Manages the Order. This is the function of Genomic Order Management Service and/or GLH LIMS

From ISO-13606 The set of information committed to one EHR as a result of a clinical encounter or a record documentation session. Examples of COMPOSITION are Progress note, Laboratory test result form, Radiology report, Referral letter, Clinic visit, Clinic letter, Discharge summary, Functional health assessment, Diabetes review.

North West GLH Regional Integration Engine (RIE) This is a Trust Integration Engine (TIE) working at a regional level

Fulfils the Order. The Order Filler Actor is implemented by laboratory information management systems.

Creates the Order. The Order Placer Actor is implemented by the systems used by the clinical practice.

Allows practitioners to view the Genomics Test Report (e.g. Patient Pass or EPR)

Source of the patient demographics change. The Patient Identity Source is implemented by the systems used for patient administration (e.g. PAS or EPR).

Source of the provider information change. The Provider Information Source is implemented by the systems used for patient administration (e.g. PAS or EPR) or Organisation Directories (LDAP/X.500).

Is based on FHIR Messaging to handle transformation of HL7 FHIR and v2 Messages to FHIR Workflow.

The OpenAPISwagger Definition file below, can be viewed using Swagger Editor

This is documentation on the version of HL7 FHIR process-message to be used for regional FHIR Messaging, this HL7 FHIR definition SHALL be followed.

Command Message

Conversion of HL7 v2.5.1 OML_O21

​See Patient Encounter Triggers for eventCoding codes.

Event Message

Conversion of

• NHS England HL7 v2 ADT Message Specification

Related to IHE Patient Encounter Management [ITI-31]

​See Patient Identity Triggers for eventCoding codes.

Event Message

Conversion of

• NHS England HL7 v2 ADT Message Specification
  • Create Patient HL7 v2.4 ADT_28
  • Update Patient HL7 v2.4 ADT_31
  • Update (merge) Patient HL7 v2.4 ADT_40

Related to IHE Patient Identifier Cross-referencing for mobile (PIXm)

Document Message

Conversion of HL7 v2.5.1 ORU_R01

CBC panel - Blood by Automated count

Comprehensive metabolic 2000 panel - Serum or Plasma

Master HL7 genetic variant reporting panel

NHS England North West Genomics Test Order (Draft)

THIS IS FOR ANALYSIS, and is not to be used for implementation at present.

The aim of this is to support conversion of multiple Genomic Order Forms HL7 v2 and FHIR.

TODO

Placeholder for EU Lab Composition (and so IPS Composition)

Includes constraints from:

• NHS England Genomics DiagnosticReport use text descriptions only, not the rendered profile.

See also HL7 Europe Laboratory Report - DiagnosticReport: Laboratory Report

Based on UK Definitions from IHE Europe Metadata for exchange medical documents and images

Includes constraints from:

• HL7 PV1 segment definitions from NHS England HL7 v2 ADT Message Specification

DRAFT

TODO

Reference:

• part of openEHR Genomic Variant Result

See also HL7 Europe Laboratory Report - Observation Results: laboratory

Reference:

• part of openEHR Genomic Variant Result

For reference:

• NHS England Genomics Education - Visual communication aid: Variants of uncertain significance (VUS)

DRAFT Extension of OperationOutcome

Includes elements from:

• HL7 v2 XON – Extended Composite Name and Identification Number for Organisations
• XON definition from NHS England HL7 v2 ADT Message Specification
• IHE Mobile Care Services Discovery (mCSD)

Includes constraints from:

• NHS England Genomics Patient use text descriptions only, not the rendered profile.
• HL7 PID segment definitions from NHS England HL7 v2 ADT Message Specification

Includes elements from:

• HL7 v2 XCN Extended Composite ID Number and Name for Persons
• XCN definition from NHS England HL7 v2 ADT Message Specification
• IHE Mobile Care Services Discovery (mCSD)

TODO

Initial elaboration extending SDC Questionnaire

DRAFT Initial elaboration

Includes constraints from:

• NHS England Genomics ServiceRequest use text descriptions only, not the rendered profile.

See also HL7 Europe Laboratory Report - ServiceRequest: Laboratory Order

Includes constraints from:

• NHS England Genomics Specimen use text descriptions only, not the rendered profile.

See also HL7 Europe Laboratory Report - Specimen: Laboratory

Based on FHIR Workflow

Usually assigned by the order filler.

DRAFT: Additional conformance on FHIR Attachment data type. In HL7 FHIR this is likely to be a Binary resource and in HL7 v2 the OBX segment. When laboratory reports include a url link in DiagnosticReport, the FHIR Bundle should also include a FHIR DocumentReference providing additional document metadata.

Backport of FHIR R5 CodeableReference. (copied from BE eHealth Platform Federal Core Profiles). Extension able to hold a reference and a concept (Temporary solution until https://jira.hl7.org/browse/FHIR-44661 is solved and see Zulip: https://chat.fhir.org/#narrow/stream/179280-fhir.2Finfrastructure-wg/topic/Backporting.20CodeableReference)

See Enterprise Integration Patterns - Correlation Identifier and Rule 3: Reference Other Aggregates by Identity (Implementing Domain Driven Design)

NHS Data Dictionary CONSULTANT CODE and GENERAL MEDICAL PRACTITIONER PPD CODE.

