Manages the Order. This is the function of Genomic Order Management Service and/or GLH LIMS

From ISO-13606 The set of information committed to one EHR as a result of a clinical encounter or a record documentation session. Examples of COMPOSITION are Progress note, Laboratory test result form, Radiology report, Referral letter, Clinic visit, Clinic letter, Discharge summary, Functional health assessment, Diabetes review.

North West GLH Regional Orchestration Engine (RIE) This is a Trust Integration Engine (TIE) working at a regional level

Fulfils the Order. The Order Filler Actor is implemented by laboratory information management systems.

Creates the Order. The Order Placer Actor is implemented by the systems used by the clinical practice.

Allows practitioners to view the Genomics Test Report (e.g. Patient Pass or EPR)

Source of the patient demographics change. The Patient Identity Source is implemented by the systems used for patient administration (e.g. PAS or EPR).

Source of the provider information change. The Provider Information Source is implemented by the systems used for patient administration (e.g. PAS or EPR) or Organisation Directories (LDAP/X.500).

The Actor ran by a private or hospital laboratory that subcontracts a part of an Order or of an Order Group to another laboratory. This actor may also be referred to as Order Placer

The Actor ran by a laboratory performing tests upon request from other laboratories. This actor may also be referred to as Order Filler

Is based on FHIR Messaging to handle transformation of HL7 FHIR and v2 Messages to FHIR Workflow.

The OpenAPISwagger Definition file below, can be viewed using Swagger Editor

Is based on EURIDICE Health Data API, which we are using as FHIR R4 version of Care Connect API

The OpenAPISwagger Definition file below, can be viewed using Swagger Editor

This is documentation on the version of HL7 FHIR process-message to be used for regional FHIR Messaging, this HL7 FHIR definition SHALL be followed.

OperationOutcome is required for rejected messages.

Search parameter for searching resource identifier for assigning authority

NHS England North West Genomics Test Order (Draft)

The aim of this is to support conversion of Genomic Report (HL7 v2 ORU) for use by several NHS Trusts (as HL7 v2 or FHIR).

Audit

Health Document

FHIR Document

FHIR Messaging

Diagnostic - Laboratory

Patient Care

Diagnostic - Genomics Reporting Implication

Diagnostic - Core

Messaging Document Message

Health Document

Patient Administration Base, for implementation see

• Account Number Hospital Spell - an admission (inpatient or outpatient)
• Visit Number Visit - an A&E attendance, a community contract, an OP attendance (Appointment), etc

Messaging Event Messsage

Patient Care

Diagnostic - Genomic Reporting

Diagnostic - Genomics

Diagnostic - Genomics Reporting Finding

Diagnostic - Genomics Reporting Finding

Patient Administration Related to Yorkskhire and Humberside - EncounterGrouping

Diagnostic - Laboratory

Diagnostic - Genomics Reporting

Diagnostic - Core

Diagnostic - Core for use with test orders. Does not define categories

Diagnostic Reference - HL7 Europe Laboratory Report - Observation Results: laboratory

DRAFT Extension of OperationOutcome

Care Directory HL7 Europe Core - Organizationhttp://hl7.eu/fhir/base/StructureDefinition/organization-eu-core

Patient Administration HL7 Europe Core - Patient

Care Directory HL7 Europe Core - Practitioner

Care Directory HL7 Europe Core - PractitionerRole

Patient Care

Data Capture Initial elaboration extending SDC Questionnaire

Data Capture DRAFT Initial elaboration

Patient Administration

Diagnostic - Laboratory

Diagnostic - Laboratory Specimen Collection

Diagnostic Based on FHIR Workflow

Diagnostic - Genomics Reporting Implication

Diagnostic - Genomics Reporting Finding

Patient Administration Equivalent to Yorkskhire and Humberside - Encounter

Diagnostic iGene Work Order Management

DRAFT: Additional conformance on FHIR Attachment data type.

