NHS North West Genomics, published by NHS North West Genomics. This guide is not an authorized publication; it is the continuous build for version 0.2.2 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

Laboratory Testing Workflow (LTW)

References

1. IHE Pathology and Laboratory Medicine (PaLM) Technical Framework - Volume 1 HL7 v2

Actors and Transactions

Actor	Definition
Order Placer	Commonly known as the Electronic Patient Record (EPR) System or Order Communications System
Order Filler	Genomic Laboratory Hub (GLH), Laboratory Information System (LIMS)
Automation Manager	Performed by Laboratory Information System (LIMS)
Order Result Tracker	This is often provided by Electronic Patient Record (EPR) Systems
Laboratory Report (Clinical Document)	See Clinical Document
Intermediary	E.g. Regional or Trust Integration Engine
Automation Manager	Often software associated with analysers and Laboratory Analytical Workflow (IHE LAW)

See also Ref A Section 3 Laboratory Testing Workflow (LTW) Profile for detailed description of actors.

IHE LTW Actor Diagram

Initially only the IHE LAB-1 and LAB-3 is in focus.

Later stages will include the use of Genomic Order Management Service.

Overview

Genomic LTW Business Process

The sample may not need collecting by the ordering clinician for 2 reasons

• it has already been sent to the GLH and extracted DNA is already stored there
• the sample is somewhere else in the country. In this instance the ordering clinician will need to arrange the sample transfer to the GLH.

The processes above are described in more detail in:

• Use Case 1: Genomic Test Order for the order
• Use Case 2: Genomic Test Report for the report

From a high level perspective the process is

Genomics Simplified Sequence Diagram

Where the Order Placer sends the Laboratory Order to the Order Filler, the lab performs the test and then sends the Laboratory Report back to the Order Placer. However, variations can exist such as the order is updated or the order is entered directly on the Order Fillersystem (these are currently out of scope).

Laboratory Order (LAB-1)

graph TD;
    OrderPlacer["<b>Order Placer</b><br/>(EPR or Order Comms)"] --> |1. Send Genomic Laboratory Order<br/>HL7 v2 ORM_O01 or OML_O21| OR[Acute Hospitals<br/>Trust Integration Engine]
       OrderPlacer --> |"2. Asks for (Order)"| SpecimenCollection
    SpecimenCollection[Specimen Collection] --> |3. Sends Specimen| OrderFiller
    OR --> |"1a. HL7 FHIR Message O21<br/>(IHE LTW)"| RIE[Middleware<br/>Regional Orchestration Engine] 
    RIE --> |"1c. Send Genomic Laboratory Order<br/>HL7 FHIR Message O21<br/>(IHE LTW)"| CDR[NW Genomics<br/>Clinical Data Repository]
    CDR --> |1d. Send FHIR Event Notification| Any["Any <br/>(future)"]
    RIE --> |"1b. Send Genomic Laboratory Order<br/>HL7 v2 OML_O21<br/>(IHE LTW)"| EHRTIE[NW Genomics<br/>Laboratory Information Management System] 
    RIE --> |"1b. Send Genomic Laboratory Order<br/>FHIR Transaction<br/>via NHS England Genomic Order Management Service"| GOMS["External<br/>Laboratory Information Management System<br/>(Future)"] 
    EHRTIE --> OrderFiller[<b>Order Filler</b>]
    GOMS --> OrderFiller

    classDef green fill:#D5E8D4;
    classDef yellow fill:#FFF2CC;
    class RIE green;
    class OR green;
    class CDR yellow;

Use Case: Genomic Test Order

An order is created by the clinical practice and placed to the laboratory.

Genomics Test Order Activity

Select Genomic Test Order Form

Within the system creating the genomics order, the practitioner will select a form for the test required. Below are several examples from North West Genomic Laboratory Hub - Test Request Forms. How this is implemented will vary between different NHS organisations and systems they use.

NW GLH Genomic Testing Request Form – Rare Disease

Request for Genetic Testing for Haemoglobinopathies

Complete Genomic Test Order Form

These forms may (/will?) will have a computable definition called an template (FHIR Questionnaire) which will list the technical content requirements for the form. At present only one archetype has been defined:

• NW GMSA Genomics Test Order Panel

This archetype definition can also support HL7 Structured Data Capture should the Order Placer system support these features.

