NHS North West Genomics - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

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[<b>Order Placer</b><br/>Genomics Test Order]--> |"Sends Laboratory Order - LAB-1<br/>FHIR Message O21"| AN;
    T --> |Asks for| S
    S[Specimen Collection] --> |Sends Specimen| AN;
    AN["<b>Order Filler</b><br/>Diagnostic Testing"] --> |"Requests further tests <br/>(reflex order)"| T;
    AN --> |"Creates Laboratory Report - LAB-3<br/>HL7 v2 ORU_R01"| B;
    AN --> |Sends Laboratory 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.

Laboratory Workflow (LTW)

Test Order

graph TD;

    Practitioner[fas:fa-user-md Practitioner] --> |1. Selects Order Form| FormManager
    FormManager --> OrderEntry
    Practitioner --> |3. Completes| OrderEntry[Order Form]
    EPR[fas:fa-database Electronic Patient Record] --> |2. Pre Populates with existing data| OrderEntry 
    OrderEntry --> |4. Submits Order| EPR
    EPR --> |5. Sends Laboratory Order| DiagnosticTesting[fas:fa-stethoscope Diagnostic Testing]

For more details see:

• Send Laboratory Order (IHE LTW) NHS Trust
• Read & Search Laboratory Order (HIE)

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]
    EPR --> |GC1. 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[fas:fa-database  Genomic Clinical Data Repository]
    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 (Genomic Disorder) <br/>or Observation (Genomic Disorder Carrier) <br/>based on Diagnostic Implication"| GPEPR[fas:fa-database GP Electronic Patient Record]
    
    GeneticCounseling --> |GC2. Obtains Family Structure and History| Patient
    GeneticCounseling --> |GC3. Records FamilyMemberHistory| EPR
    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.

For more details see:

• Send Laboratory Report Data (IHE LTW) - NHS Trust
• Send Laboratory Report Document (HIE) - ICS/ICB
• Read & Search Laboratory Report Data (HIE)
• Read & Seerch Laboratory Report Documents (HIE)

Inter Laboratory Workflow (ILW)

For illustration purposes only, see Inter Laboratory Workflow

Specimen Event Tracking (SET)

For illustration purposes only, see Specimen Event Tracking

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