DRAFT Extension to FHIR Reference to include Codes (i.e. SNOMED Concepts)

Core Data Contract for FHIR Identifier, v2 CX and EI

Patient Administration HL7 IdentifierType: PI Patient Identifier 'NHS Data Model and Dictionary' GS1 Global Service Relation Number GS1 Pathology GS1 Code 8018

Diagnostic Workflow HL7 IdentifierType: STN Shipment Tracking Number GS1 Serial Shipping Container Code (SSCC) GS1 Pathology

Patient Administration HL7 IdentifierType: AN/VN Account/Visit number 'NHS Data Model and Dictionary' GS1 SERVICE RELATION INSTANCE NUMBER GS1 Pathology GS1 Code 8019

Patient Administration

Patient Administration HL7 IdentifierType: AN Account Number 'NHS Data Model and Dictionary' HOSPITAL PROVIDER SPELL IDENTIFIER Accession ID

Patient Administration HL7 IdentifierType: MR Medical record number 'NHS Data Model and Dictionary' LOCAL PATIENT IDENTIFIER

Patient Administration HL7 IdentifierType: NH National Health Plan Identifier NHS Data Model and Dictionary England/Wales NHS NUMBER, Northern Ireland HEALTH AND CARE NUMBER and Scotland COMMUNITY HEALTH INDEX NUMBER Only traced NHS Number SHOULD be used, un-traced NHS Numbers MUST be clearly indicated.

Diagnostic Workflow HL7 IdentifierType: PGN Placer Group Number

Diagnostic Workflow HL7 IdentifierType: Placer/Filler Identifier

Patient Administration 'NHS Data Model and Dictionary' ORGANISATION_CODE

Care Directory 'NHS Data Model and Dictionary' ORGANISATION SITE IDENTIFIER

Patient Administration HL7 IdentifierType: PI Patient Identifier NHS Data Model and Dictionary LOCAL PATIENT IDENTIFIER NHS England Canonical Data Model Not applicable, use MedicalRecordNumber only.

'Care Directory' 'NHS Data Model and Dictionary' CONSULTANT CODE and GENERAL MEDICAL PRACTITIONER PPD CODE.

Diagnostic Workflow HL7 IdentifierType: FILL Filler Identifier

Diagnostic Workflow HL7 IdentifierType: STN Shipment Tracking Number

Diagnostic Workflow HL7 IdentifierType: ACSN Accession ID Uniquely identifies a Specimen across multiple laboratory systems. This is related to RADIOLOGICAL ACCESSION NUMBER which applies to Imaging Studies.

Patient Administration HL7 IdentifierType: VN Visit Number

(copied from BE eHealth Platform Federal Core Profiles) Extension able to hold a reference and a concept (Temporary solution until https://jira.hl7.org/browse/FHIR-44661 is solved and see Zulip: https://chat.fhir.org/#narrow/stream/179280-fhir.2Finfrastructure-wg/topic/Backporting.20CodeableReference )

NHS Data Model and Dictionary ADMISSION METHOD

NHS Data Model and Dictionary ADMISSION SOURCE

• UKCoreSourceOfAdmission

NHS Data Model and Dictionary DESTINATION OF DISCHARGE

• UKCoreDischargeDestination

NHS Data Model and Dictionary DISCHARGE METHOD CODE

• UKCoreDischargeMethod

• Switzerland DocumentEntry.classCode
• NHS England NRL - Record Category

• Digital Health and Care Scotland (EH4001) CLINICAL DOCUMENT INDEXING STANDARDS LA Labs
• NHS England NRL -Record Type

• Switzerland DocumentEntry.mimeType

NHS Data Model and Dictionary ETHNIC CATEGORY This extends UKCoreEthnicCategory to include other categories for reasons stated in Wikipedia: Classification of ethnicity in the United Kingdom

NHS Data Model and Dictionary ACTIVITY LOCATION TYPE CODE

• See National genomic test directory for cancer on Genomic Test Directory

1st level classification of NHS England Genomic Test Directory codes

Genomic Disorder Carrier

Genomic Finding

Genomic Finding Detected

• See National genomic test directory for rare and inherited disease on Genomic Test Directory

