North West Genomics Testing Workflow (GTW)
0.0.1 - ci-build
North West Genomics Testing Workflow (GTW)
0.0.1 - ci-build
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
(and ORM_O01 General Order)
| Segment HL7 | Optionality |
|---|---|
| MSH | 1..1 |
| PID | 1..1 |
| PV1 | 1..1 |
| ORC | 0..* |
| OBR | 1..* |
| OBX | 1..* |
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values | ||
|---|---|---|---|---|---|---|---|
| MSH-1 | Field Separator | R | ` | ||||
| MSH-2 | Encoding Characters | R | ^~\& | ||||
| MSH-3 | Sending Application | R | iGene | ||||
| MSH-4 | Sending Facility | HD | R | ODS Code | 699X0 | ||
| MSH-5 | Receiving Application | HD | R | EPIC | |||
| MSH-6 | Receiving Facility | R | ODS Code | R0A | |||
| MSH-7 | Date/Time Of Message | R | 20170126143602 | ||||
| MSH-9 | Message Type | R | ORU^R01^ORU_R01 | ||||
| MSH-10 | Message Control ID | R | 2017012614360280000 | ||||
| MSH-11 | Processing ID | R | P | ||||
| MSH-12 | Version ID | R | 2.5.1 | ||||
| MSH-13 | Accept AcknowledgmentType | R | AL |
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values |
|---|---|---|---|---|---|
| PID-1 | Set ID-PID | R | 1 | ||
| PID-3 | Patient Identifier List | CX | R | NHS Number Medical Record Number. | 633^^^R0A^MR~9449305552^^^NHS^NH |
| PID-5 | Patient Name | R | CHISLETT^Octavia^^Miss | ||
| PID-7 | Date/Time of Birth | R | 20080920 | ||
| PID-8 | Administrative Sex | R | F | ||
| PID-11 | Patient Address | R | 1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST | ||
| PID-13 | Phone Number - Home | R | 01656 123123^PRN^PH~07927655295^ORN^CP^NET^X.400^abc@home.com~01656 123123~01656123123^PRN^PH^^^abc@home.com~01656123123^PRN^PH | ||
| PID-32 | Identity Reliability Code | O | Mandatory if the the NHS Number tracing status is not known. | 01 |
The PV1 segment should represent the sending organisations encounter, i.e. the one that created the order or report. This differs from DHCW definition.
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values |
|---|---|---|---|---|---|
| PV1-1 | Set ID - PV1 | PL | R | 1 | |
| PV1-3 | Assigned Patient Location | R | ^^^R0A09^^^^^^^R0A ^^^P1S8J^^^^^^^699X0 |
||
| PV1-8 | Referring Doctor | XCN | R | Practitioner Identifier | C3456789^Darwin^Samuel^^^Dr^^^GMC |
| PV1-10 | Hospital Service | R | Service | 311 |
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values |
|---|---|---|---|---|---|
| ORC-2 | Placer Order Number | EI | R | Placer Order Number | 1601737^ R0A^150^L |
| ORC-3 | Filler Order Number | EI | R | Filler Order Number | 1001166717^699X0^^255^ISO |
| ORC-4 | Placer Group Number | EI | R | Placer Group Number | 1001166717^699X0^^255^ISO |
| ORC-5 | Order Status | O | |||
| ORC-9 | Date/Time of Transaction | O | |||
| ORC-12 | Ordering Provider | XCN | R | Practitioner Identifier | C3456789^Darwin^Samuel^^^Dr^^^GMC |
| ORC-21 | Ordering Facility Name | XON | R | ODS Code |
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values |
|---|---|---|---|---|---|
| OBR-1 | Set ID - OBR | R | 1 | ||
| OBR-2 | Placer Order Number | EI | R | Placer Order Number | 1601737^ R0A^150^L |
| OBR-3 | Filler Order Number | EI | R | Filler Order Number | 1001166717^699X0^^255^ISO |
| OBR-4 | Universal Service Identifier | R | Genomic Test Directory | R240.1^Diagnostic testing for known variant(s)^England-GenomicTestDirectory | |
| OBR-7 | Observation Date/Time | R | 20170126135745 | ||
| OBR-16 | Ordering Provider | R | Practitioner Identifier | C3456789^Darwin^Samuel^^^Dr^^^GMC | |
| OBR-22 | Results Rpt/Status Chng -Date/Time | R | 20170126135745 |
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values |
|---|---|---|---|---|---|
| OBX-1 | Set ID – OBX | R | 1 | ||
| OBX-2 | Value Type | R | ED | ||
| OBX-3 | Observation Identifier | CE | R | Document Entry Type | 1054161000000101^Genetic report^SNM |
| OBX-5 | Observation Value | ED | R | MOL^IM^PDF^Base64^JVBERI0X… | |
| OBX-11 | Observation Result Status | R | F | ||
| OBX-14 | Date/Time of the Observation | 20190514102417+0000 |
This applies to HL7 v2 ORU_R01 feeds to the RIE.
