NHS North West Genomics
2.2.0 - ci-build United Kingdom flag

NHS North West Genomics - Local Development build (v2.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Table of Contents

.. 0 Table of Contents
... 1 Home
... 2 How To Engineer (scale and deliver) Interoperability
... 3 Laboratory Testing Workflow (LTW)
... 4 Inter Laboratory Workflow (ILW)
... 5 Specimen Transportation and Management
... 6 Genetic Referrals
... 7 Health Data API (HIE/EURDICE)
... 8 API Security
... 9 Resource Access [IPA/QEDm]
... 10 Message Exchange [LTW/MQ]
... 11 Document Exchange [MHD]
... 12 Patient Identity Matching (PDQm)
... 13 Authorisation [IUA]
... 14 HL7 v2 Standards
... 15 Distributed Whole Genome Sequencing (dWGS)
... 16 Use Case: Histocompatibility and Immunogenetics (Clatterbridge to Histotrac)
... 17 Testing
... 18 Support
... 19 Overview - Data Contracts
... 20 Use Case: BCR-ABL Monitoring
... 21 Use Case: Whole Genome Sequencing (Proposed - Alder Hey, MFT, Liverpool)
... 22 Use Case: Cytogenetics and Haemato-Oncology Diagnostic Pathway (Shire to HODS)
... 23 Use Case: Cheshire and Merseyside Pathology
... 24 Use Case: Cancer Background Information for Use Cases
... 25 Developer Guides
... 26 Use Case: OMICS DSS Result Integration
... 27 Use Case: Clarity LIMS Integration (Proposed - Replacing Omics DSS and DLIMS)
... 28 Use Case: NHS England Genomic Order Management Service (GOMS)
... 29 Use Case: ctDNA Management Information (NW to NE&Y Genomics)
... 30 Use Case: ctDNA NHS England Unified Genomic Record (UGR)
... 31 Use Case: Regional Integration Engine (RIE)
... 32 Use Case: iGene Orders and Reports (Alder Hey, MFT, Liverpool)
... 33 Use Case: Regional Shared Care Records
... 34 Use Case: StarLIMS / iGene Integration
... 35 Architecture
... 36 Architecture - Enterprise Integration Patterns (EIP)
... 37 Diagnostic Model Overview
... 38 Artifacts Summary
.... 38.1 Automation Manager
.... 38.2 Clinical Document
.... 38.3 Document Access Provider
.... 38.4 Document Consumer
.... 38.5 Document Publisher
.... 38.6 Intermediary
.... 38.7 Order Filler
.... 38.8 Order Placer
.... 38.9 Order Result Tracker
.... 38.10 Patient Identity Source
.... 38.11 Provider Information Source
.... 38.12 Requestor (ILW)
.... 38.13 Resource Access Provider
.... 38.14 Subcontractor (ILW)
.... 38.15 CapabilityStatement for NW Genomics Genomic Data Platform (EURIDICE Health Data API)
.... 38.16 CapabilityStatement for NW GMSA Regional Orchestration Engine for Genomics
.... 38.17 Process Message
.... 38.18 Message Definition - Acknowledgement
.... 38.19 Message Definition - Document and Document Notification
.... 38.20 Message Definition - Laboratory Order
.... 38.21 Message Definition - Unsolicited Observation
.... 38.22 assigner
.... 38.23 BCR-ABL Monitoring Result Panel
.... 38.24 Cancer Test Additional Ask At Order Entry Questions
.... 38.25 Chimerism Test Additional Ask At Order Entry Questions
.... 38.26 Chimerism Testing Result Panel
.... 38.27 CYP2C19 Mavacamten (R454) Ask At Order Entry Questions
.... 38.28 Cystic Fibrosis Carrier Testing Ask At Order Entry Questions
.... 38.29 Deafness (R67) Ask At Order Entry Questions
.... 38.30 dWGS Ask At Order Entry Questions
.... 38.31 Genetic Clinical Referral
.... 38.32 Genetic Clinical Referral - Consultand (RelatedPerson)
.... 38.33 Genomic Variant Review Ask At Order Entry Questions
.... 38.34 GMS WGS Cancer Ask At Order Entry Questions
.... 38.35 GMS WGS Rare Disease
.... 38.36 H&I Haematopoietic Stem Cell Transplantation (Recipients & Donors) Ask At Order Entry
.... 38.37 H&I Organ Transplant (Patients and Donors) Ask At Order Entry
.... 38.38 Haemato-Oncology Ask At Order Entry Questions
.... 38.39 Haemoglobinopathy Genetic Testing Ask At Order Entry Questions
.... 38.40 HLA Tests - Transplant Ask At Order Entry
