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 v1.04, 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 or, if supported, use the structured Pathology Lab Report guidance. 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.

It is understood the OML mesage does not cover all concepts defined within the FHIR MDS. In this case, appropriate segments in the HL7v2.5.1 spec have been provided, though how these are to be sent along with the OML message is still to be determined

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.

Healthcare Professional

Purpose

To record details regarding a HCP that is associated with a test order. To know who to contact with questions or clinical results and how they should be contacted.

Notes

Mapped to PractitionerRole. The requestor is mapped to ServiceRequest.requestor. 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
HCP - Genomic test order role Determined through where the PractitionerRole is referenced from e.g. for the requester: ServiceRequest.requestor, Additional contact: ServiceRequest.extension:additionalContact, Sample collection: Specimen.collection.collector etc. multiple possible segments e.g. ORC-12 for requester HCP's function within the genomic test ordering process.
HCP - Full name PractitionerRole.practitioner.display (full delimited name can be retrieved via identifier e.g. from SDS) ORC-12 HCP's full name.
HCP - Job Title PractitionerRole.code (display can be used to capture human readable job role code) CTD-1 HCP's job title.
HCP - Current Specialty PractitionerRole.specialty Additional CTD-1 segments HCP's current specialty.
HCP - Phone PractitionerRole.telecom:system=phone ORC-14 HCP's phone number.
HCP - Email address PractitionerRole.telecom:system=email CTD-5.4 HCP's email address.
HCP - Organization name. PractitionerRole.organization.display (full delimited name can be retrieved via identifier e.g. from ODS) ORC-21 HCP's organization name.
HCP - Organization address. PractitionerRole.organization (retrieved via ODS) ORC-22 HCP's organization address.
HCP - Organization ODS code. PractitionerRole.organization.identifier ORC-21.10 HCP's organization ODS code.
HCP - Department name PractitionerRole.healthcareService.identifier, could alternatively use PractitionerRole.healthcareService.display to record human readable version or PractitionerRole.specialty if mapped to clinical specialty TBC Additional CTD-1 segments HCP's department name.
HCP - Professional registration number PractitionerRole.practitioner.identifier ORC-12.1 HCP's professional registration number such as their GMC number.
HCP - Professional registration number type PractitionerRole.practitioner.identifier.system ORC-12.9 HCP's professional registration number type such GMC.
HCP - Genomic report delivery method PractitionerRole.telecom.rank=1 CTD-6 HCP report preferred delivery method.
HCP - Central email for address and reporting (many) Additional PractitionerRole.telecom:system=email marked with extension:contactpoint-comment indicating reporting, may need to be additionally indicated in NEMS subscription depending on notification method used TBC Additional CTD segment (CTD-5.4) Central email address provided by the HCP.

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.

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 - 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 - Observed sex Patient.gender PID-8 Fetus' phenotypic sex classification. Estimated physical characteristic. Currently determined by ultrasound. Gender for PLCM.
Fetus - Chromosomal sex Observation.code( subject=Patient, code = code under 734840008 or 95462004 as examples ) OBX-5 with appropriate SNOMED/READ/LOINC code Fetus' genomic / karyotypic characteristic. Determined by genomic testing.
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 NTE 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 - Life status at time of request 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. PID-30 (OBX segments should be used for types of fetal death) Fetus' alive or deceased status details at the point of test ordering.