ORC-3, ORC-12 (XCN) and ORC-21 (XON) SHALL be populated.
Coded Element. UK SNOMED CT is preferred and may be mandatory depending on use, for example for OXB Type ED, it will be required.
SNOMED
1054161000000101^Genetic report^SNM
LOINC (from HL7 International)
53577-3^Reason for study^LN
51967-8^Genetic disease(s) assessed^LN
48018-6^Gene studied^LN
Extended Composite ID with Check Digit CX.1 - Id Number, CX-4 - Assigning authority and CX.5 - Identifier Type Code are mandatory
NHS Number
9449305552^^^NHS^NH
Medical Record Number
633^^^R0A^MR
Entity Identifier. EI.1 - Entity Identifier and EI.2 - Namespace Id are mandatory
Manchester University NHS Foundation Trust
1601737^R0A
North West GLH Hub
1001166717^699X0
This is baed on the definition of PL from NHS England HL7 v2 ADT Message Specification SHOULD be followed and SHALL be used in ORC-12. In addition, this includes of PL.11 to hold organisation ODS code.
The ODS Site Code SHALL belong to the ODS Code. This is to help avoid data issues in this codesystem.
| Field HL7 | Fieldname | Data Type | Optionality | Table and Notes | Example Values |
|---|---|---|---|---|---|
| PL.4 | Facility | HD | R | Organisation Site Code | R0A09 |
| PL.11 | Assigning Authority For Location | HD | R | Organisation Code | R0A |
Extended Composite ID Number and Name for Persons. The definition of XCN from NHS England HL7 v2 ADT Message Specification SHOULD be followed and SHALL be used in ORC-12.
Example
GMC Code
C3456789^Darwin^Samuel^^^Dr^^^GMC
Extended Composite Name and Identification Number for Organizations. The definition of XON from NHS England HL7 v2 ADT Message Specification SHOULD be followed and SHALL be used in ORC-21.
Example
MANCHESTER UNIVERSITY NHS FOUNDATION TRUST^^R0A^^^ODS
MSH|^~\&|EPIC|R0A|iGene|699X0|20190514102527+0200||OML^O21^OML_O21|9612365d-52a4-4fab-87e7-8a09d753f095|T|2.5.1|||AL
PID|1||633^^^R0A^MR~9449305552^^^NHS^NH||CHISLETT^Octavia^^Miss||20080920|F|||1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST
PV1|1|N|^^^R0A09^^^^^^^R0A|||||C3456789^Darwin^Samuel^^^Dr^^^GMC||311
ORC|RE|1601737^R0A|1001166717^699X0||SC||||20170126143602|||C3456789^Darwin^Samuel^^^Dr^^^GMC|||||||||MANCHESTER UNIVERSITY NHS FOUNDATION TRUST^^R0A^^^ODS
OBR|1|1601737^R0A||R240.1^Diagnostic testing for known variant(s)^England-GenomicTestDirectory|||20190514102000+0200|||SCC|O|||20190514102000+0200||C3456789^Darwin^Samuel^^^Dr^^^GMC||||||20190514102417+0200
OBX|1|ED|721965002^Laboratory order^SNM||MOL^IM^PDF^Base64^JVBERi0x...||||||F
SPM|1|25GEN-029GN00001^R0A||||||||||||||||||Y
MSH|^~\&|iGene|699X0|EPIC|R0A|20190514102527+0200||ORU^R01^ORU_R01|5051095-201905141025|T|2.5.1|||AL
PID|1||633^^^R0A^MR~9449305552^^^NHS^NH||CHISLETT^Octavia^^Miss||20080920|F|||1 RAVENSFIELD GARDENS^^EPSOM^SURREY^KT19 0ST
PV1|1|N|^^^P1S8J^^^^^^^699X0|||||C3456789^Darwin^Samuel^^^Dr^^^GMC||311
ORC|RE|1601737^R0A|1001166717^699X0||CM||||20170126143602|||C3456789^Darwin^Samuel^^^Dr^^^GMC|||||||||MANCHESTER UNIVERSITY NHS FOUNDATION TRUST^^R0A^^^ODS
OBR|1|1601737^R0A|1001166717^699X0|R240.1^Diagnostic testing for known variant(s)^England-GenomicTestDirectory|||20190514102000+0200|||SCC|O|||20190514102000+0200||C3456789^Darwin^Samuel^^^Dr^^^GMC||||||20190514102417+0200
OBX|1|ED|1054161000000101^Genetic report^SNM||MOL^IM^PDF^Base64^JVBERi0x...||||||F
IG © 2024+ Manchester University NHS Foundation Trust. Package nhs.mft.fhir#0.0.1 based on FHIR 4.0.1. Generated 2025-02-22
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