Clinical headings

Clinical headings are created by bodies such as the PRSB and are used to add structure to the FHIR instance.

Across the GLHs, there is a lack of standardisation within paper based Non-WGS Test Order Forms used for both Cancer and Rare Disease. To enable interoperability and ensure the provision of end-to-end visibility on the test order, a standardised master data set (MDS) has been compiled, which serves all scenarios and test types. The MDS has been mapped to each test type in the genomic test directory, effectively creating a by-test mapping and therefore the minimum data set requirements for each permutation of the future test order forms.

The standardisation of the Non-WGS Test Order form is currently underway. Fields within the test order forms (Non-WGS and WGS) are specified as Mandatory, Optional, or Mandatory-if (applicable to test type) based on the MDS. The functional requirements for test ordering include an ability to configure forms based on the MDS and an ability to update forms (including introduction and modification of data fields through change control processes) at a regional level. For further details, refer to the draft copies of the Non-WGS Test Order forms in the links to documentation section.

In the case of Genomics, no PRSB clinical headings have been used but sections from the core Genomics Minimum Dataset and their mappings have been recreated on the following pages. The current dataset is based on MDS v1.0, available on the NHS Futures website. These include designations of mandatory vs. optional fields per test category, which have been excluded from the following tables for readability.

The sub pages provide guidance about the heading and the structure required when representing this information in FHIR.

For preliminary reports included in a test order, e.g. Pathology etc. These should be included as "presentedForm" attachments in DiagnosticReports with a small clinical conclusion included in the "conclusion" field. If supported, sending systems can also send coded Observations following the Genomics-Observation profile.

Specialist Testing Requirements

The Master Data Set (MDS) sets out the data required by both the requester and lab, to accept and progress the test request. In addition to the mandatory and optional fields identified on the Non-WGS and WGS test order forms, there may be additional specialist testing requirements needed to progress the test.

For example, to request an NIPD test the following additional information is required:

  • Identification of Foetal Phenotypic sex (Mandatory)- Male/Female/ Undetermined/ Unknown (free text field)
  • Foetal Count (Mandatory) -identification of number of fetuses
  • Foetal ID: practices for recording the ID may vary across local organisations
  • Pregnancy details including capture of pregnancy type (spontaneous pregnancy, IVF or surrogacy and age of egg donor)
  • Ultrasound or MRI Reports (Optional)

The requirement for electronic test order forms is to allow for configuration and inclusion of additional specialist testing needs. The by test mapping is currently in progress and requires input from the GMS to progress with inclusion of the additional requirements into the alpha phase.

Mapping to HL7v2/IHE

The current genomics space largely uses HL7 v2. There are multiple versions of HL7 v2 being used and many local variations on the standards.

The long term plan is to move to FHIR R4 UK Core, but as this is a risk to delivering the alpha for the test order service the following options for transforming the HL7 v2 messages to FHIR for the test order service are being considered:

  1. Transform HL7 v2 messages within the test order service
  2. Suppliers perform their own mapping of HL7 v2 to FHIR and interact with the test order service using the FHIR APIs
  3. Centrally define a mapping from one or two of the most common HL7 v2 versions to FHIR, so that it can be given to suppliers to implement.
  4. Transformation Component/Service, deployed locally

The following are currently inside the scope of this work (matched to IHE Pathology and Laboratory Medicine, PaLM, profiles):

  • Test requesting procedure - IHE Laboratory Testing Workflow (LTW)
  • DiagnosticReport distribution - IHE Sharing Laboratory Reports (XD-LAB)
  • Send-away test communications - IHE Inter-Laboratory Workflow (ILW)
  • Requests for further clinical information - IHE Laboratory Clinical Communications (LCC)
  • Sample event tracking - IHE Specimen Event Tracking (SET)

The following are currently outside the scope of this work

  • Laboratory device integration - IHE Laboratory Device Automation (LDA)
  • Internal laboratory procedures - IHE Laboratory Analytical Workflow (LAW)
  • Point of care testing - IHE Laboratory Point of Care Testing (LPOCT)
  • Sample identification - IHE Laboratory Specimen Barcode Labelling (LBL)
  • Local lab code sharing - IHE Laboratory Code Set Distribution (LCSB)
  • Structured reporting - IHE Anatomic Pathology Structured Report (APSR)

The original order message in FHIR has been mapped to the HL7v2.5.1 OML Laboratory Order Message (event O21). as defined withing the IHE PaLM Laboratory Testing Workflow Technical Framework. The mappings provided in the following tables are meant as a guide to support uplifting current HL7v2 interfaces within the Genomic Order Comms ecosystem, not as a recommendation on the representation of FHIR concepts within HL7v2.

Further pages may be added to include additional mappings to FHIR, such as:

  • Mapping another data standard to FHIR
  • Mapping from another version of a HL7 standard
  • Mapping data items defined in a clinical domain to FHIR

The mapping may be at a resource level or Bundle level.

These pages provide mapping of the business entities and data to FHIR resources. The constraints that need to be applied to each FHIR resource using the UK Core profiles is provided on the individual profile pages elsewhere within this Implementation Guide.

Requesting Clinician

Purpose

To know who to contact with questions or clinical results and how they should be contacted.

Notes

Mapped to the requestor of the ServiceRequest. Usage of HealthcareService and Location resources still to be determined.

It is expected that practitioner and organization details will be referenced from PractitionerRole resources (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.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Requestor - Full name ServiceRequest.requester( PractitionerRole.practitioner( Practitioner.name ) ) ORC-12 Requestor's full name.
Requestor - Job Title ServiceRequest.requester( PractitionerRole.code ) STF-18 Requestor's job title.
Requestor - Current Specialty ServiceRequest.requester( PractitionerRole.specialty ) PRA-5 Requestor's current specialty.
Requestor - Phone ServiceRequest.requester( PractitionerRole.telecom:system=phone ) ORC-14 Requestor's phone number.
Requestor - Email address ServiceRequest.requester( PractitionerRole.telecom:system=email ) STF-15 Requestor's email address.
Requestor - Organization name. ServiceRequest.requester( PractitionerRole.organization( Organization.name ) ) ORC-21 Requestor's organization name.
Requestor - Organization address. ServiceRequest.requester( PractitionerRole.organization( Organization.address ) ) ORC-22 Requestor's organization address.
Requestor - Organization ODS code. ServiceRequest.requester( PractitionerRole.organization( Organization.identifier ) ) ORC-21.10 Requestor's organization ODS code.
Requestor - Department name ServiceRequest.requester( PractitionerRole.healthcareService( HealthcareService.name ) ), could alternatively use PractitionerRole.healthcareService.display to reduce resources in message or PractitionerRole.specialty if mapped to clinical specialty TBC STF-8 Requestor's department name.
Requestor - Professional registration number ServiceRequest.requester( PractitionerRole.practitioner( Practitioner.identifier ) ) ORC-12.1 Requestor's professional registration number such as their GMC number.
Requestor - Professional registration number type ServiceRequest.requester( PractitionerRole.practitioner( Practitioner.identifier.system ) ) ORC-12.9 Requestor's professional registration number type such GMC.
Requestor - Genomic report delivery method ServiceRequest.requester( PractitionerRole.telecom.rank=1 ) STF-16 Requestors report preferred delivery method.
Requestor - Central email for address and reporting (many) Additional ServiceRequest.requester( PractitionerRole.telecom:system=email ) optionally marked with extension:contactpoint-comment indicating reporting, may need to be additionally indicated in NEMS subscription TBC STF-15 Central email address provided by the requestor.