This is a Correlation Identifier definition compatible with Yorkskhire and Humberside - Interweave-EncounterGrouping

See also 5.6.3 Alternate Visit ID (CX) from NHS England HL7 v2 ADT Message Specification PV1 documentation.

• an admission
• an A&E attendance
• a community contract
• an outpatient number (note this is not an individual attendance number which is the NHS England HL7 v2 PV1 definition)

HL7 v2 Filler Order Number (ORC-3)

TODO

Only use in References Data Type if the NHS Number is not known or unverified.

Only traced NHS Number SHOULD be used, un-traced NHS Numbers MUST be clearly indicated.

NHS Data Dictionary ORGANISATION_CODE

NHS Data Dictionary ORGANISATION SITE IDENTIFIER

Use ODS Site code relevant for organisation. E.g. Use Mid Yorkshire Hospitals NHS Trust (RXF) version of Pinderfields Hospital (RXF05) when referring to Mid Yorks, not others in the director

HL7 v2 Placer Group Number (ORC-4)

HL7 v2 Placer Order Number (ORC-2)

(copied from BE eHealth Platform Federal Core Profiles) Extension able to hold a reference and a concept (Temporary solution until https://jira.hl7.org/browse/FHIR-44661 is solved and see Zulip: https://chat.fhir.org/#narrow/stream/179280-fhir.2Finfrastructure-wg/topic/Backporting.20CodeableReference )

DRAFT

• ADMISSION METHOD

DRAFT

• ADMISSION SOURCE
• UKCoreSourceOfAdmission

DRAFT

• DESTINATION OF DISCHARGE
• UKCoreDischargeDestination

DRAFT

• DISCHARGE METHOD CODE
• UKCoreDischargeMethod

• Switzerland DocumentEntry.classCode

• Digital Health and Care Scotland - (EH4001) CLINICAL DOCUMENT INDEXING STANDARDS LA Labs

• Switzerland DocumentEntry.mimeType

This extends UKCoreEthnicCategory to include other categories for reasons stated in Wikipedia: Classification of ethnicity in the United Kingdom See also NHS Data Model and Dictionary ETHNIC CATEGORY

DRAFT

• ACTIVITY LOCATION TYPE CODE

• See National genomic test directory for cancer on Genomic Test Directory

2nd level classification of Genomic Test Directory

• See National genomic test directory for rare and inherited disease on Genomic Test Directory

IdentifierType work around to bypass lack of NH in based definition

Top level classification of Genomic Test Directory

IHE Patient Encounter Management [ITI-31]

A28/A31/A40

PractitionerIdentifiers

ValueSet for Request Priority

DRAFT

• TREATMENT FUNCTION CODE
• UKCoreCareSettingType

• MAIN SPECIALTY CODE
• UKCorePracticeSettingCode

A subset of HL7 Europe Laboratory Report ValueSet: Specimen Types

ValueSet for Yes/No answers

ValueSet for Yes/No/Unknown answers

2nd level Genomic Test Directory Codes

• Genomic Test Directory

Bucket for local codes

Bucket for local codes

UK Professional License

For demonstration purposes only - THIS HAS NOT BEEN VALIDATED

For Implementation Guide see SNOMED CT Implementation Guide for the LOINC Ontology

For demonstration purposes only - THIS HAS NOT BEEN VALIDATED

For Implementation Guide see SNOMED CT Implementation Guide for the LOINC Ontology

Influenced by HL7 v2 ADT_A31

Genomic Order Entry Optional Questions - THIS IS FOR ANALYSIS, and is not to be used for implementation.

Genomic Report BRCA1 Variant Example

Genomic Report Ovarian Carcinoma Diagnostic Implication Example

This is based on US Core Example Observation: MCV Example and incorporates extra coding from NHS England Pathology - PATH-R4-10: Bundle Example - Full Blood Count Report

For coding descriptions see

• 1022491000000106 and 1491000237105 SNOMED UK Edition
• 613061010000108 and 787-2 SNOMED LOINC Edition

TODO

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Organization MANCHESTER UNIVERSITY NHS FOUNDATION TRUST

Organization North West GMSA

Parameters Expansion Profile

TODO

TODO

Genomic Record of Discussion Example

Influenced by HL7 v2 OML_O22

Influenced by HL7 v2 OML_O21

Influenced by HL7 v2 OML_O21

FHIR Message Query Example for use with Asynchronous Message Delivery

TODO

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Example NHS England PDS Test Pack

TODO

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Genomic Report PDF Example

Influenced by HL7 v2 ORU_R01

First draft is based on Royal College of Radiologists HL7 v2 ORU converted to HL7 FHIR. Will be converted to a Genomics example

TODO

TODO

FHIR Document Genetic Report for Jack Dawkins

Composition - Genomics Report Octavia CHISLETT

TODO

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