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.
Patient
Purpose
To track a patient, identify within shared systems and maintain complete records. To apply processes applicable to deceased patient requests, patient contact and urgency purposes. Data needed to support genetic interpretation, for PLCM to locate further patient ODS codes for a given test and to link patients to potential family members and their genetic results.
Notes
Mapped to Patient resource, extensions not in UKCore are under review. Representation of Karyotypic Sex is through an Observation with code under Karyotype (cell structure) - SCTID: 734840008 or Anomaly of sex chromosome (disorder) - SCTID: 95462004 (these codes are under review). Representation of pregnancy and gestation is under discussion.
It is expected that practitioner and organization details for GPs will be referenced from Patient.generalPractitioner (e.g. using ODS/SDS identifiers) rather than be included as FHIR resources within Test Request payloads, though the full FHIR mapping has been provided below for completeness.
Profiling for Procedure is currently in progress
Mapping
Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description |
---|---|---|---|
Patient - First name | Patient.name.given | PID-5.2 | Patient's first name. |
Patient - Surname | Patient.name.family | PID-5.1 | Patient's last name. |
Patient - Date of birth | Patient.birthDate | PID-7 | Patient's date of birth. |
Patient - Address | Patient.address | PID-11 | Patient's home address. |
Patient - Postcode | Patient.address.postalCode | PID-11.5 | Patient's home postcode. |
Patient - Country | Patient.address.country | PID-11.6 | Patient's home country. |
Patient - Life status at time of request | Patient.deceasedBoolean (would be replaced by deceasedDateTime if date of death is known), representation of unknown implied by deceasedBoolean not being present | PID-30 | Patient's alive or deceased status. |
Patient - Ethnicity | Patient.extension:EthnicCategory | PID-22 | Patient's ethnicity. Will have the option 'unknown' available. |
Patient - Sex assigned at birth | Patient.extension:birthSex | PID-8 | Patient's phenotypic sex classification. The external physical characteristics of the person. Currently determined by the Dr at birth. Gender for PLCM. |
Patient - Organisation responsibile for GP practice ODS code | N/A obtained through parent of GP Practice as recorded within ODS, obtained through Patient.generalPractitioner | PD1-4.14 | ODS code of organisation responsible for the GP Practice where the patient is registered. |
Patient - GP Practice ODS Code | Patient.generalPractitioner.identifier (with system matching ODS NamingSystem) | PD1-4.14 | Patient's GP practice ODS code. |
Patient - Gender Identity same as at birth | N/A inferred through difference between Patient.extension:birthSex and Patient.extension:patient-genderIdentity | N/A - not part of the HL7v2 standard, though PID-8 or an OBX segment could be used | Confirmation if the patient's gender is the same as at birth. |
Patient - Is from consanguinous union | FamilyMemberHistory.extension = family-member-history-genetics-observation( Observation.code=842009 ) or Observation attached to Patient | OBX-5 with appropriate SNOMED/READ/LOINC code | The fact of biological parents being descended from the same ancestor. |
Patient - GP full name | Patient.generalPractitioner.display for general practitioner reference to practitioner (SDS identifier), not practice | PD1-4.2 and PD1-4.3 | Patient's GP's full name. |
Patient - NHS number | Patient.identifier:system = https://fhir.nhs.uk/Id/nhs-number | PID-3 where PID-3.5=2.16.840.1.113883.2.1.3.2.4.18.23 | Patient NHS number. |
Patient - Local identifier | Patient.identifier:system != https://fhir.nhs.uk/Id/nhs-number (local NamingSystem can be used, assigner determined through assigner field) | PID-3 where PID-3.5 = 2.16.840.1.113883.2.1.3.2.4.18.24 | Patient identification code such as an NHS number. |
Patient - Reason for unavailable NHS number | Patient.extension:nhsNumberUnavailableReason | N/A, could use PID-32 as surrogate | Reason for an NHS number not being provided. |
Patient - Relationship to proband | RelatedPerson.relationship (alingment to MDS valueset pending review) | NK1-3 | Relative's relationship to proband/index. |
Patient - Gender Identity | Patient.extension:patient-genderIdentity | N/A - not part of the HL7v2 standard, though PID-8 or an OBX segment could be used | Patient's stated gender. The gender by which the person is addressed. Determined by the patient. |
Patient - Date of death | Patient.deceasedDateTime | PID-29 | Patient's date/time of death. |
Patient - Karyotypic sex | Observation.code( subject=Patient, code = code under 734840008 or 95462004 as examples ) | OBX-5 with appropriate SNOMED/READ/LOINC code | Patient's genomic / karyotypic characteristics. Determined after laboratory testing. |
Patient - Pregnancy gestation period | Observation.component.valueDuration with code for gestation | OBX-14 (subtracted from ORC-9) | Patient's term of active pregnancy at point of test request. |
Patient - Fetal gestation | As above, 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. |
Patient - 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. |
Patient - Pregnancy type | Inferred through presence of Procedure with codes under IUI/IVF (e.g. codes under 63487001) | OBR segments with appropriate codes | Type of conception. |
Patient - 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") | OBR segments with appropriate codes | The age of the patient who donated the egg at the time of donation. |
Patient - Diagnosed with or being treated for cancer | TBC Inferred through attached Condition resources with code under 363346000 or Procedure etc. with reasonCode under same concept | OBR segments with appropriate codes | Has the patient been diagnosed with or are they being treated for cancer. |
Patient - Had transplant | Inferred through presence of Procedure( subject=Patient ) with code under 77465005 - Transplantation, alternatively, Observation with code 77465005 with valueBoolean=false | Presence of OBR segment with OBR-44 code for transplant | Has the patient ever had a transplant. |
Patient - Type of transplant | Procedure.code( subject=Patient, code= code under 77465005 ) | OBR-44 | What type of transplant the patient had. (Bone marrow / Stem cell) |
Patient - Transplant date | Procedure.performedDateTime( subject=Patient ) | OBR-7 | When the patient had the transplant. |
Patient - Had transfusion | Inferred through presence of Procedure( subject=Patient ) with code under 5447007 - Transfusion, alternatively, Observation with code 5447007 with valueBoolean=false | Presence of OBR segment with OBR-44 code for transplant | Has the patient ever had a transfusion. |
Patient - Type of transfusion | Procedure.code( subject=Patient, code= code under 5447007 ) | OBR-7 | What type of transfusion the patient has had. (Packed Red Cells /Plasma / Platelets) |
Patient - Transfusion date | Procedure.performedDateTime( subject=Patient ) | OBR-7 | When the patient had the transfusion. |
Patient - Height (m) | Observation.valueQuantity( code=54871000237100, subject=Patient) | OBX-5 | Patient's height. |
Patient - Sexual orientation (pending review) | Observation.value( subject=Patient, code=66621004) | OBX-5 with appropriate SNOMED/READ/LOINC code | Patient's sexual orientation. |
Patient - Withheld identity reason | Additional codes to be part of Patient.extension:nhsNumberUnavailableReason ValueSet (as per NHS Data Model and Dictionary, pending addition) | N/A, could use PID-32 as surrogate | Confirmation why the patient is withholding identity details. |
Patient - GP's professional registration number | Patient.generalPractitioner.identifier with system for appropriate registration authority | PD1-4.1 | Patient's GP's professional registration number. |
Patient - Pedigree/Family Identifier | Patient.identifier:pedigreeNumber | Additional identifiers under PID-3 | Patient's genetic/pedigree number which links their family. |
Patient - Pregnancy status | Observation.code( subject=Patient, code=77386006 ) | OBX-5 with appropriate SNOMED/READ/LOINC code | Patient's pregnancy status. |