Additional Contact

Purpose

To know who additionally should be contacted with questions or clinical results and how they should be contacted.

Notes

Mapped to an extension on the ServiceRequest, in review.

It is expected that practitioner and organization details will be referenced from PractitionerRole resources (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.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Additional contact - Full name ServiceRequest.extension:additionalContact( PractitionerRole.practitioner( Practitioner.name ) ) Additional STF segment (STF-3), possibly referenced from the STF segment for the requester via STF-14 Additional contact's full name.
Additional contact - Job Title ServiceRequest.extension:additionalContact( PractitionerRole.code ) STF-18 Additional contact's job title.
Additional contact - Current Specialty ServiceRequest.extension:additionalContact( PractitionerRole.specialty ) PRA-5 Additional contact's current specialty.
Additional contact - Phone ServiceRequest.extension:additionalContact( PractitionerRole.telecom:system=phone ) STF-10 Additional contact's phone number.
Additional contact - Email address ServiceRequest.extension:additionalContact( PractitionerRole.telecom:system=email ) STF-15 Additional contact's email address.
Additional contact - Organization name, address and ODS code. ServiceRequest.extension:additionalContact( PractitionerRole.organization( Organization.name ) ) STF-9.2 Additional contact's organization name.
Additional contact - Organization address. ServiceRequest.extension:additionalContact( PractitionerRole.organization( Organization.address ) ) STF-11 Additional contact's organization address.
Additional contact - Organization ODS code. ServiceRequest.extension:additionalContact(PractitionerRole.organization( Organization.identifier ) ) STF-9.1 Additional contact's organization ODS code.
Additional contact - Department name ServiceRequest.extension:additionalContact(PractitionerRole.healthcareService( HealthcareService.name ) ), could alternatively use PractitionerRole.healthcareService.display to reduce resources in message STF-8 Additional contact's department name.
Additional contact - Professional registration number ServiceRequest.extension:additionalContact(PractitionerRole.practitioner( Practitioner.identifier ) ) STF-2.1 Additional contact's professional registration number such as their GMC number.
Additional contact - Professional registration number type ServiceRequest.extension:additionalContact(PractitionerRole.practitioner( Practitioner.identifier.system ) ) STF-2.3 Additional contact's professional registration number type such GMC.
Additional contact - Genomic report delivery method ServiceRequest.requester( PractitionerRole.telecom.rank=1 ) STF-16 Additional contact's report preferred delivery method.
Additional contact - Central email for address and reporting (many) Additional ServiceRequest.extension:additionalContact( PractitionerRole.telecom:system=email ), may need to be additionally indicated in NEMS subscription STF-15 Central email address provided by the additional contact.

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 - Is relative N/A determined through patient attached to ServiceRequest.subject N/A determined though first PID segment in OML message (relatives referenced through NK1 segments) Confirmation if this patient is the reported-on patient or a supplementary relative.
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 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 - 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 - 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 PID-30 Patient's alive or deceased status.
Patient - Date of death Patient.deceasedDateTime PID-29 Patient's date/time of death.
Patient - Relationship to proband RelatedPerson.relationship NK1-3 Relative's relationship to proband/index.
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. Determined by the Dr / birth gender.
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 - 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 - Sexual orientation Observation.code( subject=Patient ) OBX-5 with appropriate SNOMED/READ/LOINC code Patient's sexual orientation.
Patient - Karyotypic sex Observation.code( subject=Patient ) OBX-5 with appropriate SNOMED/READ/LOINC code Patient's genomic / karyotypic characteristics. Determined after laboratory testing.
Patient - GP Practice ODS Code Patient.generalPractitioner( PractitionerRole.organization( Organization.identifier ) ) PD1-4.14 Patient's GP practice ODS code.
Patient - GP full name Patient.generalPractitioner( PractitionerRole.practitioner( Practitioner.name ) ) PD1-4.2 and PD1-4.3 Patient's GP's full name.
Patient - GP GMC number Patient.generalPractitioner( PractitionerRole.practitioner( Practitioner.identifier ) ) 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 ) OBX-5 with appropriate SNOMED/READ/LOINC code Patient's pregnancy status.
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 OBR segments with appropriate codes Type of conception.
Patient - Fetal karyotypic sex Observation.code( subject.display="fetus" ) OBX-5 with appropriate SNOMED/READ/LOINC code Absence or presence of Y chromosome in the fetus.
Patient - Had transplant Inferred through presence of Procedure( subject=Patient ) with code under 77465005 - Transplantation 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 ) 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 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 ) 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 - 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 - Height (m) Observation.valueQuantity( code=54871000237100, subject=Patient) OBX-5 Patient's height.

Fetus

Purpose

To support genetic interpretation of tests and samples for fetuses. To provide a clear divide between mother and fetus and support the management of multiple fetuses.

Notes

Mapped to its own Patient resource, optionally tagged via a proposed birthStatus extension or future dated EDD in place of birthDate, as well as linked observations.