Submit Genomic Test Order Form

The completed form is submitted to the Regional Orchestration Engine using:

Genomics Test Order Sequence Diagram - LAB-1

For submission, this form will be converted by the Order Placer to a communication format called HL7 FHIR (and for compatability reasons HL7 v2. If the Order Placer has a FHIR enabled Electronic Patient Record (e.g. EPIC, Cerner, Meditech, etc), they may use HL7 SDC - Form Data Extraction to assist with this process.

Order Test Form - Data Extraction Overview

The FHIR exchange style used FHIR Message following laboratory-order message definition. This definition is based on HL7 v2 OML_O21 Laboratory Order which simplifies conversion to/from pipe+hat (v2) and json (FHIR) formats.

At present, the NW GLH Laboratory Information Management System (LIMS) will not support HL7 FHIR. The Regional Integration Exchange (RIE) will perform conversion between v2 and FHIR formats.

This message is an aggregate (DDD)/archetype and so is a collection of FHIR Resources (similar to v2 segements) which is described in Genomic Test Order.

Communicating Ask at Order Entry questions and prior results

See also HL7 Europe Laboratory Report - ServiceRequest This message can be extended by template (FHIR Questionnaire) which allows the definition of additional questions to be defined for the laboratory order.

The detail of this form/template defines:

Order Text Form Example (extract)

Question	CodeSystem	Code	FHIR Profile	HL7 v2 Segment	FHIR Questionniare item.type	FHIR Observation value[x]	v2 OBX-2
Does This Test Relate to a Pregnancy	SNOMED	77386006	Observation	OBX	boolean	valueBoolean	CE (code 0136)
Sample	LOINC	68992-7	Observation-Panel	OBR
High Infection Risk Sample	SNOMED	281269004	Observation	OBX	boolean	valueBoolean	CE (code 0136)

It is not expected the NW GLH Laboratory Information Management System (LIMS) will support UK SNOMED CT, and the RIE will handle the conversion either internally using FHIR ConceptMap or a terminology service with the following capabilities IHE Sharing Valuesets, Codes, and Maps (SVCM)

Collect Sample and Update Genomic Test Order

After submitting the original order, the sample will be collected and sent to the Order Filler. The Order Filler will update the Test Order to include details such as a specimen collection date, order filler number, etc.

Relationship to NHS England Pathology

This guide builds on the use cases described in the NHS England Pathology FHIR Implementation Guide, extending them to support a wider range of stakeholders and introducing standards for the Laboratory Order LAB-1.

Key differences include:

• Workflow foundation: The IHE Laboratory and Testing Worflow LTW is used as the reference model for describing laboratory testing processes.
• Order Placer role: The GP Electronic Patient Record (EPR) System and the Order Communications System together form the Order Placer role, which may also be fulfilled by other EPR systems.
• Intermediary between Order Placer and Order Filler: This intermediary performs message translation and code conversion.
• Order Result Tracker role: For results, the GP EPR System acts as the Order Result Tracker, though other systems (e.g. Secondary Care EPR) can provide this function.
• Intermediary between Order Filler and Order Result Tracker: This intermediary also handles message translation and code conversion.
• Canonical model: A standardised model (Canonical model), expressed in HL7 FHIR, that can be implemented using HL7 v2, FHIR, and IHE XDS. It aligns with the latest HL7 UK Core and NHS England Data Model and Dictionary. While primarily focused on genomics, it incorporates elements from pathology and radiology for compatibility, and mandates the use of NHS England National Procedure Codes.

