Patient Clinical Information

Purpose

To know known/suspected disease including status and traits to support testing and interpretation. Further details which may support testing and interpretation including the family history of a disease.

Notes

Mapped to Condition and Observation resources linked to the patient. The primary condition being tested for SHOULD be referenced via ServiceRequest.reasonReference, additional relevant conditions SHOULD be referenced via ServiceRequest.supportingInfo. SNOMED CT is preferred for Condition.code, though Genomic Test Directory codes MAY be used, where a SNOMED CT concept cannot be found, until the Test Directory is aligned to SNOMED CT.

Condition codes such as the type of cancer SHALL be recorded as a Condition.code referencing the Patient resource. Absence of a condition is represented through lack of a Condition resource added to the request (rather than an explicit negative finding, unless related to phenotypic details). Treatment details SHOULD be represented as Procedure resources recording the actual details of the treatment, though if details are not known this MAY be recorded as Observations, e.g. with code= 395073001 | Cancer treatment started | TBC. Treatment history SHOULD use the most appropriate FHIR resource, though requirements for structuring of data have not been elaborated so MAY be recorded against ServiceRequest.note using appropriately annotated entries, see Genomics-ServiceRequest.

Mapping

ID Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
PCI-001 Genomic ethnicity Observation.valueString( code=723621000000103 ) OBX-5 Patient's ethnicity where 'Patient - Ethnicity field' doesn't provide an adequate description. E.g Ashkenazi Jewish
PCI-002 Disease status Condition.clinicalStatus, Condition.verificationStatus Potentially mapped to DG1-17 If the patient is affected, uncertain, unaffected, or it is unknown.
PCI-004 Age at disease onset Condition.onsetAge PRB-16, note not included within OML message The age when a change in patients' health was first noted in line with suspected diagnosis.
PCI-005 Confirmed diseases Condition where verificationStatus=confirmed DG1-6 Disease a patient is known to have.
PCI-049 Suspected diseases Condition where verificationStatus=provisional DG1-6 Disease a patient is believed to have.
PCI-006 Present phenotypes Observation.code with HPO system and valueCodeableConcept = 52101004 Present Additional OBX segments The HPO (or alternative ontology as appropriate) term names for observable disease traits.
PCI-051 Absent phenotypes Observation.code with HPO system and valueCodeableConcept = 2667000 Absent For just consultands, the HPO (or alternative ontology as appropriate) term names for absent disease traits evident in the proband.
PCI-052 Unknown phenotypes Observation.code with HPO system and valueCodeableConcept = 261665006 Unknown For just consultands, the HPO (or alternative ontology as appropriate) term names for unconfirmed disease traits evident in the proband.
PCI-010 Count of tumours Inferred through number of Condition/Condition.bodysite entries for tumours Multiple DG1 segments (bodySite for condition not in scope for HL7v2) How many tumours the patient has.
PCI-011 Site of tumour (many) codes used for Condition.bodysite entries Multiple DG1 segments (bodySite for condition not in scope for HL7v2) Location of the tumours on the body.
PCI-014 Tumour sites - Body image diagram DocumentReference, MAY be referenced from Condition.evidence.detail N/A - not in scope for HL7v2 Image attachment of body with tumour sites highlighted.
PCI-015 Pedigree details / Relevant family history FamilyMemberHistory referenced from ServiceRequest.supportingInfo, optionally referenced from Condition.evidence.detail N/A not in scope for HL7v2, could be added as additional DG1 segments related to relatives (representation of family history in HL7v2 still pending investigation) The patient's pedigree details/diagram (inc family history of cancer).
PCI-016 Pedigree diagram Media referenced from ServiceRequest.supportingInfo, optionally referenced from Condition.evidence.detail N/A not in scope for HL7v2, could be added as additional DG1 segments related to relatives (representation of family history in HL7v2 still pending investigation) Image attachment of pedigree details.
PCI-017 Laterality of hearing loss Specific Condition.code under Hearing loss e.g. 473424007 DG1-2 Laterality of the hearing loss i.e. bilateral or unilateral.
PCI-018 Fetal maternal screening genotype Presence of Condition.code with appropriate code for Fetal Maternal Screening Genotype (as identified in ConceptMap) attached to Maternal Patient resource DG1-3 Maternal screening genotype for haemoglobinopathy testing.
PCI-021 Legal considerations TBC Needs more specificity to properly model, likely Consent resources attached to ServiceRequest TBC possibly DG1-18 Legal considerations for a given request.
PCI-022 Fetal paternal screening genotype Presence of Condition.code with appropriate code for Fetal Maternal Screening Genotype (as identified in ConceptMap) attached to Paternal Patient resource DG1-3 Paternal screening genotype for haemoglobinopathy testing.
PCI-023 Expected maternity unit - Organisation name TBC Future dated Encounter with referenced serviceProvider or referenced from EpisodeOfCare.managingOrganization (for pregnancy episode) potentially PV1-42.4 Requesting clinician's organisation name.
PCI-024 Expected maternity unit - Organisation address TBC Future dated Encounter with referenced serviceProvider or referenced from EpisodeOfCare.managingOrganization (for pregnancy episode) PV1-42.7 Requesting clinician's organisation address.