Correct representation of fetal data is under review within the Interoperability Standards Team ans is subject to change

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Fetus - Is sample for fetal or unregistered neonate Patient indicated as fetus through either birthStatus extension on Patient resource or future dated birthDate, Specimen.subject N/A PID-7 could be used if birthDate discrimination is chosen Confirmation that the test is for a fetus or an unregistered neonate.
Fetus - Local identifier Patient.identifier:system != https://fhir.nhs.uk/Id/nhs-number PID-3 where PID-3.5 = 2.16.840.1.113883.2.1.3.2.4.18.24 Fetus identification code other than NHS number.
Fetus - Karyotypic sex Observation.code( subject=Patient ) OBX-5 with appropriate SNOMED/READ/LOINC code Absence or presence of X chromosome in the fetus.
Fetus - Observed sex Patient.gender PID-8 Fetus phenotypic sex classification. Estimated physical characteristics determined by ultrasound. Gender for PLCM.
Fetus - Are multiple fetuses being tested N/A Inferred through inclusion of multiple Patient resources attached to test order N/A inferred though inclusion of multiple PID segments attached to OML message Confirmation that multiple fetuses are being tested.
Fetus - Is testing for fetal loss from 24 weeks of gestation Inferred through inclusion observation/condition for fetal loss (code under 363681007) with date later than 24 weeks after pregnancy observation Inferred though difference in OBX-14 for pregnancy and miscarriage/loss observations Confirmation that the test is for a loss of pregnancy after 24 weeks gestation.
Fetus - Additional details Clinical resources referencing fetal Patient resource NTE/PRB/OBX segments related to PID for fetus Further details for a fetal test.

Record of Discussion

Purpose

For recording consent of patient data for research, based off the paper form available from the Genomics GitHub repository

Notes

WGS Only RoD forms will be stored as QuestionnaireResponse resources following the structure of the RoD Questionnaire resource, Questionnaire-Genomic Testing. Answers are not currently linked to structured identifiers, e.g. for patient and responsible clinician, this will be reviewed in a future release.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
RoD - Included N/A - Inferred through inclusion of RoD Questionnaire Response N/A - Inferred through inclusion of CON segment Has RoD been included with request.
RoD - Patient category Answer to RoD question with linkId patientCategory CON-16 Confirmation of who made the RoD decisions.
Test type Answer to RoD question with linkId testType CON-2 If the test is WGS Cancer or WGS rare disease.
RoD - Research opt out reason Answer to RoD question with linkId reasonsforChoiceA CON-22 Why patient has opted out of research.
RoD - Remote consent Answer to RoD question with linkId remoteConsent CON-10 Where consent has been recorded on behalf of the patient via remote confirmation.
RoD - Recording clinician Answer to RoD question with linkId healthcareProfessionalName STF segment attached to CON Name of the clinician who recorded the RoD details.
RoD - Responsible clinician Answer to RoD question with linkId responsibleClinician STF segment attached to CON Name of the clinician who is responsible for the patient's genomic test request.
RoD - Record of discussion form - copy attached Consent.sourceAttachment (or QuestionnaireResponse attached directly to message, TBC) CON-19 Marker to confirm on a test request form that an RoD has been included.
RoD - Patient conversation taken place, ROD form to follow Consent.status (TBC) Inferred through CON-19 value Marker to confirm RoD conversation has taken place but will be sent separately.
RoD - Patient choice status Answer to RoD question with linkId researchConfirmation2 CON-11 Indication of the patient consenting to the genomic test request.
RoD - Has research participation been discussed Answer to RoD question with linkId researchConfirmation1 Inferred through CON-12 Marker to confirm RoD conversation has taken place.
RoD - Signature Answer to RoD question with linkId patientSignature N/A not in scope for HL7v2 Copy of wet signature or valid e-signature.
RoD - Document/Link N/A - Presence of DiagnosticReport in message N/A not in scope for HL7v2 A copy of/or link to the previous genomic or non genomic report.

Test Request

Purpose

Elements are included for the billing approach, TAT/SLA tracking and prioritisation. To confirm validity of urgency and apply lower level prioritisation. To know which test has been requested, which further tests are required within this request and how many patients are being tested within this request.

Notes

Mapped to ServiceRequest, extensions are still in review. CI and CITT codes for genomic tests are pending addition to SNOMED-CT

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Test request - Test request id ServiceRequest.identifier ORC-2 Unique id to identify this test request.
Test request - Payment status ServiceRequest.extension:coverage IN1-15 How the test request is funded. The current ValueSet for this field needs expansion, pending finalization of the MDS
Test request - Date and time request sent ServiceRequest.authoredOn ORC-9 Date and time the test request was made.
Test request - Is urgent ServiceRequest.priority TQ1-9 Confirmation if the test request is urgent.
Test request - Urgency reason ServiceRequest.extension:priorityReason N/A could possibly use TQ1-10 If urgent, the test request urgency reason.
Test request - Test Directory version Inferred though version included in system URL, ServiceRequest.code.coding.system OBR-4.3 The version of Test Directory the requested CI/CITT code relates to.
Test request - CI code ServiceRequest.code OBR-4 The code which identifies the requested test. Provided by Test Directory.
Test request - CITT code ServiceRequest.code OBR-4 The code (including decimal) which identifies the requested test. Provided by Test Directory.
Test request - CI code for multipurpose CITT ServiceRequest.orderDetail NTE segment attached to OBR The code which identifies the test to be actioned when the CITT code is multipurpose.
Test request - Reason for testing ServiceRequest.reasonCode ORC-16 The reason for a genomic test.
Test request - Reason for reanalysis Additional ServiceRequest.reasonCode/reasonReference elements OBR-13 segment linked to ORC The reason for a genomic test.
Test request - Detail of reason for reanalysis ServiceRequest.supportingInfo elements NTE segments linked to OBR segment for reanalysis reason The detail associated to the reason reanalysis has been requested.
Test request - Type of reanalysis ServiceRequest.orderDetail Additional NTE segments attached to OBR The type of reanalysis which has been requested.
Test request - DNA storage information ServiceRequest.orderDetail Additional NTE segments attached to OBR If the reason for testing is DNA storage, this captures further detail.
Test request - Patient set to be tested N/A - Determined through number of ServiceRequests in the test order N/A - determined through number of ORC segments within OML^O21 message Confirmation if the test is a singleton, duo or trio.
Test request - Count of patients to be tested N/A - Determined through number of Patients referenced in ServiceRequests in test order N/A - determined through number of PID segments referenced from ORC segments within OML^O21 message Count of patients to be tested.
Test request - Date report required by ServiceRequest.occurrenceDateTime OBR-8 The date a completed genomic report is required by.
Test request - Further information ServiceRequest.supportingInfo Additional segments attached to ORC/OBR Further information regarding the test request.

PLCM activity

Purpose

For PLCM activity submissions.