Relationship to NHS England Pathology

Laboratory Report (LAB-3)

graph TD;
    OrderFiller["<b>Order Filler</b><br/>Diagnostic Testing (LIMS)"] --> |"1. Sends HL7 v2 ORU_R01<br/>(IHE LTW)"| RIE[Middleware<br/>NW Genomics<br/>Regional Orchestration Engine] 
    RIE --> |"1a. Sends HL7 v2 ORU_R01<br/>(IHE LTW)"| TIE[Middleware<br/>Acute Hospitals<br/>Trust Integration Engine] 
    TIE--> |"1a. Sends HL7 v2 ORU_R01<br/>(IHE LTW)"| EHRTIE[North West<br/>NHS Trust<br/>EHR] 
    RIE--> |"1a. Sends HL7 v2 ORU_R01<br/>(IHE LTW)"| BOARD["NHS Wales<br/>Health Board<br/> (future?)"]
    RIE --> |"1a. Sends FHIR Transaction<br/>via NHS England Genomic Order Management Service"| GOMS["NHS England<br/>NHS Trust<br/>EHR (Future)"] 
    RIE --> |1b. Sends HL7 v2 MDM_T02 or IHE XDS| ICSTIE[Integrated Care System <br/> Document Repository]
    RIE --> |1c. Sends HL7 FHIR R4<br/>Message O21| CDR[NW Genomics<br/>Clinical Data Repository]
    CDR --> |1d. Sends FHIR Event Notification| Any["Any <br/>(future)"]
    GOMS --> OrderPlacer[<b>Order Placer</b>]
    EHRTIE --> OrderPlacer
    BOARD--> OrderPlacer

    classDef green fill:#D5E8D4;
    classDef yellow fill:#FFF2CC;
    class RIE green;
    class TIE green;
    class CDR yellow;

Use Case: Genomic Test Report

A report is created by the clinical practice and sent to the order result tracker.

Genomic Test Report Description

Genomics Test Report Activity

Send/Share Genomic Test Report

Genomic Report Example

Genomics Test Report Sequence Diagram - LAB-3

Main Process Flow

• Optional Preliminary Report Stage
  • Perform Diagnostic Test → Write Preliminary Report (Order Filler).
  • Send (Preliminary) Genomic Test Report IHE LAB-3 from the Order Filler to the Intermediary (RIE).
  • RIE sends HL7 v2 message Laboratory Report ORU_R01 to the Order Placer.
  • The same HL7 v2 message is also sent from the Intermediary to the Order Placer.
• Final Report Stage
  • Complete Report (Order Filler).
  • Send (Final) Genomic Test Report IHE LAB-3 from the Order Filler to the Intermediary (RIE).
  • RIE sends HL7 v2 message Laboratory Report ORU_R01 to the Order Placer.
• Completion Notification
  • When all tests in the order are complete, a Task Complete Notification is sent to the Order Placer.
    • This notification can be sent via email or another messaging system.

Order and Report Use Case Summary

Genomic Order and Report Summary

Genomic Test Order and Report use cases form part of a broader diagnostic testing workflow, which is guided by:

• NICE standards
• Getting It Right First Time (GIRFT) best practice pathways (e.g. Getting It Right First Time (GIRFT) Best Practice Timed Diagnostic Cancer pathways
• Local Diagnostic Pathway Guidance.

These pathways are technically implmented and generally align with the IHE Laboratory and Testing Worflow LTW (for Imaging workflows see IHE Radiology (RAD))

Within EHR systems, test orders are usually created through an Order Entry Form (also referred to in health informatics as a Template). Reports are typically displayed in the EPR as a Composition (health informatics terminology).

Between the Order Placer (e.g., consultant and EPR) and the Order Filler (e.g., laboratory and LIMS), various intermediary systems are used. These are often called Trust Integration Engines (TIEs). The most widely used messaging standard is HL7 v2.

To modernise these workflows, the North West GMSA is also introducing FHIR. Alongside this, a regional canonical data model—compatible with HL7 v2, FHIR, and IHE XDS—is being developed. This model aims to reduce the need for multiple message transformations by establishing a common (regional) NHS core data standard.