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 NTE segment attached to patient with NTE-4=PI Has RoD been included with request.
RoD - Patient category Answer to RoD question with linkId patientCategory CON-16 (for OML, included in RoD, referenced from NTE-3) Confirmation of who made the RoD decisions.
RoD - Recording clinician name Answer to RoD question with linkId healthcareProfessionalName STF segment attached to CON (for OML, included in RoD, referenced from NTE-3) Name of the clinician who recorded the RoD details.
RoD - Record of discussion form - copy attached Consent.sourceAttachment (or QuestionnaireResponse attached directly to message, TBC) CON-19 (for OML, included in RoD, referenced from NTE-3) Marker to confirm on a test request form that an RoD has been included.
RoD - Patient choice status Answer to RoD question with linkId researchConfirmation2 CON-11 (for OML, included in RoD, referenced from NTE-3) 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 (for OML, included in RoD, referenced from NTE-3) Marker to confirm RoD conversation has taken place.
RoD - Remote consent Answer to RoD question with linkId remoteConsent CON-10 (for OML, included in RoD, referenced from NTE-3) Where consent has been recorded on behalf of the patient via remote confirmation.
RoD - Test type Answer to RoD question with linkId testType CON-2 (for OML, included in RoD, referenced from NTE-3) If the test is WGS Cancer or WGS rare disease.
RoD - Research opt out reason Answer to RoD question with linkId reasonsforChoiceA CON-22 (for OML, included in RoD, referenced from NTE-3) Why patient has opted out of research.
RoD - Responsible clinician name Answer to RoD question with linkId responsibleClinician STF segment attached to CON (for OML, included in RoD, referenced from NTE-3) Name of the clinician who is responsible for the patient's genomic test request.
RoD - Patient conversation taken place, ROD form to follow Consent.status (TBC) Inferred through CON-19 value (for OML, included in RoD, referenced from NTE-3) Marker to confirm RoD conversation has taken place but will be sent separately.
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 is pending addition to UK Core
Test request - Date and time request sent ServiceRequest.authoredOn ORC-9 Date and time the test request was made.
Test request - Reason for testing ServiceRequest.reasonCode ORC-16 The reason for a genomic test.
Test request - High level test identifier ServiceRequest.code.coding.code OBR-4.1 The high level id which identifies the requested test. Options provided by Test Directory.
Test request - High level test identifier description ServiceRequest.code.coding.display OBR-4.2 The high level id which identifies the requested test. Options provided by Test Directory.
Test request - Low level test identifier ServiceRequest.code.coding.code OBR-4.1 The low level id which identifies the requested test. Options provided by Test Directory.
Test request - Low level test identifier description ServiceRequest.code.coding.display OBR-4.2 The low level id which identifies the requested test. Options provided by Test Directory.
Test request - Low level multipurpose test identifier ServiceRequest.orderDetail.coding.code OBR-4.1 The low level code which identifies the test to be actioned when the CITT code is multipurpose.
Test request - Low level multipurpose test identifier description ServiceRequest.orderDetail.coding.display OBR-4.2 The low level name of the test to be actioned when the CITT code is multipurpose.
Test request - Count of patients to be tested N/A - Determined through number of Patients referenced in ServiceRequests in test order N/A - for HL7v2, each patient test request SHOULD be sent using a new OML^O21 message Count of patients to be tested.
Test request - Urgency reason ServiceRequest.extension:priorityReason N/A could possibly use TQ1-10 If urgent, the test request urgency reason.
Test request - Reason for reanalysis Additional ServiceRequest.reasonCode elements OBR-13 segment linked to ORC The reason for a genomic test.
Test request - Detail of reason for reanalysis ServiceRequest.supportingInfo elements (if structured, ServiceRequest.note if unstructured TBC) 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 - Is urgent ServiceRequest.priority TQ1-9 Confirmation if the test request is urgent.
Test request - Date report required by ServiceRequest.occurrenceDateTime OBR-8 The date a completed genomic report is required by.
Test request - Recipient ODS code ServiceRequest.performer Normally the recipient of the OML message, potentially could be recorded under ORC-3.2 ODS code of the first organisation which receives the genomic test request.

Primary Sample

Purpose

For samples directly obtained from a patient. 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 v1.04 mappings are still under review