Notes

Derived from existing fields used for clinical/operational purposes in the test order/response.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
PLCM activity - NGIS referral identifier ServiceRequest.identifier ORC-3 NGIS referral identifier
PLCM activity - Financial month Derived from ServiceRequest.authoredOn Derived from ORC-9 The month in which the PLCM activity occurred.
PLCM activity - Financial year Derived from ServiceRequest.authoredOn Derived from ORC-9 The financial year in which the PLCM activity occurred.
PLCM activity - Date and time dataset created Derived from DiagnosticReport.effectiveDateTime based on ServiceRequest Derived from OBR-7 in the ORL response message for the activity based on the OML request The date and time a file was created prior to submission to Data Landing Portal (DLP).
PLCM activity - Activity start date and time Derived from Task.executionPeriod.start for activity based on ServiceRequest Derived from TQ1-7 in the ORL response message for the activity based on the OML request The date and time of the defined PLCM activity start date for the relevant activity.
PLCM activity - Activity end date and time Derived from Task.executionPeriod.end for activity based on ServiceRequest Derived from TQ1-8 in the ORL response message for the activity based on the OML request The date and time of the defined PLCM activity end date for the relevant activity.
PLCM activity - Patient age at activity date Derived from the difference between Patient.birthDate and Task.executionPeriod.start for the relevant activity Derived from the difference between PID-7 and TQ1-7 for the relevant activity Age of the patient at the date a PLCM activity is undertaken.
PLCM activity - ODS code of organisation submitting to PLCM Task.owner if pulled directly from broker system OBR-32.7 if sourced from principle results interpreter ODS code of the organisation submitting the PLCM data specification.
PLCM activity - ODS code of organisation commissioned to deliver requested test ServiceRequest.performer if pulled directly from broker system PRD-7 where PRD-1=RT ODS code of the organisation commissioned by NHS England to deliver the service.
PLCM activity - ODS code of organisation delivering requested test Task.owner OBX-32.10 ODS code of the organisation delivering the service.
PLCM activity - ODS code of the laboratory site delivering requested test Task.owner( PractitionerRole.healthcareService( HealthcareService.identifier ) ) AFF-2.10 associated with performing organization ODS code of the site on which the laboratory delivering the service is based.
PLCM activity - ODS code of commissioning region Organization.partOf N/A - not in scope for HL7v2 ODS code of the commissioning region.
PLCM activity - Commissioned service category code Derived from ServiceRequest.requester( PractitionerRole.healthcareService ) Derived from STF-8 for requester PLCM category code for the service commissioning the test request.
PLCM activity - Service code Derived from ServiceRequest.code Derived from OBR-4 PLCM Service code to confirm if the test request is for a specialised service.
PLCM activity - Point of delivery code Derived from ServiceRequest.code Derived from OBR-4 PLCM point of delivery code.
PLCM activity - Local point of delivery code Derived from ServiceRequest.code Derived from OBR-4 PLCM local point of delivery code.
PLCM activity - Turnaround time (calendar days) Derived from difference between ServiceRequest.authoredOn and resulting DiagnosticReport.effectiveDateTime Derived from difference between ORC-9 and OBR-7 for resulting report To be populated with the actual turnaround time for the activity expressed in calendar days.
PLCM activity - Turnaround time standard (calendar days) N/A fixed dependent on test type N/A fixed dependent on test type To be populated with the relevant turnaround time standard for the activity expressed in calendar days at TESTREPORT activity stage, else blank.
PLCM activity - Compliant with turnaround time standard (calendar days) N/A derived from fixed standard and current turnaround time N/A derived from fixed standard and current turnaround time To be populated with Y=Yes, N=No at TESTREPORT activity stage, else blank.
PLCM activity - Test method code Derived from ServiceRequest.code Derived from OBR-4 PLCM test method code.
PLCM activity - Sample plating quality control Implied though completion of SpecimenProcessing Task Implied through status recorded in ORC-25 indicating plating quality control had passed Confirmation if the sample plating has passed quality control.
PLCM activity - Sample plating quality control fail code Task.statusReason for SpecimenProcessing Task ORC-25 Sample plating, quality control, fail code.
PLCM activity - Sample volume Specimen.collection.quantity SPM-12 Sample volume in (µl).
PLCM activity - DNA concentration Observation attached to Specimen with code 13925004 and appropriate UCUM unit OBR attached to SPM segment with code 13925004 and appropriate UCUM unit DNA concentration in (ng/ul).
PLCM activity - DNA quantification Observation attached to Specimen with code 13925004 and appropriate UCUM unit OBR attached to SPM segment with code 13925004 and appropriate UCUM unit DNA quantification in (µg).
PLCM activity - Sample category code Derived from Specimen.type Derived from SPM-4 PLCM sample category code.
PLCM activity - Quality score for sequencing N/A Derived from DNA concentration/quantification N/A Derived from DNA concentration/quantification Quality score for sequencing.
PLCM activity - Local report identifier DiagnosticReport.identifier OBR-3 for report Identifier for the issued report
PLCM activity - Test outcome code (Many) DiagnosticReport.result( Observation.code ) OBX-3 elements for resulting report PLCM test outcome codes.

Sample/Biopsy inc germline

Purpose

To track samples, direct storage, handling and testing decisions including ensuring volumes received match what was sent. Further detail which may support testing and interpretation. To enable patient to opt out of having a sample/biopsy stored.

Notes

Mapped to Specimen. Extensions lifted from mCODE are currently under review. Observation codes linked to samples are pending addition to SNOMED-CT

Additional observation code fields from MDS v0.55 mappings are still under review