Relationship to NHS England Genomic Order Management Service FHIR API

This guide builds on the use cases outlined in NHS England Genomic Order Management Service FHIR API - Background, expanding them to support a broader range of participants and introducing standards for the Laboratory Order LAB-1. Key differences include:

• Workflow basis: The IHE Laboratory and Testing Worflow LTW serves as the primary reference for describing laboratory testing processes.
• Message translation and code conversion: The Regional Orchestration Engine (RIE) handles translations and code mappings to and from the Genomic Order Management Service FHIR API.
• Routing of orders and reports: The RIE routes orders and reports for other GMSAs through the Genomic Order Management Service FHIR API.
• Regional workflow consistency: Existing regional workflows remain largely unchanged, with both HL7 v2 and FHIR standardised across the region.
• Report compatibility: Reports are aligned with neighbouring Welsh NHS systems, using DHCW HL7 v2 ORU as the core model for both HL7 v2 and FHIR in the North West.

Relationship to NHS England Genomic Order Management Service

Filler Order Management (LAB-2)

See interaction to North East and Yorkshire Genomics in the following section.

Work Order Management (LAB-4)

In Progress

Genomics Work Order Simplified Sequence Diagram

graph TD


subgraph GenomicLIMS["Order Filler"];
    iGene[LIMS<br/>IGene]
end

subgraph HIE["Genomic Archiving and Communication System (GACS)"];
    RIE4["RIE Workflow Orchestration"]
end


subgraph Analyser["Automation Manager"];
    Cepheid[Analyser - Cepheid]
    StarLIMS[LIMS - StarLIMS]
    NEY["Repository - North East and Yorkshire Genomics"]
end

iGene --> |"Work Order Management (LAB-4)<br/>i. Worksheet (iGene SQL data-pipeline)"| RIE4
RIE4 <--> |"Work Order Management (LAB-4)<br/>ii. Lab Orders HL7 QBP Query"| Cepheid
RIE4 <--> |"Work Order Management (LAB-4)<br/>ii. Lab Orders HL7 FHIR Query"| StarLIMS
RIE4 <--> |"Order Notification (LAB-2)<br/> Lab Order O21<br/>HL7 FHIR Query"| NEY 


classDef purple fill:#E1D5E7;
classDef pink fill:#F8CECC;

class GDR,RIE4,VCFFHIR pink;

Test Results Management (LAB-5)

graph TD

subgraph GenomicLIMS["Order Filler"];
    iGene[LIMS<br/>IGene]
end

subgraph Analyser["Automation Manager"];
    Cepheid[Analyser - Cepheid]
    StarLIMS[LIMS - StarLIMS]
end

subgraph HIE["Genomic Archiving and Communication System (GACS)"];
    RIE["Regional Orchestration Engine (RIE)"]
end

Cepheid --> |"Test Results Management (LAB-5/LAB-32)<br/>a. Lab Reports HL7 ORU_R32"| RIE
StarLIMS --> |"Test Results Management (LAB-5)<br/>a. SQL data-pipeline"| RIE

RIE --> |"Test Results Management (LAB-5)<br/>b. CSV  Import"| iGene

classDef purple fill:#E1D5E7;
classDef pink fill:#F8CECC;

class GDR,RIE,VCFFHIR pink;

In Progress

Security Considerations

TODO - is OAuth2 based using client credentials flow.

This may include IHE Internet User Authentication [IUA] and IHE Basic Audit Log Patterns[BALP] which includes use of:

• OAuth2 Standard for Authorisation
  • including use of JWT access tokens and including future support for SMART-on-FHIR Scopes)
• FHIR AuditEvent for Logging Access
• TLS for Transport Security

Cross-Profile Considerations

It is recommended that the actors receive patient demographic and encounter updates only within the context of a work order. Whenever patient data changes, due to:

• Update patient information (A31 or A08)
• Patient transfer (A02)
• Transfer cancelled (A12)
• Patients merge (A40)

Note: Event trigger definitions based on NHS England HL7 v2 ADT Message Specification which is NHS England's supplement to IHE Technical Framework Volume2: Patient Identity Management [ITI-30] and Patient Encounter Management [ITI-31].

It is common for this requirement to be answered by a combination of:

• Patient Administration (PAM)
• IHE Patient Administration Management (PAM)//HL7 v2 ADT Patient Encounter Management (A02, A08 and A12)
  • (Denmark) HL7 FHIR version DK MedCom HospitalNotification