Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
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 v1.03, 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:
- Transform HL7 v2 messages within the test order service
- Suppliers perform their own mapping of HL7 v2 to FHIR and interact with the test order service using the FHIR APIs
- 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.
- 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.
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) | STF-18 | HCP's job title. |
| HCP - Current Specialty | PractitionerRole.specialty | PRA-5 | HCP's current specialty. |
| HCP - Phone | PractitionerRole.telecom:system=phone | ORC-14 | HCP's phone number. |
| HCP - Email address | PractitionerRole.telecom:system=email | STF-15 | 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 | STF-8 | 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 | STF-16 | 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 | STF-15 | 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.
Profiling for Procedure is currently in progress
Mapping
| Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description |
|---|---|---|---|
| Patient - First name | Patient.name.given | PID-5.2 | Patient's first name. |
| Patient - Surname | Patient.name.family | PID-5.1 | Patient's last name. |
| Patient - Date of birth | Patient.birthDate | PID-7 | Patient's date of birth. |
| Patient - Address | Patient.address | PID-11 | Patient's home address. |
| Patient - Postcode | Patient.address.postalCode | PID-11.5 | Patient's home postcode. |
| Patient - Country | Patient.address.country | PID-11.6 | Patient's home country. |
| Patient - Life status at time of request | Patient.deceasedBoolean (would be replaced by deceasedDateTime if date of death is known), representation of unknown implied by deceasedBoolean not being present | PID-30 | Patient's alive or deceased status. |
| Patient - Ethnicity | Patient.extension:EthnicCategory | PID-22 | Patient's ethnicity. Will have the option 'unknown' available. |
| Patient - Sex assigned at birth | Patient.extension:birthSex | PID-8 | Patient's phenotypic sex classification. The external physical characteristics of the person. Currently determined by the Dr at birth. Gender for PLCM. |
| Patient - Organisation responsibile for GP practice ODS code | N/A obtained through parent of GP Practice as recorded within ODS, obtained through Patient.generalPractitioner | PD1-4.14 | ODS code of organisation responsible for the GP Practice where the patient is registered. |
| Patient - GP Practice ODS Code | Patient.generalPractitioner.identifier (with system matching ODS NamingSystem) | PD1-4.14 | Patient's GP practice ODS code. |
| Patient - Gender Identity same as at birth | N/A inferred through difference between Patient.extension:birthSex and Patient.extension:patient-genderIdentity | N/A - not part of the HL7v2 standard, though PID-8 or an OBX segment could be used | Confirmation if the patient's gender is the same as at birth. |
| Patient - Is from consanguinous union | FamilyMemberHistory.extension = family-member-history-genetics-observation( Observation.code=842009 ) or Observation attached to Patient | OBX-5 with appropriate SNOMED/READ/LOINC code | The fact of biological parents being descended from the same ancestor. |
| Patient - GP full name | Patient.generalPractitioner.display for general practitioner reference to practitioner (SDS identifier), not practice | PD1-4.2 and PD1-4.3 | Patient's GP's full name. |
| Patient - NHS number | Patient.identifier:system = https://fhir.nhs.uk/Id/nhs-number | PID-3 where PID-3.5=2.16.840.1.113883.2.1.3.2.4.18.23 | Patient NHS number. |
| Patient - Local identifier | Patient.identifier:system != https://fhir.nhs.uk/Id/nhs-number (local NamingSystem can be used, assigner determined through assigner field) | PID-3 where PID-3.5 = 2.16.840.1.113883.2.1.3.2.4.18.24 | Patient identification code such as an NHS number. |
| Patient - Reason for unavailable NHS number | Patient.extension:nhsNumberUnavailableReason | N/A, could use PID-32 as surrogate | Reason for an NHS number not being provided. |
| Patient - Relationship to proband | RelatedPerson.relationship (alingment to MDS valueset pending review) | NK1-3 | Relative's relationship to proband/index. |
| Patient - Gender Identity | Patient.extension:patient-genderIdentity | N/A - not part of the HL7v2 standard, though PID-8 or an OBX segment could be used | Patient's stated gender. The gender by which the person is addressed. Determined by the patient. |
| Patient - Date of death | Patient.deceasedDateTime | PID-29 | Patient's date/time of death. |
| Patient - Karyotypic sex | Observation.code( subject=Patient, code = code under 734840008 or 95462004 as examples ) | OBX-5 with appropriate SNOMED/READ/LOINC code | Patient's genomic / karyotypic characteristics. Determined after laboratory testing. |
| Patient - Pregnancy gestation period | Observation.component.valueDuration with code for gestation | OBX-14 (subtracted from ORC-9) | Patient's term of active pregnancy at point of test request. |
| Patient - Fetal gestation | As above, though could be inferred through difference between Observation.effectiveDateTime for pregnancy and Procedure.performedDateTime for termination | OBX-14 (subtracted from OBR-7 for termination procedure) | Stage during patient pregnancy at which it terminated. |
| Patient - Estimated Delivery Date (EDD) | As above, though could be inferred through Observation.effectiveDateTime for pregnancy + 40 weeks or new observation with code 161714006 | OBX-14 + 40 weeks | Patient's estimated delivery date. |
| Patient - Pregnancy type | Inferred through presence of Procedure with codes under IUI/IVF (e.g. codes under 63487001) | OBR segments with appropriate codes | Type of conception. |