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Raw specimen/biopsy - Id assigning authority ODS code (many) Specimen.identifier.assigner SPM-2.1.2 Authority who assigned the sample id (e.g. histopathology, SHIMDS, etc). Occurs multiple times.
Raw specimen/biopsy - Is assigning authority a histopathology laboratory (many) Derived from ODS - Specimen.identifier.assigner Derived from ODS - SPM-2.1.2 Confirmation of an assigning authority ODS code being from a histopathology laboratory.
Raw specimen/biopsy - Id (many) Specimen.identifier.value SPM-2 Id of sample provided linked to the previously stated assigning authority. Occurs multiple times.
Raw specimen/biopsy - Sample well identifier Specimen.container.identifier SAC-3 Id of the sample well.
Raw specimen/biopsy - Location details Not in scope for FHIR r4, could use Specimen.note SAC-15 Where a raw specimen/biopsy is in storage and not provided with a request.
Raw specimen/biopsy - WGS specimen type category Specimen.extension:sampleCategory SPM-5 WGS cancer high level category for the specimen.
Raw specimen/biopsy - Type Specimen.type SPM-4 Tissue of origin.
Raw specimen/biopsy - State Specimen.condition SPM-24 How has the specimen been preserved/fixed. Note: The ValueSet for this field is pending review to align with MDSv1.0
Raw specimen/biopsy - Sample preparation (submitted to GLH) Specimen.processing Combination of SPM-6/SPM-24 or NTE segments if other processing How has the specimen has been prepared for the GLH.
Raw specimen/biopsy - Obtained date Specimen.collection.collectedDateTime SPM-17 The time at which the sample/biopsy was obtained from the patient.
Raw specimen/biopsy - Blood component Specific codes under Specimen.type SPM-4 For a blood specimen, confirmation of which blood component the specimen consists of.
Raw specimen/biopsy - Received date Specimen.receivedTime SPM-18 Date at which a specimen was received at a laboratory.
Raw specimen/biopsy - High risk reason Specimen.collection.extension:specimen-specialHandling.valueCoding.code SPM-16.2 The high contamination risk reason for a sample/biopsy.
Raw specimen/biopsy - Solid tumour morphology BodyStructure.morphology( patient=Patient ) Additional SPM-4/5 qualifiers The histology and likely course of development of a tumour.
Raw specimen/biopsy - Solid tumour histological type (topography) BodyStructure.location(patient=Patient) SPM-8 The patient's solid tumour histological type (topography), where the tumour arose.
Raw specimen/biopsy - Biopsy site Specimen.collection.bodySite SPM-8/SPM-9 Site of biopsy.
Raw specimen/biopsy - Skin/Bone affected status Observation.valueBoolean ( code=22201000087104, specimen=Specimen ), assume unaffected if not provided OBX segment with appropriate code If the skin or bone provided is unaffected or affected.
Raw specimen/biopsy - Blasts % Observation.code( code=1022601000000101, specimen=Specimen ) OBX segment with appropriate code Blast count in the specimen/biopsy (Haemonc) - sourced at local SIHMDS.
Raw specimen/biopsy - Neoplastic cell content (%) Observation.code( code=444901007 (TBC), specimen=Specimen ) OBX segment with appropriate code Neoplastic cell content in the specimen/biopsy (Solid Tumour) - sourced at local lab. (%)
Raw specimen/biopsy - Necrosis Observation.code( code=6574001 (TBC), specimen=Specimen ) OBX segment with appropriate code % necrotic cells in specimen volume.
Raw specimen/biopsy - Nucleated cell count Observation.code( code=1022461000000100, specimen=Specimen ) OBX segment with appropriate code Nucleated cell count in the specimen/biopsy (Solid Tumour and Haem-Onc).
Raw specimen/biopsy - Tumour cellularity Observation.code( code=TBC, specimen=Specimen ) The proportion which is tumour nuclei.
Raw specimen/biopsy - Volume Specimen.collection.quantity SPM-12 Volume of provided sample.
Raw specimen/biopsy - Taken alive/post mortem Observation.valueBoolean( code=839021000000109, specimen=Specimen ), true=post-mortem sample, assume taken alive if not provided OBX segment with appropriate code If a sample/biopsy was taken when the patient was alive or deceased.
Raw specimen/biopsy - Maternal cell contamination (MCC) Observation.valueBoolean( code=726741007, specimen=Specimen ), assume no MCC if not provided OBX segment with appropriate code Confirmation if MCC has been excluded from sample.
Raw specimen/biopsy - Family member provided by Specimen.subject PID segment attached to SPM Which family member the specimen is provided by.
Raw specimen/biopsy - Option for products of conception Additional Specimen.collection.extension:specimen-specialHandling with appropriate code/text SPM-15 Future management for products of conception.
Raw specimen/biopsy - Sample to follow N/A implied through absence of Specimen in Test Order message, or Specimen.status=unavailable and missing Specimen.collection.collectedDateTime samples ordered but not collected N/A implied through absence of SPM segment in test order Confirmation that the sample will be sent separately to, and after the test request.
Raw specimen/biopsy - Sample to follow reason Text in ServiceRequest.note field NTE segment attached to ORC Confirmation as to why the sample is being sent after the test request.
Raw specimen/biopsy - Additional specimen/biopsy information Observation resources referencing Specimen for coded information or Specimen.note OBX segments attached to SPM Raw specimen/biopsy - Additional specimen/biopsy information.

Extracted Specimen

Purpose

For testing, obtained from raw specimen To support storage, testing and interpretation.

Notes

Mapped to Specimen. It is expected extracted specimens will be additional specimens referencing the parent specimen via the Specimen.parent field.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Extracted specimen - Id assigning authority ODS code (many) Specimen.identifier.assigner SPM-2.1.2 Authority who assigned the specimen id.
Extracted specimen - Id (many) Specimen.identifier.value SPM-2 Id of sample provided linked to the previously stated assigning authority. Occurs multiple times.
Extracted specimen - Location details Not in scope for FHIR r4, could be attached to Tasks assigned to particular organizations SAC-15 Where a raw specimen is in storage and not provided with a request.
Extracted specimen - Type Specimen.type SPM-4 Tissue of origin.
Extracted specimen - State Specimen.condition SPM-24 How has the specimen been preserved/fixed.
Extracted specimen - Extracted date Specimen.processing.timeDateTime where Specimen.processing.procedure = 62972009, alternatively, could use Specimen.collection.collectedDateTime for the new Specimen OBR-7 attached to processing procedure in SAC-30 Date at which a specimen was extracted from a previous specimen.
Extracted specimen - Additional specimen information Observation resources referencing Specimen for coded information or Specimen.note OBX segments attached to SPM Raw specimen/biopsy - Additional specimen/biopsy information.

Previous Genomic Report

Purpose

To locate previous genomic test reports linked to this service request.

