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.

Patients registered with PDS (those that have an NHS number) will not have their demographics stored on the Genomic Order Management system. This is to avoid data duplication and data currency issues where PDS is considered the master patient index.

Profiling for Procedure is currently in progress

Life Status

For Life Status at time of request for Foetal records, as per PRSB guidance, this should be inferred through outcome codes attached to the Pregnancy observation.

e.g. under Observation with code 77386006, Observation.component.valueCodeableConcept (with Observation.component.code = 267013003 | Past pregnancy outcome (observable entity) |)

The component SNOMED codes SHOULD match the following list to map from foetal life statuses:

PRSB Prgnancy Outcome GEL Foetal Life Status SNOMED CT Pregnancy Outcome Code
01 Live birth N/A - not included in GEL list 281050002 - Livebirth (finding) (or captured through Patient.extension:bornStatus)
02 Antepartum Stillbirth stillborn 713202001 - Antepartum stillbirth (finding)
03 Intrapartum Stillbirth stillborn 921611000000101 - Intrapartum stillbirth (finding)
04 Stillbirth – timing unknown stillborn 237364002 - Stillbirth (finding)
05 Termination of Pregnancy equal to or greater than 24 weeks aborted 57797005 - Induced termination of pregnancy (disorder)
98 Other (not listed) N/A not part of GEL life status ValueSet potentially captured through Patient.extension:bornStatus = unknown
N/A not mapped exactly to PRSB ValueSet miscarriage 17369002 - Miscarriage (disorder)
N/A no pregnancy outcome code unborn N/A no pregnancy outcome code (captured through Patient.extension:bornStatus)

Sex/Gender representations

There are currently multiple FHIR fields for representation of gender and sex related observations, the following table outlines the usage of each field/resource.

FHIR element Usage
Patient.extension:birthSex The patient's sex as registered at birth, this is used to denote the phenotypic sex of the patient
Patient.gender The patient's gender, used for administrative purposes, some services record sex within this field, which is incorrect
Patient.extension:genderIdentity The gender the patient identifies with, has a larger valueset than the Patient.gender field, including trans and intersex options, may not match the administrative gender assigned to the patient
Observation.code Used for recording the Karyotypic sex of the patient, as determined through genetic testing, codes used SHOULD be from SNOMED CT, such as codes under 734840008 or 95462004 as examples

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Patient - Title Patient.name.prefix (for PDS registered patients, will only be recorded within PDS) PID-5.5 Patient's title.
Patient - First name Patient.name.given (for PDS registered patients, will only be recorded within PDS) PID-5.2 Patient's first name.
Patient - Surname Patient.name.family (for PDS registered patients, will only be recorded within PDS) PID-5.1 Patient's last name.
Patient - Date of birth Patient.birthDate (for PDS registered patients, will only be recorded within PDS) PID-7 Patient's date of birth.
Patient - Address Patient.address (for PDS registered patients, will only be recorded within PDS) PID-11 Patient's home address.
Patient - Postcode Patient.address.postalCode (for PDS registered patients, will only be recorded within PDS) PID-11.5 Patient's home postcode.
Patient - Country Patient.address.country (for PDS registered patients, will only be recorded within PDS) 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. For Foetal records, foetal death SHOULD be recorded through the Patient.extension:bornStatus field. The type of death can be inferred through Observation components related to the mother's pregnancy observation (as in table above). (for PDS registered patients, will only be recorded within PDS) 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 registered 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 responsible 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). (for PDS registered patients, will only be recorded within PDS) PD1-4.14 Patient's GP practice ODS code.
Patient - Is from consanguinous union Observation valueBoolean with code=160475008 (NOTE: The SNOMED CT code used is not specific to direct 1st generation ancestors of the subject, a more specific code has been requested. Until release of a SNOMED CT version with a more specific code, use of this code within Genomic Order Management SHALL be used to imply whether the subject's parents are consanguinous.) 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. (for PDS registered patients, will only be recorded within PDS) 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. (for PDS registered patients, will only be recorded within PDS TBC) PID-29 Patient's date/time of death.
Patient - Chromosomal 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 (Order Prior) 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 (Order Prior) 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 (Order Prior) 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 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.
Patient - 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)
Patient - Transplant date Procedure.performedDateTime( subject=Patient ) OBR-7 When the patient had the transplant.
Patient - 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.
Patient - 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)
Patient - Transfusion date Procedure.performedDateTime( subject=Patient ) OBR-7 (Order Prior) When the patient had the transfusion.
Patient - Height (m) Observation.valueQuantity( code=54871000237100, subject=Patient) OBX-5 Patient's height.
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. (for PDS registered patients, will only be recorded within PDS) 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 for pregnant / 60001007 for not pregnant) OBX-5 with appropriate SNOMED/READ/LOINC code Patient's pregnancy status.