| Patient - IVF age of egg donor | TBC Observation referencing IVF procedure (through partOf) with code = 433475001 (if category of over 35 is sufficient, otherwise code.display of "IVF age of egg donor") | OBR segments with appropriate codes | The age of the patient who donated the egg at the time of donation. |
| Patient - Diagnosed with or being treated for cancer | TBC Inferred through attached Condition resources with code under 363346000 or Procedure etc. with reasonCode under same concept | OBR segments with appropriate codes | Has the patient been diagnosed with or are they being treated for cancer. |
| Patient - Had transplant | Inferred through presence of Procedure( subject=Patient ) with code under 77465005 - Transplantation, alternatively, Observation with code 77465005 with valueBoolean=false | Presence of OBR segment with OBR-44 code for transplant | Has the patient ever had a transplant. |
| Patient - Type of transplant | Procedure.code( subject=Patient, code= code under 77465005 ) | OBR-44 | What type of transplant the patient had. (Bone marrow / Stem cell) |
| Patient - Transplant date | Procedure.performedDateTime( subject=Patient ) | OBR-7 | When the patient had the transplant. |
| Patient - Had transfusion | Inferred through presence of Procedure( subject=Patient ) with code under 5447007 - Transfusion, alternatively, Observation with code 5447007 with valueBoolean=false | Presence of OBR segment with OBR-44 code for transplant | Has the patient ever had a transfusion. |
| Patient - Type of transfusion | Procedure.code( subject=Patient, code= code under 5447007 ) | OBR-7 | What type of transfusion the patient has had. (Packed Red Cells /Plasma / Platelets) |
| Patient - Transfusion date | Procedure.performedDateTime( subject=Patient ) | OBR-7 | When the patient had the transfusion. |
| Patient - Height (m) | Observation.valueQuantity( code=54871000237100, subject=Patient) | OBX-5 | Patient's height. |
| Patient - Sexual orientation (pending review) | Observation.value( subject=Patient, code=66621004) | OBX-5 with appropriate SNOMED/READ/LOINC code | Patient's sexual orientation. |
| Patient - Withheld identity reason | Additional codes to be part of Patient.extension:nhsNumberUnavailableReason ValueSet (as per NHS Data Model and Dictionary, pending addition) | N/A, could use PID-32 as surrogate | Confirmation why the patient is withholding identity details. |
| Patient - GP's professional registration number | Patient.generalPractitioner.identifier with system for appropriate registration authority | PD1-4.1 | Patient's GP's professional registration number. |
| Patient - Pedigree/Family Identifier | Patient.identifier:pedigreeNumber | Additional identifiers under PID-3 | Patient's genetic/pedigree number which links their family. |
| Patient - Pregnancy status | Observation.code( subject=Patient, code=77386006 ) | OBX-5 with appropriate SNOMED/READ/LOINC code | Patient's pregnancy status. |
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 (pending backport of R5 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 - Observed sex | TBC Patient.birthSex | PID-8 | Fetus phenotypic sex classification. Estimated physical characteristics determined by ultrasound. Gender for PLCM. |
| Fetus - Phenotypic sex | Patient.gender | PID-8 | Fetus' sex classification determined by ultrasound. |
|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 to match MDSv1.03 |
| 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 - Is test identifier multipurpose | N/A inferred through ServiceRequest.code (as this is defined within the Test Directory) | OBR-4 | Confirmation if the test identifier (TD code) is multipurpose and therefore also requires additional test identifiers. |
| Test request - Is test identifier for requested, attempted or delivered | N/A inferred through ServiceRequest.code (changes to ServiceRequest are expected as part of order fulfillment. History of changes, capturing requested code vs. attempted and delivered, are expected to be recorded within ServiceRequest resource history, reasons for changes SHOULD be captured witihn associated Provenance resources) | OBR-4 | Confirmation if a provided test identifier was requested, attempted or delivered. |
| Test request - High level test identifier version | ServiceRequest.code.coding.version | OBR-4.3 | The version of the high level CI referred to. |
| 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 - High level test identifier system ref | ServiceRequest.code.coding.system | OBR-4.4 | The high level system reference for the considered test. |
| Test request - Low level test identifier version | ServiceRequest.code.coding.version | OBR-4.3 | The version of the low level CITT referred to. |
| 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 test identifier system ref | ServiceRequest.code.coding.system | OBR-4.4 | The low level system reference for the considered test. |
| Test request - Patient set to be tested (pending review) | 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 - 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/reasonReference elements | OBR-13 segment linked to ORC | The reason for a genomic test. |
| 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 - 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 - Date report required by | ServiceRequest.occurrenceDateTime | OBR-8 | The date a completed genomic report is required by. |
| Test request - Further information | ServiceRequest.supportingInfo (if structured, ServiceRequest.note if unstructured TBC) | Additional segments attached to ORC/OBR | Further information regarding the test request. |