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Primary Sample - Destination organization ODS code Not in scope for FHIR R4, could use Specimen.note or record this information against Task, e.g. inferred through the Task.owner who is intended to receive the specimen (TBC, if required a request to backport Specimen.container.location will be made to support capture of this information) SAC-15 Destination for primary sample.
Primary Sample - Id (many) Specimen.identifier.value SPM-2 Id of sample provided linked to the previously stated assigning authority. Occurs multiple times.
Primary Sample - 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.
Primary Sample - Received date Specimen.receivedTime SPM-18 Date at which a specimen was received at a laboratory.
Primary Sample - Sample storage details Not in scope for FHIR R4, could use Specimen.note or record this information against Task.input (TBC, if required a request to backport Specimen.container.location will be made to support capture of this information) SAC-15 Where a primary sample is in storage or where it needs to be stored.
Primary Sample - Volume Specimen.collection.quantity SPM-12 Volume of provided sample.
Primary Sample - Test Request Id Specimen.request ORC-2, included within the same OML message The id of the associated genomic test being requested.
Primary Sample - 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, within same OML message Patient NHS number.
Primary Sample - 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, within same OML message Patient identification code other than NHS number.
Primary Sample - Obtained date Specimen.collection.collectedDateTime SPM-17 The time at which the sample/biopsy was obtained from the patient.
Primary Sample - Primary Sample Specimen.type SPM-4 Tissue of origin.
Primary Sample - Primary Sample State Specimen.condition SPM-24 How has the specimen been preserved/fixed. Note: The ValueSet for this field is pending review to align with MDSv1.04
Primary Sample - Necrosis Observation.code( code=6574001 (TBC), specimen=Specimen ) OBX segment with appropriate code % necrotic cells in specimen volume.
Primary Sample - 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).
Primary Sample - Tumour nuclear 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. (%)
Primary Sample - Tumour cellularity Observation.code( code=TBC, specimen=Specimen ) OBX segment with appropriate code The proportion which is tumour nuclei.
Primary Sample - Solid tumour morphology BodyStructure.morphology( patient=Patient ), referenced from Specimen.collection.bodysite.extension:bodySiteReference if in reference to a specimen, or referenced from a Condition if in relation to the patient's condition (pending profiling of bodySiteReference backport to R4 Condition) Additional SPM-4/5 qualifiers The histology and likely course of development of a tumour.
Primary Sample - Solid tumour topography BodyStructure.location(patient=Patient), referenced from Specimen.collection.bodysite.extension:bodySiteReference if in reference to a specimen, or referenced from a Condition if in relation to the patient's condition (pending profiling of bodySiteReference backport to R4 Condition) SPM-8 The tumour sample site. eg from colon, stomach etc.
Primary Sample - Biopsy site Specimen.collection.bodySite SPM-8/SPM-9 Site of biopsy.
Primary Sample - 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.
Primary Sample - 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.
Primary Sample - Option for all products of conception Additional Specimen.collection.extension:specimen-specialHandling with appropriate code/text SPM-15 Future management for products of conception.
Primary Sample - Blasts % Observation.code( code=1022601000000101, specimen=Specimen ) OBX segment with appropriate code Blast count in the specimen/biopsy (Haemonc) - sourced at local SIHMDS.
Primary Sample - High infection risk reason Specimen.collection.extension:specimen-specialHandling.valueCoding.code SPM-16.2 The high contamination risk reason for a sample/biopsy.

Sample Preparation

Purpose

Where cell separation is to be applied to a primary sample

Notes

Mapped to Specimen. It is expected processing performed on a specimen will be added to the original Specimen resource unless daughter samples are taken (splitting of the sample prior to processing), in which case a new Specimen resource SHOULD be created

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Sample Preparation - Parent primary sample id Specimen.parent SPM-3 Id of primary sample this derived from
Sample Preparation - Id (many) Specimen.identifier.value SPM-2 Id of sample provided linked to the previously stated assigning authority. Occurs multiple times.
Sample Preparation - 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.
Sample Preparation - Sample storage details Not in scope for FHIR R4, could use Specimen.note or record this information against Task.input (TBC, if required a request to backport Specimen.container.location will be made to support capture of this information) SAC-15 Where a sample preparation is in storage or where it needs to be stored.
Sample Preparation - Volume Specimen.collection.quantity SPM-12 Volume of provided sample.
Sample Preparation - Performed date Specimen.processing.timeDateTime N/A not in scope for HL7v2, may need to replace SPM-17 Date at which the sample preparation was completed.
Sample Preparation - Received date Specimen.receivedTime SPM-18 Date at which a specimen was received at a laboratory.
Sample Preparation - Sample preparation Specimen.processing.procedure N/A not in scope for HL7v2, may need to be captured within SPM-6 Cell separation applied to a primary sample.

Final Sample

Purpose

For testing, obtained from raw specimen, material to be genomically tested. 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
Final Sample - Parent primary sample id Specimen.parent (may be inferred through sample preparation parent, if this is not the primary sample resource) SPM-3 Id of primary sample this derived from
Final Sample - Parent sample preparation id Specimen.parent SPM-3 Id of sample preparation this derived from
Final Sample - Id (many) Specimen.identifier.value SPM-2 Id of final sample provided, linked to the associated assigning authority. Occurs multiple times.
Final Sample - Id assigning authority ODS code (many) Specimen.identifier.assigner SPM-2.1.2 Authority who assigned the final sample id.
Final Sample - Sample storage details Not in scope for FHIR R4, could use Specimen.note or record this information against Specimen.container.identifier (TBC, if required a request to backport Specimen.container.location will be made to support capture of this information) SAC-15 Where a final sample is in storage or where it needs to be stored.
Final Sample - Volume Specimen.collection.quantity SPM-12 Volume of provided final sample.
Final Sample - Performed date Specimen.processing.timeDateTime N/A not in scope for HL7v2, may need to replace SPM-17 Date at which the final sample was extracted.
Final Sample - Received date Specimen.receivedTime SPM-18 Date at which a final specimen was received at a laboratory.
Final Sample - Final sample Specimen.type SPM-4 Material to be genomically tested.

