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.

Restricted Patients: PDS guidance on managing the data of sensitive patient shall be followed. Some patients are tagged as restricted and are sometimes known as sensitive patients. Restricted patients can be retrieved; however, location-sensitive fields such as address, telecom and generalPractitioner are removed.

The restricted flag can be found in the data under meta/security on the patient resource. See in Example: Patient-SensitivePatient-Example

Profiling for Procedure is currently in progress

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

ID Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
P-1 Patient - Title Patient.name.prefix (for PDS registered patients, will only be recorded within PDS) PID-5.5 Patient's title.
P-2 Patient - First name Patient.name.given (for PDS registered patients, will only be recorded within PDS) PID-5.2 Patient's first name.
P-40 Patient - Middle name Additional Patient.name.given elements (for PDS registered patients, will only be recorded within PDS) PID-5.3 Patient's middle name.
P-3 Patient - Surname Patient.name.family (for PDS registered patients, will only be recorded within PDS) PID-5.1 Patient's last name.
P-41 Patient - Name use Patient.name.use (for PDS registered patients, will only be recorded within PDS) PID-5.7 Links each patient name entry to confirm if current, previous or what the patient is known as.
P-4 Patient - Date of birth Patient.birthDate (for PDS registered patients, will only be recorded within PDS) PID-7 Patient's date of birth.
P-6 Patient - Postcode Patient.address.postalCode (for PDS registered patients, will only be recorded within PDS) PID-11.5 Patient's home postcode.
P-7 Patient - Country of residence Patient.address.country (for PDS registered patients, will only be recorded within PDS) PID-11.6 Patient's home country.
P-9 Patient - Ethnicity Patient.extension:EthnicCategory PID-22 Patient's ethnicity. Will have the option 'unknown' available.
P-10 Patient - Sex defined at birth Patient.extension:birthSex PID-8 Patient's phenotypic sex classification as defined at birth based on physical characteristic.
P-12 Patient - GP Practice's 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.
P-13 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.
P-15 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.
P-16 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.
P-42 Patient - ODS code of organisation which assigned local identifier Patient.identifier.assigner.identifier.value PID-3.4 ODS code of the organisation which assigned the local identifier P-16.
P-17 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.
P-18 Patient - Relationship to proband RelatedPerson.relationship NK1-3 Relative's relationship to proband/index.
P-19 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, determined by the patient.
P-20 Patient - Deceased date Patient.deceasedDateTime (for PDS registered patients, will only be recorded within PDS TBC) PID-29 Patient's date of death.
P-21 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 characteristic. Determined by genomic testing.
P-35 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.
P-37 Patient - Local pedigree/family identifier Group.identifier Additional identifiers under PID-3 Patient's genetic/pedigree number which links their family.
P-39 Patient - Reason for inclusion in genomic test request ServiceRequest.note (tagged with MDS question code via extension) N/A though could be added to NTE elements related to OML_O21 Reason patient has been included in genomic test request, such as to support proband testing or providing own genomic reporting.