Notes

Mapped to DiagnosticReport. It is expected previous genomic reports will be attached as PDF documents or references to their location will be provided within the genomic test order. Structured genomic reports will be investigated in future stages of the Genomic Medicine Service. Metadata regarding patient/performer details are expected to match previous mappings for these headings above.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Previous genomic report - Report referral summary DiagnosticReport.conclusion OBX-5 Referring clinician's summary of the previous genomic report to support test request.
Previous genomic report - Report file/link DiagnosticReport.presentedForm OBX-5 where OBX-2=ED or RP A copy of/or link to the previous genomic report.
Previous genomic report - Test performed date DiagnosticReport.effectiveDateTime OBX-19 The date a previous genomic test was performed.
Previous genomic report - Report identifier DiagnosticReport.identifier OBX-3 The identifier for the previous genomic report.
Previous genomic report - Patient's first name DiagnosticReport.subject( Patient.name.given ) PID-5.2 attached to OBR The first name of the patient on the previous genomic report.
Previous genomic report - Patient's surname DiagnosticReport.subject( Patient.name.family ) PID-5.1 attached to OBR The surname of the patient on the previous genomic report.
Previous genomic report - Patient's address DiagnosticReport.subject( Patient.address ) PID-11 attached to OBR The address of the patient on the previous genomic report.
Previous genomic report - Patient's post code DiagnosticReport.subject( Patient.address.postalCode ) PID-11.5 attached to OBR The postcode of the patient on the previous genomic report.
Previous genomic report - Patient's country DiagnosticReport.subject( Patient.address.country ) PID-11.6 attached to OBR The country of the patient on the previous genomic report.
Previous genomic report - Patient's date of birth DiagnosticReport.subject( Patient.birthDate ) PID-7 attached to OBR The date of birth of the patient on the previous genomic report.
Previous genomic report - Patient's NHS number DiagnosticReport.subject( 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 The NHS number of the patient on the previous genomic report.
Previous genomic report - Patient's alternative identifier DiagnosticReport.subject( 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 The alternative identifier of the patient on the previous genomic report.
Previous genomic report - Patient's relationship to requesting patient DiagnosticReport.subject( Patient.link( RelatedPerson.relationship ) ) NK1-3 The relationship of the patient on the previous genomic report to the requesting patient.
Previous genomic report - Patient's clinical genetics number DiagnosticReport.subject( Patient.identifier:system = TBC ) PID-3 The individual clinical genetic number of the patient on the previous genomic report.
Previous genomic report - Patient's pedigree number DiagnosticReport.subject( Patient.identifier:system = https://fhir.nhs.uk/Id/genomics-pedigree-number ) PID-3, system TBC The pedigree number of the patient on the previous genomic report which links their family.
Previous genomic report - Report lab test number DiagnosticReport.basedOn( ServiceRequest.identifier ) ORC-2 The lab test number from the previous genomic report.
Previous genomic report - Report of genetic analysis DiagnosticReport.conclusionCode OBR-5 The clinical outcomes from the previous genomic report.
Previous genomic report - Report performer full name DiagnosticReport.performer( PractitionerRole.practitioner( Practitioner.name ) ) OBX-16 The full name of the individual that authored the previous genomic test report.
Previous genomic report - Report performer organisation ODS code DiagnosticReport.performer( PractitionerRole.organization( Organization.identifier ) ) OBX-23.10 The organisation ODS code of the individual that authored the previous genomic test report.
Previous genomic report - Original requester full name DiagnosticReport.basedOn( ServiceRequest.requester( PractitionerRole.practitioner( Practitioner.name ) ) ) ORC-12 The full name of the individual that requested the previous genomic test report.
Previous genomic report - Original requester organisation ODS code DiagnosticReport.basedOn( ServiceRequest.requester( PractitionerRole.organization( Organization.identifier ) ) ) ORC-21.10 The organisation ODS code of the individual that requested the previous genomic test report.
Previous genomic report - Original requester reason for request DiagnosticReport.basedOn( ServiceRequest.reasonCode ) ORC-16 The reason for requesting the previous genomic test report.

Previous Diagnostic Report

Purpose

To locate previous Non-Genomic diagnostic test reports linked to this service request.

Notes

Mapped to DiagnosticReport. Observations/test results within the DiagnosticReport are expected to be included as referenced Observation resources. It is expected previous diagnostic reports will have a minimal amount of information coded for automated interpretation but reports can be attached as PDF documents or references to their location provided, as with Genomic reports.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Previous non genomic report - Report referral summary DiagnosticReport.conclusion OBX-5 Referring clinician's summary of the previous non genomic report to support test request.
Previous non genomic report - Report file/link DiagnosticReport.presentedForm OBX-5 where OBX-2=ED or RP A copy of/or link to the previous non genomic report.
Previous non genomic report - Test performed date DiagnosticReport.effectiveDateTime OBX-19 The date a previous non genomic test was performed.
Previous non genomic report - Report identifier DiagnosticReport.identifier OBX-3 The identifier for the previous non genomic report.
Previous non genomic report - Test type DiagnosticReport.code OBR-4 A name that describes the previous non genomic report.
Previous non genomic report - Test result value comparator DiagnosticReport.result( Observation.valueQuantity.comparator ) OBX-5 A comparator that may used to indicate whether the actual value is greater or less than the stated value. Applies to numeric values only.
Previous non genomic report - Test result value unit of measure DiagnosticReport.result( Observation.valueQuantity.unit ) OBX-6 The name and code of the unit of measure associated with the test result value. Applies to numeric values only.
Previous non genomic report - Test result reference range low DiagnosticReport.result( Observation.referenceRange.low ) OBX-7 (before operator) The reference range low value.
Previous non genomic report - Test result reference range high DiagnosticReport.result( Observation.referenceRange.high ) OBX-7 (after operator) The reference range high value.
Previous non genomic report - Test result test method DiagnosticReport.result( Observation.method ) OBX-17 The method of testing/observation that was used.
Previous non genomic report - Test result reference range text DiagnosticReport.result( Observation.referenceRange.text ) OBX-7 A human readable text-based description to provide additional information about the reference range. For example, the target population that the reference range applies to and/or differences based on factors such as age or sex.
Previous non genomic report - Test result clinical summary DiagnosticReport.result( Observation.interpretation ) OBX-8 A human readable text-based clinical interpretation of the test result and any additional notes provided by the performing organisation.
Previous non genomic report - Report result DiagnosticReport.conclusionCode OBR-5 Reference to the result(s)/result groups contained in the report.
Previous non genomic report - Report performer full name DiagnosticReport.performer( PractitionerRole.practitioner( Practitioner.name ) ) OBX-16 The full name of the individual that authored the previous non genomic test report.
Previous non genomic report - Report performer organisation ODS code DiagnosticReport.performer( PractitionerRole.organization( Organization.identifier ) ) OBX-23.10 The organisation ODS code of the individual that authored the previous non genomic test report.
Previous non genomic report - Original requester full name DiagnosticReport.basedOn( ServiceRequest.requester( PractitionerRole.practitioner( Practitioner.name ) ) ) ORC-12 The full name of the individual that requested the previous non genomic test report.
Previous non genomic report - Original requester organisation ODS code DiagnosticReport.basedOn( ServiceRequest.requester( PractitionerRole.organization( Organization.identifier ) ) ) ORC-21.10 The organisation ODS code of the individual that requested the previous non genomic test report.
Previous non genomic report - Original requester reason for request DiagnosticReport.basedOn( ServiceRequest.reasonCode ) ORC-16 The reason for requesting the previous non genomic test report.