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 (all previous results should be part of Order Prior/Observation Prior sections of OML message) 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 Patient Prior 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 Patient Prior The surname of the patient on the previous genomic report.
Previous genomic report - Patient's address DiagnosticReport.subject( Patient.address ) PID-11 attached to Patient Prior 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 Patient Prior 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 Patient Prior 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 Patient Prior 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 ) ) N/A Could be captured though NTE on Order Prior ORC 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.display ) 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.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.display ) ) 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.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.

Relevant Clinical 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
Relevant clinical report - Report title DiagnosticReport.code OBR-4 (for the request the report is in relation to) Referring clinician's summary of the previous non genomic report to support test request.
Relevant clinical report - Report referral summary DiagnosticReport.conclusion OBX-5 Referring clinician's summary of the previous non genomic report to support test request.
Relevant clinical 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.
Relevant clinical report - Test performed date DiagnosticReport.effectiveDateTime OBX-19 The date a previous non genomic test was performed.
Relevant clinical report - Report identifier DiagnosticReport.identifier OBX-3 The identifier for the previous non genomic report.
Relevant clinical report - Test type DiagnosticReport.code OBR-4 A name that describes the previous non genomic report.
Relevant clinical 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.
Relevant clinical 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.
Relevant clinical report - Test result reference range low DiagnosticReport.result( Observation.referenceRange.low ) OBX-7 (before operator) The reference range low value.
Relevant clinical report - Test result reference range high DiagnosticReport.result( Observation.referenceRange.high ) OBX-7 (after operator) The reference range high value.
Relevant clinical report - Test result test method DiagnosticReport.result( Observation.method ) OBX-17 The method of testing/observation that was used.
Relevant clinical 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.
Relevant clinical 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.
Relevant clinical report - Report result DiagnosticReport.conclusionCode OBR-5 Reference to the result(s)/result groups contained in the report.
Relevant clinical report - Report performer full name DiagnosticReport.performer( PractitionerRole.practitioner.display ) OBX-16 The full name of the individual that authored the previous non genomic test report.
Relevant clinical report - Report performer organisation ODS code DiagnosticReport.performer( PractitionerRole.organization.identifier ) OBX-23.10 The organisation ODS code of the individual that authored the previous non genomic test report.
Relevant clinical report - Original requester full name DiagnosticReport.basedOn( ServiceRequest.requester( PractitionerRole.practitioner.display ) ) TBC, need to review recording/referencing of original request where this is not in an electronic format ORC-12 The full name of the individual that requested the previous non genomic test report.
Relevant clinical report - Original requester organisation ODS code DiagnosticReport.basedOn( ServiceRequest.requester( PractitionerRole.organization.identifier ) ) ORC-21.10 The organisation ODS code of the individual that requested the previous non genomic test report.
Relevant clinical report - Original requester reason for request DiagnosticReport.basedOn( ServiceRequest.reasonCode ) ORC-16 The reason for requesting the previous non genomic test report.

Patient Clinical Information

Purpose

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

Notes

Mapped to Condition and Observation resources linked to the patient. The primary condition, being tested for SHOULD be referenced via ServiceRequest.reasonReference, additional relevant conditions SHOULD be referenced via ServiceRequest.supportingInfo.