| Test request - Item sent | N/A indicated through Tasks related to ServiceRequest changing owner, Tasks may reference Specimen resources through Task.input if they relate to samples being sent | TBC Status updates as part of test order fulfillment are not expected to represented within HL7v2 messages | Item being sent to another location. |
| Test request - Item destination ODS code | Task.owner | As above | Subsequent ODS code of destination for stipulated item. |
Raw Specimen/Biopsy
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 v1.03 mappings are still under review
Mapping
| Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description |
|---|---|---|---|
| Raw specimen/biopsy - Received date | Specimen.receivedTime | SPM-18 | Date at which a specimen was received at a laboratory. |
| Raw specimen/biopsy - Type | Specimen.type Note: The ValueSet for this field is pending review to align with MDSv1.03 | 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 MDSv1.03 |
| 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 - Is assigning authority a histopathology laboratory (many) | Derived from ODS - Specimen.identifier.assigner (it is assumed ODS would have the necessary metadata to confirm lab type, this is pending internal review) | Derived from ODS - SPM-2.1.2 | Confirmation of an assigning authority ODS code being from a histopathology laboratory. |
| Raw specimen/biopsy - Sample preparation (submitted to GLH) | Specimen.processing Note: The ValueSet for this field is pending review to align with MDSv1.03 | 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 - WGS specimen type category | Specimen.extension:sampleCategory | SPM-5 | WGS cancer high level category for the specimen. |
| 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 - 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. |
| Raw specimen/biopsy - Biopsy site | Specimen.collection.bodySite | SPM-8/SPM-9 | Site of biopsy. |
| 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 - Family member provided by | Specimen.subject (links between Patient/RelatedPerson resources in test order would indicate family relationships) | PID segment attached to SPM | Which family member the specimen is provided by. |
| 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 - 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 - 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 - 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 - 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 - Option for products of conception | Additional Specimen.collection.extension:specimen-specialHandling with appropriate code/text Note: specific concepts may be called out to align with MDSv1.03 enums | 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 - 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 - 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. |
| Raw specimen/biopsy - Location 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 raw specimen/biopsy is in storage or where it needs to be stored.. |
| Raw specimen/biopsy - High infection risk reason | Specimen.collection.extension:specimen-specialHandling.valueCoding.code Note: specific concepts may be called out to align with MDSv1.03 enums | SPM-16.2 | The high contamination risk reason for a sample/biopsy. |
| 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 - Additional specimen/biopsy information | Observation resources referencing Specimen for coded information or Specimen.note if unstructured | 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 - Type | Specimen.type Note: The ValueSet for this field is pending review to align with MDSv1.03 | SPM-4 | Tissue of origin. |
| Extracted specimen - State | Specimen.condition Note: The ValueSet for this field is pending review to align with MDSv1.03 | 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 - 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, see also location details field under Raw Specimen/Biopsy | SAC-15 | Where a raw specimen is in storage and not provided with a request. |
| 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. |
| Extracted specimen - Sample well identifier | Specimen.container.identifier | SAC-3 | Id of the sample well. |
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.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
Mapping
| Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description |
|---|---|---|---|
| Disease status | Condition.clinicalStatus (Needs mapping to MDS enums) | 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. |
| Has multiple tumours | 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) | codes used for Condition.bodysite entries | Multiple PRB 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 | 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. |
| 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. |
| 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 PRB segments related to relatives | 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 PRB segments related to relatives | Image attachment of pedigree details. |
| Disease penetrance | Inferred through FamilyMemberHistory.condition.outcome elements for each individual e.g. 29679002 for carriers | 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. |
| 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. |
| 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 | Media TBC | N/A - not in scope for HL7v2 | Image attachment of body with tumour sites highlighted. |
| Date of disease onset | Condition.onsetDateTime | PRB-16 | The date when a change in patients health was first noted in line with suspected diagnosis. |
| 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. |
| 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 | 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. |
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 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. |