Patient Clinical Presentation

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

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Further clinical information Linked Condition/Observation resources Linked PRB/OBR segments Clinical information which has not been captured elsewhere.
Further non clinical information. ServiceRequest.note NTE segments in OML message Non-clinical information which has not been captured elsewhere.
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
Tumour sites - Body image diagram TBC Media TBC N/A - not in scope for HL7v2 Image attachment of body with tumour sites highlighted.
Has multiple primary tumours TBC Inferred through multiple Condition.bodySite entries Multiple PRB segments (bodySite for condition not in scope for HL7v2) Does the patient have multiple tumours.
Count of tumours Inferred through number of Condition/Condition.bodysite entries for tumours Multiple PRB segments (bodySite for condition not in scope for HL7v2) How many tumours the patient has.
Site of tumour (many) Condition.bodysite entries Multiple PRB segments (bodySite for condition not in scope for HL7v2) Location of the tumours on the body.
Known/suspected disease Condition.verificationStatus PRB-13 Disease a patient is believed, known to have, or be at risk of developing.
Date of diagnosis Condition.recordedDate PRB-7 The patient's date of diagnosis.
Disease status Condition.clinicalStatus PRB-14 If the patient is affected, unaffected, or it is unknown.
Phenotypic details (Many) Condition.code with HPO system Additional PRB segments (PRB-3) The HPO (or alternative ontology as appropriate) term names for the observable disease traits.
Date of disease onset Condition.onsetDateTime PRB-16 The date when a change in patients health was first noted in line with suspected diagnosis.
Pedigree details/diagram Condition.evidence.detail( reference( FamilyMemberHistory, Media ) ) N/A not in scope for HL7v2, could be added as additional PRB segments related to relatives The patient's pedigree details/diagram (inc family history of cancer).
Disease penetrance Inferred through Condition.evidence.detail( reference( FamilyMemberHistory.condition ) ) elements for each individual PRB segments related to relatives, though PRB-12 could be used Confirms if all individuals with a disease show clinical symptoms or if there are carriers who do not.
Solid tumour type Specific Condition.code e.g. child concepts of 128462008 for metastatic tumours PRB-3 The patient's solid tumour type.
Liquid tumour type Specific Condition.code, e.g. 91861009 for AML PRB-3 The patient's liquid tumour type.
Laterality of hearing loss Specific Condition.code under Hearing loss e.g. 473424007 PRB-3 Laterality of the hearing loss i.e. bilateral or unilateral.
Fetal maternal screening genotype Presence of Condition.code 62621000119107 for Fetal hemoglobinopathy (disorder) PRB-3 Maternal screening genotype for haemoglobinopathy testing.
Is patient on TKI therapy Presence of in-progress Procedure with code 1237262009 for Receptor tyrosine-protein kinase erbB-2 inhibitor therapy (procedure) OBR-44 If the patient is on tyrosine kinase inhibitor therapy.
Is patient in treatment free remission Condition.clinicalStatus = remission PRB-14 If the patient in treatment free remission.
Legal considerations TBC Needs more specificity to properly model TBC Legal considerations for a given request.
Symptoms at onset Condition.evidence.code OBX segments attached to PRB The patient's symptoms at onset.
ISTH BAT score Observation.valueQuantity (note: no SNOMED code currently exists for the ISTH-BAT tool so this will need to be coded as text within Observation.code) OBX-5 Bleeding score - high bleeding score is associated with the presence of an inherited bleeding disorder
Fetal paternal screening genotype Condition.code 80141007 for Hemoglobinopathy (disorder) attached to paternal Patient resource (or associated carrier code) PRB-3 Paternal screening genotype for haemoglobinopathy testing.
Expected maternity unit - Organisation name TBC Future dated Encounter with referenced serviceProvider ROL segment attached to PV1 Requesting clinician's organisation name.
Expected maternity unit - Organisation address TBC Future dated Encounter with referenced serviceProvider ROL segment attached to PV1 Requesting clinician's organisation address.
Expected maternity unit - Organisation ODS code TBC Future dated Encounter with referenced serviceProvider ROL segment attached to PV1 Requesting clinician's organisation ODS code.
Expected maternity unit - Department name TBC Future dated Encounter with referenced serviceProvider ROL segment attached to PV1 Requesting clinician's department name.
MODY probability calculator score Observation with code under 609561005 for Maturity-onset diabetes of the young (disorder) OBX-5 Exeter's diabetic risk calculator
Insulin treated within 6 months of diagnosis Presence of Procedure with appropriate Insulin Therapy code with performed[x] within six months of the ServiceRequest.authoredOn date OBR-44 Has the patient been treated for insulin within the last 6 months of diagnosis.
Diagnosis during pregnancy Overlap of Condition.recordedDate with Observation.effectivePeriod for pregnancy PRB segment overlapping OBC for pregnancy Was the patient diagnosed during pregnancy
Patient BMI at time of genomic test request Observation with code 60621009 for Body mass index (observable entity) with effectiveDateTime same as ServiceRequest.authoredOn OBX-5 Patient BMI at time of genomic test request
Patient BMI at time of diagnosis Observation with code 60621009 with effectiveDateTime same Condition.recordedDate OBX-5 Patient BMI at time of diagnosis
Maternal BMI at time of request Observation with code 60621009 attached to maternal Patient resource with effectiveDateTime same as ServiceRequest.authoredOn OBX-5 Maternal body mass index at time of request.
Paternal BMI at time of request Observation with code 60621009 attached to paternal Patient resource with effectiveDateTime same as ServiceRequest.authoredOn OBX-5 Paternal body mass index at time of request.
Initial therapy: Insulin subtype - Units per dose First MedicationStatement.dosage.doseAndRate.doseQuantity with appropriate medicationCodeableConcept for Insulin RXA-6 Initial therapy: Insulin subtype - Units per dose
Initial therapy: Insulin subtype - Frequency First MedicationStatement.dosage.timing.repeat with appropriate medicationCodeableConcept for Insulin RXA-12 Initial therapy: Insulin subtype - Frequency
Initial therapy: Insulin subtype - Oral hypoglycemic agents (OHA) subtype units per dose First MedicationStatement.dosage.doseAndRate.doseQuantity with appropriate medicationCodeableConcept for Insulin OHA (codes under 420100005) RXA-6 Initial therapy: Insulin subtype - Oral hypoglycemic agents (OHA) subtype units per dose
