obtained from patient.
PS-011 Primary Sample - Primary Sample Specimen.type SPM-4 The primary sample material.
PS-012 Primary Sample - Primary Sample State Specimen.condition SPM-24 The state of the primary sample.
PS-025 Primary Sample - Preservative/Container Specimen.container.additiveCodeableConcept SPM-6 (TBC) How the primary sample is preserved.
PS-030 Primary Sample - Block identifier Specimen.parent.identifier SPM-3 Sample block identifier.
PS-031 Primary Sample - Fixative type Specimen.processing.additive SPM-6 Sample fixative type.
PS-032 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-033 Primary Sample - Hours in fixative Specimen.processing.timePeriod N/A, though SPM-6.9 could be used (TBC) Sample hours in fixative.
PS-034 Primary Sample - Tumour enrichment method Additional Specimen.processing elements N/A Not part of the HL7v2 spec Method used for tumour enrichment.
PS-013 Primary Sample - Necrosis Observation.code( code=405921002 (TBC), focus=Specimen ) OBX segment with appropriate code % necrotic (dead) cells in primary sample.
PS-014 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-015 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-026 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-017 Primary Sample - Solid tumour morphology BodyStructure.morphology( patient=Patient ), referenced from Specimen.collection.bodySite.extension:BodyStructureReference if in reference to a specimen, or referenced from a Condition if in relation to the patient's condition. Additional SPM-4/5 qualifiers The histology and likely course of development of a tumour.
PS-018 Primary Sample - Solid tumour topography BodyStructure.location(patient=Patient), referenced from Specimen.collection.bodySite.extension:BodyStructureReference if in reference to a specimen, or referenced from a Condition if in relation to the patient's condition. SPM-8 The tumour sample site. eg from colon, stomach etc.
PS-036 Primary sample - Solid tumour stage Observation.valueCodeableConcept where code is a member of the CancerStage ValueSet OBX segment with appropriate code The size and spread of the cancer.
PS-037 Primary sample - Solid tumour grade Observation.valueCodeableConcept where code = 371469007 Histologic grade of neoplasm (observable entity) OBX segment with appropriate code The abnormality of the cancer cells.
PS-029 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-039 Primary sample - Biopsy type Specimen.collection.method SPM-7 with appropriate SNOMED CT/LOINC code for Biopsy type The method a biopsy taken by.
PS-019 Primary Sample - Biopsy site Specimen.collection.bodySite SPM-8/SPM-9 Site where the primary sample was taken from.
PS-021 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-027 Primary Sample - Test confirmed maternal cell contamination (MCC) Observation.valueQuantity( code=726741007, focus=Specimen ) OBX segment with appropriate code Analytically confirmed MCC levels
PS-022 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-023 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-024 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-028 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-035 Primary Sample - Solid tumour type BodyStructure.morphology( patient=Patient ) where code is specifically either a child of 14799000 | Neoplasm, metastatic (morphologic abnormality) or another code not specifically marked as metastatic Additional SPM-4/5 qualifiers The origin or context of a tumour sample.