NHS North West Genomics - Local Development build (v2.0.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. 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).

sequenceDiagram
    participant clinician as Order Placer<br/>Clinician (EHR)
    participant nurse as Specimen Collection<br/>Clinician/Nurse
    participant LIMS as Order Filler<br/>LIMS 

    clinician ->> clinician: Creates Order
    clinician ->> LIMS: Sends Laboratory Order
    clinician ->> nurse: Requests specimen collection
    nurse ->> nurse: Collect Specimen
    nurse ->> LIMS: Ship Specimen
    LIMS ->> LIMS: Perform Test
    LIMS ->> LIMS: Write Report
    LIMS ->> clinician: Sends Laboratory Report

Laboratory Order (LAB-1)

Process Flow

graph TD;
    subgraph OrderPlacer;
        EHR["EPR or Order Comms"] 
        SpecimenCollection[Specimen Collection]
        OR[Acute Hospitals<br/>Trust Integration Engine]
        EHR --> |HL7 v2 O01/O21| OR
        EHR --> |"2. Asks for (Order)"| SpecimenCollection    
    end

    RIE["Regional Orchestration Engine (RIE)"]
    GDP["Genomic Data Platform"]
    PubSub["Subscription Service (Future?)"]

    subgraph OrderFiller;
        iGene[LIMS<br/>IGene]
        GOMS["NHS England Genomic Order Management System"] 
        ExtLIMS[External GMSA/LIMS]
    end 

    SpecimenCollection[Specimen Collection] --> |3. Sends Specimen| OrderFiller
    OR --> |HL7 FHIR O21| RIE
    RIE --> |Update| GDP
    RIE --> |HL7 v2 O21| iGene
    RIE --> GOMS
    GOMS --> ExtLIMS
    GDP --> |O21 Event Notification| PubSub
    
    classDef green fill:#D5E8D4;
    classDef yellow fill:#FFF2CC;
    classDef pink fill:#F8CECC;
    class RIE,GDP,PubSub pink;
    class OR green;

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 following:

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.

Laboratory Report (LAB-3)

Process Flow

graph TD;

    subgraph OrderFiller;
        iGene[LIMS<br/>IGene]
        GOMS["NHS England Genomic Order Management System"] 
        ExtLIMS[External GMSA/LIMS]
    end 

    subgraph OrderPlacer;
        EHR["EPR or Order Comms"] 

        OR[Acute Hospitals<br/>Trust Integration Engine]
        OR --> |HL7 v2 R01| EHR

    end
     RIE["Regional Orchestration Engine (RIE)"]
     GDP["Genomic Data Platform"]
    PubSub["Subscription Service (Future?)"]

    RIE --> |HL7 v2 R01| OR
    RIE --> |Update| GDP
    iGene --> |HL7 v2 R01| RIE
    GOMS --> RIE
    ExtLIMS --> GOMS
    GDP --> |R01 Event Notification| PubSub
    
    classDef green fill:#D5E8D4;
    classDef yellow fill:#FFF2CC;
    classDef pink fill:#F8CECC;
    class RIE,GDP,PubSub pink;
    class OR green;

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

Filler Order Management (LAB-2)

LAB-2 is aimed at sending a copy of the order back to the Order Placer, and this will include updated data items such as Order Filler Number. It is envisaged this design will also extend to Laboratory Reports (R01).

Process Flow

graph TD


OrderFiller[Order Filler]
GDP["Genomic Data Platform"]
PubSub["Subscription Service (Future?)"]
RIE[RIE Message Distribution]
OrderPlacer[Order Placer or Interested Party]

OrderFiller --> GDP
GDP --> |O21 Event Trigger| PubSub
GDP --> |O21 Event Trigger| RIE
RIE --> |HL7 v2 OML_O21| OrderPlacer
PubSub --> |Event Notification| OrderPlacer

classDef purple fill:#E1D5E7;
classDef pink fill:#F8CECC;
classDef yellow fill:#FFF2CC;

class GDP,RIE,PubSub pink;
class OrderFiller,OrderPlacer yellow

Work Order and Test Result Management

In Progress

usecase

BCR-ABL1 concentration testing (M84.2) is used to monitor the amount of the fusion gene (Philadelphia chromosome) in chronic myeloid leukemia (CML) patients, with results typically reported on an International Scale (%IS) to measure treatment response.

Genomics Work Order Simplified Sequence Diagram

Work Order Management (LAB-4)

Process Flow

graph TD


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

subgraph HIE["Automation Manager"];
    RIE4["RIE Workflow Orchestration"]
 
end

subgraph OrderFiller;
Cepheid[Analyser - Cepheid]
StarLIMS[LIMS - StarLIMS]

GOMS["NHS England Genomic Order Management System"] 
ExtLIMS[External GMSA/LIMS]

end 

GDP["Genomic Data Platform"]
 PubSub["Subscription Service (Future?)"]

RIE4 --> |Update| GDP
GDP --> |O21 Event Notification| PubSub


iGene --> |"Work Order Management (LAB-4)<br/>Worksheet (iGene SQL data-pipeline)"| RIE4
RIE4 <--> |"Work Order Management (LAB-4)<br/>HL7 QBP Query"| Cepheid
RIE4 <--> |"Work Order Management (LAB-4)<br/>HL7 FHIR Query"| StarLIMS
RIE4 --> |"Work Order Management (LAB-4)<br/>FHIR Transaction"| GOMS
GOMS --> ExtLIMS

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

class GDP,RIE4,PubSub,VCFFHIR pink;

Test Results Management (LAB-5)

Process Flow

graph TD

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

subgraph Analyser["Order Filler"];
    Cepheid[Analyser - Cepheid]
    StarLIMS[LIMS - StarLIMS]
    ExtLIMS[External GMSA/LIMS]
    GOMS["NHS England Genomic Order Management System"] 
    ExtLIMS --> GOMS
end

subgraph HIE["Automation Manager"];
    RIE["Regional Orchestration Engine (RIE)"]
end

GDP["Genomic Data Platform"]
PubSub["Subscription Service (Future?)"]

RIE --> |Update| GDP
GDP --> |R01 or R32 Event Notification| PubSub

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

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

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

class GDP,RIE,PubSub pink;

In Progress

Security Considerations

Includes:

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

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