• See NHS England Genomic Test Directory

Test Outcome Codes from NHS England Genomic Test Outcome Codes

IdentifierType work around to bypass lack of NH in based definition

Top level classification of Genomic Test Directory

IHE Patient Encounter Management [ITI-31]

A28/A31/A40

PractitionerIdentifiers

ValueSet for Pregnancy answers

Copy of UKCoreReportCode

ValueSet for Request Priority

DRAFT NHS Data Model and Dictionary TREATMENT FUNCTION CODE

• UKCoreCareSettingType

NHS Data Model and Dictionary MAIN SPECIALTY CODE

• UKCorePracticeSettingCode
• HL7 Practice Setting Code Value Set

Intent is to use SNOMED CT H:7 ValueSet Body Site

• IHE Specimen Event Tracking

A subset of HL7 Europe Laboratory Report ValueSet: Specimen Types Local codes are provided for backward compatability, SNOMED codes are preferred.

NHS Number, CHI Number and Health and Care Number

ValueSet for Yes/No answers

ValueSet for Yes/No/Unknown answers

TODO

TODO

Bucket for local codes

1st level Genomic Test Directory Codes

• Genomic Test Directory"

HL7 v2 CodeSystem : England-GenomicTestDirectory

Test Outcome Code from NHS England Genomics Test Reporting Specification

Bucket for local codes

HL7 v2 CodeSystem : NWTestCode

TODO Placeholder

England/Wales NHS Number, Scotland CHI Number and Northern Ireland Health and Care Number

UK Professional License

iGene Codes

iGene Sample Sub Type

iGene Test Codes

General Medical Council Consultant Code. For more details see: NHS Data Model Dictionary

General Practitioner (GMP) number. For more details see: NHS Data Model Dictionary

NHS Number allocated to the patient in England and Wales. For more details see: NHS Data Model Dictionary

The identifier system for an Organisation registered with the Organisation Data Service (ODS).

The identifier system for an Organisation site registered with the Organisation Data Service (ODS).

Sample Body Site (SNOMED) to iGene Specimen Sub Type

Sample Type (SNOMED) to iGene Specimen Type

Overview Clinical Workflow including Genomic Diagnostic Testing

This is for background information around the specimen collection process, it is not considered part of this genomic specification.

This is for background information for genomic test ordering.

This is for background information for genomic test reporting.

AuditEvent Mobile Query Existing Data [PCC-44]

AuditEvent Placer Order Management [LAB-1] V2/FHIR O21 Order

Binary Sample PDF

Influenced by HL7 v2 ADT_A31

Example Filler Order Message for internal or external LIMS

Async response to a Genomic Order

Acknowledgement of Async response to a Genomic Order

Influenced by HL7 v2 OML_O22

Example search results for Conditions for Patient Liverpool

Example search results for a form with id of GenomicTestOrder

Example search results for a Genomic Diagnostic Implication for Patient Liverpool

Example search results for a Genomic Variant Gene = NTHL1

Example search results for a Genomic Variant LOINC 69548-6 for Patient Liverpool

Example search results for a MRN Number of A12356565

Example search results for a NHS Number of 9449305552

Composition - Genomics Report ctDNA

evidenced by pathology diagnostic testing

evidenced by genomic diagnostic testing

TODO. See also https://digital.nhs.uk/data-and-information/data-collections-and-data-sets/data-sets/maternity-services-data-set/guidance/msds-consanguinity-data-quality-guidance

Ned Liverpool Lynch Syndrome

Diagnostic Report ctDNA Example

TODO

TODO

TODO

TODO

TODO

TODO

TODO

Example Document and Document Notification Message for GMCR

Example of a Message Acknowledgement

Example of a Message Search

FHIR RESTful POST ServiceRequest

FamilyMemberHistory - Ricky LEEDS

FamilyMemberHistory - Sarah-Jane Nottingham

Genomic Report BRCA1 Variant Example

Genomic Report Ovarian Carcinoma Diagnostic Implication Example

Based on HL7 LRI Example 1 (Ref 5.9.1.2)