Initial therapy: Insulin subtype - Oral hypoglycemic agents (OHA) subtype frequency First MedicationStatement.dosage.timing.repeat with appropriate medicationCodeableConcept for Insulin OHA (codes under 420100005) RXA-12 Initial therapy: Insulin subtype - Oral hypoglycemic agents (OHA) subtype frequency
Current therapy: Insulin subtype - Units per dose MedicationStatement.dosage.doseAndRate.doseQuantity with appropriate medicationCodeableConcept for Insulin RXA-6 Current therapy: Insulin subtype - Units per dose
Current therapy: Insulin subtype - Frequency MedicationStatement.dosage.timing.repeat with appropriate medicationCodeableConcept for Insulin RXA-12 Current therapy: Insulin subtype - Frequency
Current therapy: Insulin subtype - Oral hypoglycaemic agents (OHA) subtype units per dose MedicationStatement.dosage.doseAndRate.doseQuantity with appropriate medicationCodeableConcept for Insulin OHA (codes under 420100005) RXA-6 Current therapy: Insulin subtype - Oral hypoglycaemic agents (OHA) subtype units per dose
Current therapy: Insulin subtype - Oral hypoglycaemic agents (OHA) subtype frequency MedicationStatement.dosage.timing.repeat with appropriate medicationCodeableConcept for Insulin OHA (codes under 420100005) RXA-12 Current therapy: Insulin subtype - Oral hypoglycemic agents (OHA) subtype frequency
Neonatal hypoglycemia treatment details Procedure/MedicationStatement with appropriate code for treatment and reasonCode=52767006 OBR/RXA segments Newborn hypoglycemia treatment details.
Neonatal hypoglycemia treatment start date Procedure.performedPeriod.start / MedicationStatement.effectivePeriod.start OBR-7 Newborn hypoglycemia treatment start date.
Neonatal hypoglycemia treatment end date Procedure.performedPeriod.end / MedicationStatement.effectivePeriod.end OBR-8 Newborn hypoglycemia treatment end date.
Birth weight Observation with code 364589006 OBX-5 Weight at birth in grams.
Diabetic complications Observation/Condition resources referencing original Diabetes Condition OBX/PRB segments Diabetic complications
Insulin dose at presentation MedicationStatement.dosage.doseAndRate.doseQuantity with appropriate medicationCodeableConcept for Insulin and effectivePeriod overlapping Encounter date RXA-6 Insulin dose at presentation (U/kg/day)
Insulin dose at time of genomic test request MedicationStatement.dosage.doseAndRate.doseQuantity with appropriate medicationCodeableConcept for Insulin and effectivePeriod overlapping ServiceRequest.authoredOn date RXA-6 Insulin dose at time of request (U/kg/day)
Is diabetes in remission Inferred through Condition.clinicalStatus for Diabetes Has patient's diabetes gone into remission.
Date of diabetes remission Either inferred though history of changes to Condition resource or Condition.note NTE segment attached to PRB Date patient's diabetes went into remission.
Is diabetes in relapse Inferred through Condition.clinicalStatus for Diabetes PRB-14 Has patient's diabetes relapsed.
Date of diabetes relapse Either inferred though history of changes to Condition resource or Condition.note Date of diabetes relapse.
Current exocrine pancreatic treatment Procedure/MedicationStatement for Conditions with exocrine/pancreatic codes OBR/RXA segments Is patient on exocrine pancreatic treatment.
Exocrine pancreatic treatment start date MedicationStatement.effectiveDateTime or Procedure.performedDateTime RXA-3 Date exocrine pancreatic treatment started.
Thyroid gland state Condition.code with SNOMED code for issue PRB-3 State of thyroid gland.
Pituitary tumour type Condition.code with appropriate SNOMED code under 127024001 PRB-3 Pituitary tumour type
Pancreatic tumour type Condition.code with appropriate SNOMED code under 126859007 PRB-3 Pancreatic tumour type
Phaeochromocytoma Condition.bodySite, with appropriate Condition.code under SNOMED code 302835009 Not in scope for HL7v2 Phaeochromocytoma laterality
Paraganglioma location Condition.bodySite, with appropriate Condition.code under SNOMED code 302833002 Not in scope for HL7v2 Paraganglioma location
Duration of hyperinsulism Difference between Condition.onsetDateTime and abatementDataTime for code 83469008 PRB-9 - PRB-16 Duration of hyperinsulism
Current treatment Set of MedicationStatement.medicationCodeableConcepts with effectivePeriod overlapping current time or status active RXA-5 What is their current treatment to understand responsiveness.
Current treatment dose with units MedicationStatement.dosage for treatment RXA-6 Dose with units
Had response to current treatment MedicationStatement.note (could include observations/condition resources to infer response but this may be difficult to interpret NTE attached to RXA Had response to current treatment
Name of other medications tried Additional MedicationStatement resources RXA segments Name of other medications tried
Duration other medications tried MedicationStatement.effectivePeriod RXA-3 Duration other medications tried
Subcutaneous fat loss areas Observation.bodySite with code 248316006 or child concepts of 248316006 OBX-5 Subcutaneous fat loss from:
Increased fat deposition areas Observation.bodySite with code 248313003 Not in scope for HL7v2 Increased fat deposition location
Has absent reflexes Observation with code 37280007 OBX-5 Has absent reflexes
Absent reflexes detail Observation with child code under 37280007 OBX-5 Absent reflexes detail
Progeroid features Condition.code with code 1216939003 or 1220589007 PRB-3 Progeroid features
Severity of hearing loss Condition.code with appropriate code under 15188001 or Condition.note with code 15188001 PRB-3 Free text regarding hearing loss
Retinal degeneration Condition.code with appropriate code under 95695004 or Condition.note with code 95695004 PRB-3 Free text regarding retinal degeneration
Risk factors MedicationStatement resources with certain codes TBC RXA-5 Toxic medication - Prematurity (risk factor for hearing loss) e.g. Baby early birth - Ototoxic medication.
Hepatic vs neurological presentation Condition.code with either Hepatic or Neurological SNOMED codes Outcome of either Hepatic or Neurological.
Suspected inborn error type(s) Condition.code with code under 86095007 and verificationStatus provisional/unconfirmed PRB-3 Suspected inborn error type(s)
Abnormal infection history site TBC Condition.bodySite for relevant infection entries TBC Abnormal infection history Site
Abnormal infection history site organism TBC Condition.bodySite for relevant infection entries with reference to specific body structures TBC Abnormal infection history Site organism
Is on Ig replacement TBC Procedure.code with code 698802001 with status=in-progress TBC If the patient is on immunoglobin replacement treatment.