.... 38.41 HRD and Tumour BRCA Ask At Order Entry Questions
.... 38.42 iGene Laboratory Order Export (CSV)
.... 38.43 iGene Work Order Export (CSV)
.... 38.44 Master HL7 genetic variant reporting panel
.... 38.45 North West Genomics dWGS Sub-Order Manifest
.... 38.46 North West Genomics Test Order
.... 38.47 North West Genomics Test Report
.... 38.48 NW Genomic General Ask At Order Questions
.... 38.49 Prenatal Haemoglobinopathy Ask At Order Entry Questions
.... 38.50 Rare Disease Genomic Testing Ask At Order Entry Questions
.... 38.51 Reportable Variant Result Panel
.... 38.52 WGS Local Test Order Ask At Order Entry Questions
.... 38.53 WGS Test Additional Ask At Order Entry Questions
.... 38.54 AuditEvent
.... 38.55 Binary
.... 38.56 Bundle - FHIR Document
.... 38.57 Bundle - FHIR Messaging
.... 38.58 Composition Genomic Report
.... 38.59 Condition
.... 38.60 Diagnostic Implication (Observation)
.... 38.61 Diagnostic Report
.... 38.62 Document Message (MessageHeader)
.... 38.63 DocumentReference
.... 38.64 Encounter
.... 38.65 Event Notification (MessageHeader)
.... 38.66 FamilyMemberHistory
.... 38.67 Genomic Observation
.... 38.68 Genomic Study Panel
.... 38.69 Genotype (Observation)
.... 38.70 Haplotype (Observation)
.... 38.71 Hospital Spell
.... 38.72 Laboratory Analyte Result (Observation)
.... 38.73 Molecular Biomarker
.... 38.74 Molecular Consequence (Observation)
.... 38.75 Observation
.... 38.76 Observation Order
.... 38.77 Observation Panel
.... 38.78 OperationOutcome
.... 38.79 Organization
.... 38.80 Patient
.... 38.81 Practitioner
.... 38.82 PractitionerRole
.... 38.83 Procedure
.... 38.84 Questionnaire
.... 38.85 QuestionnaireResponse
.... 38.86 RelatedPerson
.... 38.87 ServiceRequest
.... 38.88 Specimen
.... 38.89 Task
.... 38.90 Therapeutic Implication (Observation)
.... 38.91 Variant (Observation)
.... 38.92 Visit
.... 38.93 WorkOrder
.... 38.94 Attachment
.... 38.95 CodeableReference
.... 38.96 Correlation Identifier
.... 38.97 Genomics Pedigree Number
.... 38.98 GS1 Global Service Relation Number (GSRN)
.... 38.99 GS1 Serial Shipping Container Code (SSCC)
.... 38.100 GS1 Service Relation Instance Number (SRIN)
.... 38.101 Hospital Provider Spell Identifier
.... 38.102 Medical Record Number
.... 38.103 NHS Identifier
.... 38.104 Order Group Number
.... 38.105 Order Identifier
.... 38.106 Organisation Code
.... 38.107 Organisation Site Identifier
.... 38.108 Patient Identifier
.... 38.109 Practitioner Identifier
.... 38.110 Report Identifier
.... 38.111 Shipment Tracking Number
.... 38.112 Specimen Accession Number
.... 38.113 Visit Number
.... 38.114 ExtCodeableReference
.... 38.115 Admission Method
.... 38.116 Admission Source
.... 38.117 Discharge Destination
.... 38.118 Discharge Disposition
.... 38.119 DocumentEntry Class
.... 38.120 DocumentEntry mimeType
.... 38.121 DocumentEntry Type
.... 38.122 Ethnicity
.... 38.123 Facility Type
.... 38.124 Genomic Cancer Test Directory
.... 38.125 Genomic Clinical Indication Codes
.... 38.126 Genomic Disorder Carrier
.... 38.127 Genomic Finding
.... 38.128 Genomic Finding Detected
.... 38.129 Genomic Haematological Oncology Test Directory
.... 38.130 Genomic Rare and Inherited Disease Test Directory
.... 38.131 Genomic Test Codes
.... 38.132 Genomic Test Outcome Codes
.... 38.133 GMS WGS Cancer Form - Guide Test Codes
.... 38.134 GMS WGS Rare Disease Form - Guide HPO Terms
.... 38.135 GMS WGS Rare Disease Form - Guide Test Codes
.... 38.136 iGene Variant Category
.... 38.137 NGIS Test Code
.... 38.138 NW IdentifierType
.... 38.139 Order Category
.... 38.140 Patient Encounter Trigger
.... 38.141 Patient Identity Trigger
.... 38.142 Practitioner Identifiers
.... 38.143 Pregnancy
.... 38.144 ReportType
.... 38.145 Request Priority
.... 38.146 Service
.... 38.147 Specialty
.... 38.148 Specimen Body Site
.... 38.149 Specimen Tracking Events
