Sample/Biopsy inc germline

Purpose

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 v0.55 mappings are still under review

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Raw specimen/biopsy - 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.
Raw specimen/biopsy - Is assigning authority a histopathology laboratory (many) Derived from ODS - Specimen.identifier.assigner Derived from ODS - SPM-2.1.2 Confirmation of an assigning authority ODS code being from a histopathology laboratory.
Raw specimen/biopsy - Id (many) Specimen.identifier.value SPM-2 Id of sample provided linked to the previously stated assigning authority. Occurs multiple times.
Raw specimen/biopsy - Sample well identifier Specimen.container.identifier SAC-3 Id of the sample well.
Raw specimen/biopsy - Location details Not in scope for FHIR r4, could use Specimen.note SAC-15 Where a raw specimen/biopsy is in storage and not provided with a request.
Raw specimen/biopsy - WGS specimen type category Specimen.extension:sampleCategory SPM-5 WGS cancer high level category for the specimen.
Raw specimen/biopsy - Type Specimen.type SPM-4 Tissue of origin.
Raw specimen/biopsy - State Specimen.condition SPM-24 How has the specimen been preserved/fixed. Note: The ValueSet for this field is pending review to align with MDSv1.0
Raw specimen/biopsy - Sample preparation (submitted to GLH) Specimen.processing Combination of SPM-6/SPM-24 or NTE segments if other processing How has the specimen has been prepared for the GLH.
Raw specimen/biopsy - Obtained date Specimen.collection.collectedDateTime SPM-17 The time at which the sample/biopsy was obtained from the patient.
Raw specimen/biopsy - Blood component Specific codes under Specimen.type SPM-4 For a blood specimen, confirmation of which blood component the specimen consists of.
Raw specimen/biopsy - Received date Specimen.receivedTime SPM-18 Date at which a specimen was received at a laboratory.
Raw specimen/biopsy - High risk reason Specimen.collection.extension:specimen-specialHandling.valueCoding.code SPM-16.2 The high contamination risk reason for a sample/biopsy.
Raw specimen/biopsy - Solid tumour morphology BodyStructure.morphology( patient=Patient ) Additional SPM-4/5 qualifiers The histology and likely course of development of a tumour.
Raw specimen/biopsy - Solid tumour histological type (topography) BodyStructure.location(patient=Patient) SPM-8 The patient's solid tumour histological type (topography), where the tumour arose.
Raw specimen/biopsy - Biopsy site Specimen.collection.bodySite SPM-8/SPM-9 Site of biopsy.
Raw specimen/biopsy - 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.
Raw specimen/biopsy - Blasts % Observation.code( code=1022601000000101, specimen=Specimen ) OBX segment with appropriate code Blast count in the specimen/biopsy (Haemonc) - sourced at local SIHMDS.
Raw specimen/biopsy - Neoplastic cell 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. (%)
Raw specimen/biopsy - Necrosis Observation.code( code=6574001 (TBC), specimen=Specimen ) OBX segment with appropriate code % necrotic cells in specimen volume.
Raw specimen/biopsy - 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).
Raw specimen/biopsy - Tumour cellularity Observation.code( code=TBC, specimen=Specimen ) The proportion which is tumour nuclei.
Raw specimen/biopsy - Volume Specimen.collection.quantity SPM-12 Volume of provided sample.
Raw specimen/biopsy - Taken alive/post mortem Observation.valueBoolean( code=839021000000109, specimen=Specimen ), true=post-mortem sample, assume taken alive if not provided OBX segment with appropriate code If a sample/biopsy was taken when the patient was alive or deceased.
Raw specimen/biopsy - 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.
Raw specimen/biopsy - Family member provided by Specimen.subject PID segment attached to SPM Which family member the specimen is provided by.
Raw specimen/biopsy - Option for products of conception Additional Specimen.collection.extension:specimen-specialHandling with appropriate code/text SPM-15 Future management for products of conception.
Raw specimen/biopsy - Sample to follow N/A implied through absence of Specimen in Test Order message, or Specimen.status=unavailable and missing Specimen.collection.collectedDateTime samples ordered but not collected N/A implied through absence of SPM segment in test order Confirmation that the sample will be sent separately to, and after the test request.
Raw specimen/biopsy - Sample to follow reason Text in ServiceRequest.note field NTE segment attached to ORC Confirmation as to why the sample is being sent after the test request.
Raw specimen/biopsy - Additional specimen/biopsy information Observation resources referencing Specimen for coded information or Specimen.note OBX segments attached to SPM Raw specimen/biopsy - Additional specimen/biopsy information.