NHS North West Genomics, published by NHS North West Genomics. This guide is not an authorized publication; it is the continuous build for version 0.0.8 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/nw-gmsa/nw-gmsa.github.com/ and changes regularly. See the Directory of published versions

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Official URL: https://fhir.nwgenomics.nhs.uk/ImplementationGuide/fhir.nwgenomics.nhs.uk				Version: 0.0.8
Draft as of 2025-10-30				Computable Name: NWGMSA

Introduction

This guide is to support Genomic Testing Workflow at a regional level and is designed to be compatible with:

• NHS England - FHIR Genomics Implementation Guide which defines the conformance requirements for Genomics in England
• NHS England - Genomic Order Management Service FHIR API a FHIR Workflow based service for managing orders and results at a national level.

The general workflow is based on IHE LTW profiles and HL7 v2 OML and ORU.

Clinical Process

Genomic Testing Workflow is part of Diagnostic Testing, which is also part of the general clinical process.

graph TD;

    A[Assessment]-->|Creates Observations| B;
    A--> |Needs Diagnostic Testing and Completes| T;
    B[Diagnosis]-->|Creates Condition| C;
    T[Genomics Test Order Form]--> |"Sends laboratory or imaging order - LAB-1<br/>FHIR Message O21"| AN;
    T --> |Asks for| S
    S[Specimen Collection] --> |Sends Specimen| AN;
    AN["Diagnostic Testing"] --> |"Requests further tests <br/>(reflex order)"| T;
    AN --> |"Creates laboratory or imaging report - LAB-3<br/>HL7 v2 ORU_R01"| B;
    AN --> |Sends laboratory or imaging report| A;
    C[Plan]-->|Creates Goals and Tasks| D;
    D[Implement/Interventions]-->|Actions Tasks| E;
    E[Evaluate]--> |Reviews Care| A;
    
    click T Questionnaire-GenomicTestOrder.html
    click AN Questionnaire-GenomicTestReport.html
    click S ExampleScenario-BiopsyProcedure.html

    classDef purple fill:#E1D5E7;

    classDef yellow fill:#FFF2CC;
    classDef pink fill:#F8CECC
    classDef green fill:#D5E8D4;
    classDef blue fill:#DAE8FC;
    classDef orange fill:#FFE6CC;

    class A pink
    class B yellow
    class C green
    class D blue
    class E orange

    class O,S,T,AN purple

Genomic diagnostic testing follows the same standardized process defined by the IHE Laboratory Testing Workflow used in traditional laboratory testing. This workflow has been enhanced to support the sharing of laboratory reports (documents) through Integrated Care Systems (ICS). In addition, a new mechanism for sharing laboratory reports has been introduced to establish a regional genomic data repository.

Diagnostic Testing

graph TD;

    DiagnosticTesting[fas:fa-stethoscope Diagnostic Testing]  --> |Creates| DiagnosticReport[Diagnostic Report]
    DiagnosticReport --> |Reads Variant and DiagnosticImplication| Consultant[fas:fa-user-md Consultant]
    DiagnosticReport --> |Reads Variant and DiagnosticImplication| GP[fas:fa-user-md GP]
    GenomicCDR --> |Reads Variant and DiagnosticImplication| GeneticCounseling[fas:fa-user-md Genetic Counseling]
    DiagnosticReport --> |Reads Genomic Study and Variant| Oncologist[fas:fa-user-md Oncologist]
    DiagnosticReport --> |Is Persisted| GenomicCDR
    DiagnosticReport --> |"Reads DiagnosticImplication (Condition) and Variant (Gene)"| Patient[fas:fa-user Patient]

    Consultant --> |"Records Condition (from Diagnostic Implication)"| EPR[fas:fa-database Electronic Patient Record]
    GP--> |"Records Condition (from Diagnostic Implication)"| GPEPR[fas:fa-database GP Electronic Patient Record]
    
    GeneticCounseling --> |Obtains Family Structure and History| Patient
    GeneticCounseling --> |Records FamilyMemberHistory| GenomicCDR[fas:fa-database  Genomic Clinical Data Repository]
    Consultant --> |Asks for Genetic Counseling on Genetic Condition?| GeneticCounseling

A detailed example of this process can be found in the Example Scenario - Clinical and Genomic Workflow.

