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.
SNOMED CT Mappings
Below is a list of all the MDS elements (except for those to be removed in MDSv1.05) which are expected to be populated using SNOMED CT concepts. These have been pulled out into a separate list, with links to SNOMED CT, FHIR ValueSets or Genomics ConceptMaps to aid implementation.
Mapping
| Source Data item | Target FHIR Element | Binding |
|---|---|---|
| PS-11 - Primary Sample - Primary sample | Specimen.type | ConceptMap Genomic Primary Sample |
| PS-17 - Primary Sample - Solid tumour morphology | BodyStructure.morphology | SNOMED CT Morphologic Abnormalities |
| PS-18 - Primary Sample - Solid tumour topography | BodyStructure.location | SNOMED CT Body Structures |
| PS-19 - Primary Sample - Biopsy Site | Specimen.collection.bodySite | SNOMED CT Body Structures |
| PC-23 - Primary Sample - Blasts % | Observation.code | 1015521000000107 |
| P-21 -Patient - Chromosomal sex | Observation.code | ConceptMap Genomic Observation Chromosomal Sex |
| PCI-8 - Disease penetrance | Observation.code | 86426007 for complete penetrance or 87006007 for incomplete penetrance |
| F3 -Fetus - Chromosomal sex | Observation.code | 734840008 |
| F6 -Fetus - Life status at time of request | Patient.extension:fetalStatus | ConceptMap Genomic Patient Born Status |
| PS-13 - Primary Sample - Necrosis | Observation.code | 405921002 |
| PS-14 -Patient - Primary Sample - Nucleated cell count | Observation.code | 1022461000000100 |
| PS-15 - Primary Sample - Tumour nuclear content in whole section | Observation.code | 371510003 |
| PS-21 - Primary Sample - Observed maternal cell contamination (MCC) | Observation.valueBoolean | 726741007 TBC |
| PS-24 - Primary Sample - High infection risk reason | Specimen.collection.extension:specimen-specialHandling.valueCoding.code | ConceptMap Genomic Specimen Special Handling |
| PCI-1 -Patient clinical information - Genomic ethnicity | Observation.code | 723621000000103 |
| PCI-7 - Patient clinical information - Symptoms | Observation.code | SNOMED CT Clinical Findings |
| PCI-11 - Patient clinical information - Site of tumour | BodyStructure.location | SNOMED CT Body Structures |
| PCI-12 - Patient clinical information - Solid tumour type | Condition.code | ConceptMap Genomic Condition Solid Tumour Type |
| PCI-17 - Patient clinical information - Laterality of hearing loss | Condition.code | ConceptMap Genomic Condition Laterality of Hearing Loss |
| PCI-18 - Patient clinical information - Fetal haemoglobinopathy maternal screening genotype | Observation.code | ConceptMap Fetal Maternal Screening Genotype |
| PCI-22 - Patient clinical information - Fetal haemoglobinopathy paternal screening genotype | Observation.code | ConceptMap Fetal Maternal Screening Genotype |
| PCI-28 - Patient clinical information - Severity of hearing loss | Condition.code | Code under 15188001 |
| PCI-29 - Patient clinical information - Retinal degeneration | Condition.code | Code under 95695004 |
| PCI-31 - Patient clinical information - Suspected inborn error type(s) | Condition.code | Code under 86095007 |
| PCI-32 - Patient clinical information - Abnormal infection history site | TBC Condition.bodySite | SNOMED CT Body Structures |
| PCI-33 - Patient clinical information - Abnormal infection history site organism | TBC Condition.bodySite | SNOMED CT Body Structures |
| PCI-34 - Patient clinical information - Is on ig replacement | TBC Procedure.code | 698802001 |
| PCI-42 Patient clinical information - Had transplant | Procedure.code, Observation.code, Observation.valueCodeableConcept | Procedure with code under 77465005 - Transplantation, alternatively, Observation with code 416128008 with valueCodeableConcept 263903005 for no history of transplant |
| PCI-43 -Patient clinical information - Type of transplant | Procedure.code | ConceptMap Genomic Type of Transplant Procedure |
| PCI-45 -Patient clinical information - Had transfusion in the last 6 weeks | Procedure.code, Observation.code, Observation.codeableConcept | code under 5447007, alternatively,Observation with code 416128008 with valueCodeableConcept 303955003 for no history of transfusion |
| P-13 -Patient - Is from consanguineous union | Observation.code | 160475008 |
| PCI-35 -Patient clinical information - Being treated for cancer | Procedure.reasonCode | Code under 363346000 |
| PCI-36 -Patient clinical information - Pregnancy status | Observation.code | 77386006-Pregnant, 60001007-Not Pregnant |
| PCI-37 -Patient clinical information - Pregnancy type | Observation.component.code | ConceptMap Genomic Patient Pregnancy Type |
| PCI-38 -Patient clinical information - Pregnancy gestation period | Observation.component.valueDuration | 226081000000107 |
| PCI-39 -Patient clinical information - Fetal gestation | Observation.component.valueDuration | 57036006 |
| PCI-40 -Patient clinical information - Estimated delivery date (EDD) | Observation.component.code | 161714006 |
| PCI-41 -Patient clinical information - IVF age of egg donor | Observation.code | 433475001 |
| PCI-46 -Patient clinical information - Type of transfusion | Procedure.code | ConceptMap Genomic Procedure Transfusion Type |
| PCI-48 -Patient clinical information - Height (m) | Observation.valueQuantity | 54871000237100 |
| PCI-12 -Patient clinical information - Solid tumour type | Condition.code | ConceptMap Genomic Condition Solid Tumour Type |
| PCI-39 -Patient clinical information - Fetal gestation | Observation.code | 598151000005105 |
| TR-12 - Test request - Urgency reason | ServiceRequest.extension:priorityReason | Any code under 64572001 |
| SP-8 - Sample Preparation - Sample preparation | Specimen.processing.procedure | ConceptMap Genomic Specimen Sample Preparation |
| FS-9 - Final Sample - Final sample | Specimen.type | ConceptMap Genomic Specimen Final Sample |
| PGR-17 - Previous genomic report - Result of genetic analysis | DiagnosticReport.conclusionCode, DiagnosticReport.result | SNOMED CT Clinical Findings |