PCI-025 Expected maternity unit - Organisation ODS code TBC Future dated Encounter with referenced serviceProvider or referenced from EpisodeOfCare.managingOrganization (for pregnancy episode) PV1-42.10 Requesting clinician's organisation ODS code.
PCI-026 Expected maternity unit - Department name TBC Future dated Encounter with referenced serviceProvider or referenced from EpisodeOfCare.managingOrganization (for pregnancy episode) PV1-42.9 Requesting clinician's department name.
PCI-027 Growth history Observation resources for head circumference etc. OBX segments Summary passage of text to highlight patient centile history e.g head circumference, weight, etc.
PCI-028 Severity of hearing loss Condition.code with appropriate code under 15188001 or Condition.note with code 15188001 DG1-3 Free text regarding hearing loss
PCI-029 Retinal degeneration Condition.code with appropriate code under 95695004 or Condition.note with code 95695004 DG1-3 Free text regarding retinal degeneration
PCI-030 Risk factors MedicationStatement resources with certain codes TBC OBX segments detailing patient on medication etc. Toxic medication - Prematurity (risk factor for hearing loss) e.g. Baby early birth - Ototoxic medication.
PCI-031 Suspected inborn error type(s) Condition.code with code under 86095007 and verificationStatus provisional/unconfirmed DG1-3 Suspected inborn error type(s)
PCI-032 Abnormal infection history site TBC Condition.bodySite for relevant infection entries TBC Abnormal infection history Site
PCI-033 Abnormal infection history site organism TBC Condition.bodySite for relevant infection entries with reference to specific body structures TBC Abnormal infection history Site organism
PCI-034 Is on Ig replacement TBC Procedure.code with code 698802001 with status=in-progress TBC If the patient is on immunoglobin replacement treatment.
PCI-035 Patient clinical information - Current and previous treatment detail List of MedicationStatement/Procedure/Encounter resources if structured TBC likely NTE segments as part of order Detail regarding relevant current and previous medical treatments.
PCI-036 Patient clinical information - Pregnancy status Observation.code( subject=Patient, code=77386006 for pregnant / 60001007 for not pregnant) OBX-5 with appropriate SNOMED/READ/LOINC code Patient's pregnancy status.
PCI-037 Patient clinical information - Pregnancy type Inferred through presence of Procedure with codes under IUI/IVF (e.g. codes under 63487001) OBR segments with appropriate codes (Order Prior) Type of conception.
PCI-038 Patient clinical information - Pregnancy gestation period Observation.component.valueQuantity with code for gestation OBX-14 (subtracted from ORC-9) Patient's term of active pregnancy at point of test request.
PCI-039 Patient clinical information - Fetal gestation Observation.component.valueQuantity with code for gestation, though could be inferred through difference between Observation.effectiveDateTime for pregnancy and Procedure.performedDateTime for termination OBX-14 (subtracted from OBR-7 for termination procedure) Stage during patient pregnancy at which it terminated.
PCI-040 Patient clinical information - Estimated Delivery Date (EDD) As above, though could be inferred through Observation.effectiveDateTime for pregnancy + 40 weeks or new observation with code 161714006 OBX-14 + 40 weeks Patient's estimated delivery date.
PCI-041 Patient clinical information - IVF age of egg donor TBC Observation referencing IVF procedure (through partOf) with code = 433475001 (if category of over 35 is sufficient, otherwise code.display of "IVF age of egg donor" with age populated in valueQuantity) OBR segments with appropriate codes (Order Prior) The age of the patient who donated the egg at the time of donation.
PCI-042 Patient clinical information - Had transplant Inferred through presence of Procedure( subject=Patient ) with code under 77465005 - Transplantation, alternatively, Observation with code 416128008 with valueCodeableConcept=263903005 for no history of transplant Presence of OBR segment with OBR-44 code for transplant (Order Prior)) Has the patient ever had a transplant.
PCI-043 Patient clinical information - Type of transplant Procedure.code( subject=Patient, code= code under 77465005 ) OBR-44 (Order Prior) What type of transplant the patient had. (Bone marrow / Stem cell)
PCI-044 Patient clinical information - Transplant date Procedure.performedDateTime( subject=Patient ) OBR-7 When the patient had the transplant.
PCI-045 Patient clinical information - Had transfusion in the last 6 weeks Inferred through presence of Procedure( subject=Patient ) with code under 5447007 - Transfusion, with performedDateTime within 6 weeks of the ServiceRequest being submitted, alternatively, Observation with code 416128008 with valueCodeableConcept=303955003 for no history of transfusion Presence of OBR segment with OBR-44 code for transplant (Order Prior) Has the patient had a transfusion in the last 6 weeks.
PCI-046 Patient clinical information - Type of transfusion Procedure.code( subject=Patient, code= code under 5447007 ) OBR-7 (Order Prior) What type of transfusion the patient has had. (Packed Red Cells /Plasma / Platelets)
PCI-047 Patient clinical information - Transfusion date Procedure.performedDateTime( subject=Patient ) OBR-7 (Order Prior) When the patient had the transfusion.
PCI-048 Patient clinical information - Height (m) Observation.valueQuantity( code=54871000237100, subject=Patient) OBX-5 Patient's height.