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
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
Disease status Condition.clinicalStatus, Condition.verificationStatus (Needs mapping to MDS enums) Potentially mapped to DG1-17 If the patient is affected, uncertain, unaffected, or it is unknown.
Date of diagnosis Condition.recordedDate DG1-5 The patient's date of diagnosis.
Age at disease onset Condition.onsetAge PRB-16, note not included within OML message The age when a change in patients' health was first noted in line with suspected diagnosis.
Known/suspected disease Condition.verificationStatus DG1-6 Disease a patient is believed, known to have, or be at risk of developing.
Phenotypic details (Many) Condition.code with HPO system Additional DG1 segments (DG1-3) The HPO (or alternative ontology as appropriate) term names for the observable disease traits.
Symptoms at onset Condition.evidence.code Separate DG1 with DG1-17=S The patient's symptoms at onset.
Disease penetrance Observation.code = 86426007 or 87006007 OBX segments with appropriate SNOMED CT codes Confirms if all individuals with a disease show clinical symptoms or if there are carriers who do not.
Has multiple tumours Inferred through multiple Condition.bodySite entries Multiple DG1 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 DG1 segments (bodySite for condition not in scope for HL7v2) How many tumours the patient has.
Site of tumour (many) codes used for Condition.bodysite entries Multiple DG1 segments (bodySite for condition not in scope for HL7v2) Location of the tumours on the body.
Solid tumour type Specific Condition.code e.g. child concepts of 128462008 for metastatic tumours DG1-3 The patient's solid tumour type.
Liquid tumour type Specific Condition.code, e.g. 91861009 for AML DG1-3 The patient's liquid tumour type.
Tumour sites - Body image diagram Media TBC N/A - not in scope for HL7v2 Image attachment of body with tumour sites highlighted.
Pedigree details / Relevant family history FamilyMemberHistory referenced from ServiceRequest.supportingInfo, optionally referenced from Condition.evidence.detail N/A not in scope for HL7v2, could be added as additional DG1 segments related to relatives (representation of family history in HL7v2 still pending investigation) The patient's pedigree details/diagram (inc family history of cancer).
Pedigree diagram Media referenced from ServiceRequest.supportingInfo, optionally referenced from Condition.evidence.detail N/A not in scope for HL7v2, could be added as additional DG1 segments related to relatives (representation of family history in HL7v2 still pending investigation) Image attachment of pedigree details.
Laterality of hearing loss Specific Condition.code under Hearing loss e.g. 473424007 DG1-2 Laterality of the hearing loss i.e. bilateral or unilateral.
Fetal maternal screening genotype Presence of Condition.code with appropriate code for Fetal Maternal Screening Genotype (as identified in ConceptMap) attached to Maternal Patient resource DG1-3 Maternal screening genotype for haemoglobinopathy testing.
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 N/A, for non OML messages PRB-14 If the patient in treatment free remission.
Legal considerations TBC Needs more specificity to properly model, likely Consent resources attached to ServiceRequest TBC possibly DG1-18 Legal considerations for a given request.
Fetal paternal screening genotype Presence of Condition.code with appropriate code for Fetal Maternal Screening Genotype (as identified in ConceptMap) attached to Paternal Patient resource DG1-3 Paternal screening genotype for haemoglobinopathy testing.
Expected maternity unit - Organisation name TBC Future dated Encounter with referenced serviceProvider potentially PV1-42.4 Requesting clinician's organisation name.
Expected maternity unit - Organisation address TBC Future dated Encounter with referenced serviceProvider PV1-42.7 Requesting clinician's organisation address.
Expected maternity unit - Organisation ODS code TBC Future dated Encounter with referenced serviceProvider PV1-42.10 Requesting clinician's organisation ODS code.
Expected maternity unit - Department name TBC Future dated Encounter with referenced serviceProvider PV1-42.9 Requesting clinician's department name.
Growth history TBC Observation resources for head circumference etc. OBX segments Summary passage of text to highlight patient centile history e.g head circumference, weight, etc.
Severity of hearing loss Condition.code with appropriate code under 15188001 or Condition.note with code 15188001 DG1-3 Free text regarding hearing loss
Retinal degeneration Condition.code with appropriate code under 95695004 or Condition.note with code 95695004 DG1-3 Free text regarding retinal degeneration
Risk factors MedicationStatement resources with certain codes TBC OBX segments detailing patient on medication etc. Toxic medication - Prematurity (risk factor for hearing loss) e.g. Baby early birth - Ototoxic medication.
Suspected inborn error type(s) Condition.code with code under 86095007 and verificationStatus provisional/unconfirmed DG1-3 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.

Further Supporting Information

Purpose

To capture supporting information which has not been elsewhere specified

Notes

If clinical information, likely mapped to Condition and Observation resources linked to the patient and referenced via ServiceRequest.supportingInfo. Otherwise collated within ServiceRequest.note

Mapping

Source Data item Target FHIR Element HL7v2.5.1 Mapping Description
Further supporting information Linked Condition/Observation resources or ServiceRequest.note Linked DG1/OBR segments or NTE segments in OML message Supporting information which has not been captured elsewhere.

PLCM activity

Purpose

For PLCM activity submissions. This section is pending review, supporting PLCM activity reporting is not expected as part of the Genomic Order Management Alpha.

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 ORU 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 ORU 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 ORU 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 Potentially OBR-32.7 in OML message ODS code of the organisation commissioned by NHS England to deliver the service.
PLCM activity - ODS code of organisation delivering requested test Task.owner Potentially OBX-13 in ORU message 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 ) ) OBX-24 in ORU message 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 OBR-4 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 OBR-6 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 OBX 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 OBX 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.