Based on HL7 LRI Example 1 (Ref 5.9.1.2)

Based on HL7 LRI Example 3 (Ref 5.9.1.3)

Based on HL7 LRI Example 3 (Ref 5.9.1.3)

TODO

TODO

TODO

Laboratory Analyte Result BCRABL Invalid Example

Laboratory Analyte Result BCRABL Valid Example

This is based on US Core Example Observation: MCV Example and incorporates extra coding from NHS England Pathology - PATH-R4-10: Bundle Example - Full Blood Count Report

For coding descriptions see

• 1022491000000106 and 1491000237105 SNOMED UK Edition
• 613061010000108 and 787-2 SNOMED LOINC Edition

TODO

TODO

TODO

TODO

TODO

TODO

TODO

Based on HL7 LRI Example 3 (Ref 5.9.1.3)

DPD, Hermes, etc

Organization MANCHESTER UNIVERSITY NHS FOUNDATION TRUST

Organization North West GMSA

Parameters Expansion Profile

Test Patient for Birmingham and Solihull ICB.

Test Patient for Bolton

Test Patient for Congleton

Test Fetus Patient for London

Test Patient for Lancaster

Test Patient for London

Test Patient for Cheshire and Merseyside ICS

Test Patient for Northwich

Test Patient for Nottinghamshire ICS

Test Patient for West Yorkshire ICB

Test Patient for Greater Manchester ICS

Test Patient for South Yorkshire ICB

Test Patient for Warrington

Test Patient for Wrexham and Wales

TODO

TODO

TODO

RelatedPerson for Birmingham-Lancaster

RelatedPerson for Birmingham-London

RelatedPerson for Lancaster-London

RelatedPerson for London-Lancaster

RelatedPerson for Mother Cersei London to Fetus Baby London

RelatedPerson for Wrexham-Lancaster

RelatedPerson for Wrexham-London

TODO

TODO

TODO

TODO

Example Filler Order Message for internal or external LIMS

Influenced by HL7 v2 OML_O22

Influenced by HL7 v2 OML_O21

Influenced by HL7 v2 OML_O21

FHIR Message Query Example for use with Asynchronous Message Delivery

TODO

TODO

TODO

TODO

Example NHS England PDS Test Pack

TODO

TODO

TODO

TODO

Influenced by HL7 v2 ORU_R01

First draft is based on Royal College of Radiologists HL7 v2 ORU converted to HL7 FHIR. Will be converted to a Genomics example

TODO

TODO

Genomics Order ctDNA

Genomics Report ctDNA

FHIR Document Genomics Report ctDNA for Theon Sheffield

FHIR Document Genomics Report for Ned Liverpool

FHIR Document Genomics Report for Jack Dawkins

Composition - Genomics Report LynchSyndrome

Composition - Genomics Report Octavia CHISLETT

Based on HL7 LRI Example 2 (Ref 5.9.1.2)

Based on HL7 LRI Example 3 (Ref 5.9.1.3)

Based on HL7 LRI Example 1 (Ref 5.9.1.2)

Based on HL7 LRI Example 3 (Ref 5.9.1.3)

Based on HL7 LRI Example 2 (Ref 5.9.1.2)

Based on HL7 LRI Example 3 (Ref 5.9.1.3)

TODO

TODO

TODO

TODO

TODO

TODO

TODO

TODO

TODO

TODO

TODO

TODO

TODO

See Bundle-Bundle-NonWGSTestOrderForm-Reanalysis-Example

See Bundle-NonWGSTestOrderForm-CancerSolidTumor-Example

See Bundle-NonWGSTestOrderForm-FetalScenario-Example

Proof of concept example. Type, category, custodian and author are currently incorrect values

Proof of concept example. Type, category, custodian and author are currently incorrect values