DRAFT Implementation Guide

This is for collaboration and discussion purposes and is subject to change.

North West Genomics Testing Workflow (GTW) - Local Development build (v0.0.1) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Laboratory Testing Workflow (LTW)

References

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

Actors and Transactions

Actor	Definition
Order Placer	Commonly known as the Electronic Patient Record (EPR) 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

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-4 is in focus and this is probably using HL7 v2.x ORM_O01/OML_O21 as described below. This will be followed by IHE LAB-3 probably using HL7 v2.x ORU_R01 plus LAB-2 and LAB-5 Later stages will include the use of Genomic Order Management Service.

Overview

Genomic LTW Business Process

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

Use Case 1: 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 Genomics Test Order Form (Minimal Dataset)

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 Integration Engine using:

• LAB-1 for orders raised by Order Placer systems.
• LAB-4 for orders raised by Order Filler systems to another Order Filler system (typically pathology systems).

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 Request Entity Model.

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 order will be updated to include details such as a specimen collection date, order filler number, etc. This is also a method of notifying organisations of orders entered directly in the Order Filler system, see LAB-2.

Use Case 2: 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

Use Case 3: Genomic Test Order following on from Pathology Test Order

Genomic LTW Business Process - Use Case 3

In this use case the original order is raised by the Order Placer and sent to a Pathology LIMS (Pathology Order Filler). The Pathology LIMS follows the processes outlined in Use Case 1: Genomic Test Order and Use Case 2: Genomic Test Report for pathology testing.
As part of this testing, the clinical process requires a genomics test to be performed. This genomics process is largely the same except for:

• The order is sent as one interaction as the sample does not need to be collected.
• The order should contain the pathology report detailing the results of the pathology tests.

Use Case 4: Genomic Test Order entered on GLH (Order Filler)

Genomic LTW Business Process - Use Case 4

In this use case the order has been manually entered into NW GLH LIMS (as a result of an email or telephone call). The Order Filler notifies the Order Placer of the order. The Order Placer can then update the Order Filler when details change on the order such as a Order Placer Number assigned or updating details on the specimen such as collection dates. The proces then follows the same process as Use Case 2: Genomic Test Report

Security Considerations

TODO

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