Specimen Collection

Specimen collection is not performed by a Genomics service, and this shows how genomics fits into that process. The diagram here is around a biopsy procedure, but the same principles apply to other specimen collection procedures.

graph TD;

    Oncology[Specialty e.g. Oncology] --> |"Asks for a biopsy (procedure)"| SpecialistTeam[fas:fa-user-md Specialist Team]
    Oncology --> |"Asks for a diagnostic test (procedure)"| DiagnosticTesting[Diagnostic Testing]
    SpecialistTeam --> Admits[Admits Patient]
    Admits --> Performs[Performs Procedure]
    Admits --> |"Gets Patient Summary <br/>(Conditions, Allergies and Current Medications)"| Patient
    Admits --> |Update Patient Record| EPR
    Performs --> Discharge[Discharges Patient]
    Performs --> |Sends Specimen| DiagnosticTesting
    Discharge --> |Discharge Letter| Patient["fas:fa-user Patient"]
    Discharge --> |Send Discharge Letter| GP["fas:fa-user-md GP"]
    Discharge --> |"Record procedure (as completed)"| EPR["fas:fa-database <i>Electronic Patient Record</i>"]
    Discharge --> |Send Visit Notification| Consultant[fas:fa-user-md Consultant]
    GP --> |"Store Discharge Letter"| GPEPR["fas:fa-database <i>GP Electronic Patient Record</i>"]

A detailed example of this process can be found in the Example Scenario - Collect Specimen.

How to Read this IG

	Menu Item	Description	Audience
	Analysis and Design (Volume 1)	Description of the processes and corresponding technical frameworks	General
	Interfaces (Volume 2)	Description of the processes and corresponding technical frameworks (HL7 v2 and FHIR Interactions)	Detailed Technical (Integration Developer)
	Domain Archetype (Volume 3)	NHS North West Forms, Templates, Reports and Compositions	Data Modeling (Detailed Technical)
	Artefacts (Volume 4)	NHS North West Common Data Models	Detailed Technical
	Development	Testing, Suppport and Architecture	Detailed Technical (Developer)

Analysis and Design	Interfaces	Domain Archetype	Artefacts
Send Laboratory Order (LTW)	HL7 FHIR LAB-1	North West Genomics Test Order
Send Laboratory Report Data (LTW)	HL7 FHIR LAB-3 and HL7 v2 ORU LAB-3/R01	North West Genomics Test Report
Send Laboratory Report Document (HIE)	HL7 v2 MDM T02	North West Genomics Test Report
Read Laboratory Order or Report Data (HIE)	HL7 FHIR QEDm		Resource Profiles
Read Laboratory Report Documents (HIE)	HL7 FHIR MHD		Resource Profiles

Data Modelling

The data model used in this guide is a combination of data and workflow requirements from a variety of other guides.

North West GMSA IG

Testing

This implementation guide will also enable use of FHIR Testing tools such as Command Line FHIR Validation and Online FHIR Validation

SNOMED CT

UK edition of SNOMED (83821000000107)

Dependencies

Package hl7.fhir.uv.extensions.r4#5.2.0 This IG defines the global extensions - the ones defined for everyone. These extensions are always in scope wherever FHIR is being used (built Mon, Feb 10, 2025 21:45+1100+11:00)

Package fhir.r4.ukcore.stu3.currentbuild#0.0.19-pre-release UK Core FHIR profiles and Assets

Package hl7.fhir.uv.extensions.r4#5.1.0 This IG defines the global extensions - the ones defined for everyone. These extensions are always in scope wherever FHIR is being used (built Sat, Apr 27, 2024 18:39+1000+10:00)

Package hl7.fhir.uv.genomics-reporting#3.0.0 Guidelines for reporting of clinical genomics results using HL7 FHIR. (built Thu, Dec 12, 2024 20:34+0000+00:00)

Package hl7.fhir.uv.ips#1.1.0 International Patient Summary (IPS) FHIR Implementation Guide (built Tue, Nov 22, 2022 03:24+0000+00:00)

Package hl7.fhir.eu.laboratory#0.1.1 This guide describes how the Laboratory Report can be represented in the European REALM. (built Tue, Mar 25, 2025 12:00+0100+01:00)

Package hl7.fhir.uv.sdc#3.0.0 The SDC specification provides an infrastructure to standardize the capture and expanded use of patient-level data collected within an EHR. This includes two components: * Support more sophisticated questionnaire/form use-cases such as those needed for research, oncology, pathology and other clinical domains. *Support pre-population and auto-population of EHR data into forms/questionnaires for uses outside direct clinical care (patient safety, adverse event reporting, public health reporting, etc.). (built Tue, Mar 8, 2022 18:32+0000+00:00)

Package hl7.fhir.uv.tools.r4#0.8.0 This IG defines the extensions that the tools use internally. Some of these extensions are content that are being evaluated for elevation into the main spec, and others are tooling concerns (built Tue, Aug 5, 2025 20:09+1000+10:00)

Credits

Role(s)	Contributor(s)
	North West Genomic Medicine Service Alliance
	Alder Hey Children's Hospital Trust
	Manchester University NHS Foundation Trust
	Liverpool Womens NHS Foundation Trust
	The Christie NHS Foundation Trust
	NHS England
Enterprise Architect	Kevin Mayfield (Aire Logic/Mayfield IS)