.... 38.150 Specimen Type
.... 38.151 UK National Health Identifiers
.... 38.152 Yes/No
.... 38.153 Yes/No/Unknown
.... 38.154 CodeSystem for Analyser
.... 38.155 CodeSystem for Chimerism Testing (OBX-3 local codes)
.... 38.156 CodeSystem not defined or to be determined
.... 38.157 Histotrac Test Codes
.... 38.158 iGene Codes
.... 38.159 iGene Sample Sub Type
.... 38.160 iGene Test Codes
.... 38.161 iGene Variant Category
.... 38.162 MFT EPIC Question Ids
.... 38.163 NHS England Digital Genomic Test Services
.... 38.164 NHS England Genomic Clinical Indication Code
.... 38.165 NHS England Genomic Test Code
.... 38.166 NHS England Genomic Test Outcome Code
.... 38.167 North West Genomics Test Code
.... 38.168 NW GMSA Codes
.... 38.169 Task Input/Output Parameter Type
.... 38.170 UK National Health Identifiers
.... 38.171 UK Professional License
.... 38.172 GMC Number
.... 38.173 GMP Number
.... 38.174 NHS Number
.... 38.175 ODS Code
.... 38.176 ODS Site Code
.... 38.177 Genomic Clinical Indication (M*) to Digital Genomic Test Services (TP)
.... 38.178 Genomic Clinical Indication to Genomic Test Code (narrower)
.... 38.179 Genomic Test Code (M*) to Digital Genomic Test Services (GT)
.... 38.180 GMS WGS Guide HPO Terms to SNOMED CT
.... 38.181 Sample Body Site (SNOMED) to iGene Specimen Sub Type
.... 38.182 Sample Type (SNOMED) to iGene Specimen Type
.... 38.183 Clinical and Genomic Workflow
.... 38.184 Collect Specimen - Biopsy Procedure for obtaining a specimen, part of a diagnostic pathway. Day case admission.
.... 38.185 Genomic Test Order Process including order entry and transmission of the order
.... 38.186 Genomic Test Report Process
.... 38.187 AuditEvent Mobile Query Existing Data [PCC-44]
.... 38.188 AuditEvent Placer Order Management [LAB-1] V2/FHIR/V2 Order
.... 38.189 Binary Sample PDF
.... 38.190 Bundle 'Event Message' - Patient Update
.... 38.191 Bundle 'Message' - Genomics Order Reply
.... 38.192 Bundle 'Message' - Genomics Order Reply Acknowledgement
.... 38.193 Bundle 'Transaction' - Genomics Order Asynchronous Message Reply Acknowledgement
.... 38.194 Bundle - Conditions for a Patient QEDm
.... 38.195 Bundle - Form Search Results SDC
.... 38.196 Bundle - Genomic Diagnostic Implication for a Patient QEDm
.... 38.197 Bundle - Genomic Variant for a Patient QEDm
.... 38.198 Bundle - Genomic Variant Gene = NTHL1 QEDm
.... 38.199 Bundle - Patient Search Results by Medical Record Number PDQ
.... 38.200 Bundle - Patient Search Results by NHS Number PDQ
.... 38.201 Composition - Genomics Report ctDNA UGR
.... 38.202 Condition - Carcinoma
.... 38.203 Condition - Lynch Syndrome
.... 38.204 Consanguinity (type=CE)
.... 38.205 Diagnostic Report ctDNA Example
.... 38.206 Diagnostic Report Example.
.... 38.207 Document Reference Laboratory Report ctDNA
.... 38.208 Endpoint EPIC
.... 38.209 Endpoint iGene
.... 38.210 Endpoint RIE
.... 38.211 Example of a Message Acknowledgement
.... 38.212 Example of a Message Search
.... 38.213 FamilyMemberHistory - Lyarra Nottingham
.... 38.214 FamilyMemberHistory - Rob LEEDS
.... 38.215 FHIR RESTful POST ServiceRequest
.... 38.216 Genomic Report BRCA1 Variant Example
.... 38.217 Genomic Report Ovarian Carcinoma Diagnostic Implication Example
.... 38.218 Genomic Study (Panel) - Cystic Fibrosis
.... 38.219 Genomic Study (Panel) - Lynch Syndrome
.... 38.220 Genomic Study Panel - ctDNA 431 Present
.... 38.221 Genomic Study Panel - ctDNA 971 Failed
.... 38.222 Laboratory Analyte Result - BCRABL
.... 38.223 Laboratory Analyte Result BCRABL Invalid Example
.... 38.224 Laboratory Analyte Result BCRABL Valid Example
.... 38.225 MCV - Mean corpuscular volume
.... 38.226 Message Header - Genomic Order ctDNA O21
.... 38.227 Message Header - Genomic Order ctDNA R01
.... 38.228 Message Header - Genomic Order Reply fatal
.... 38.229 Message Header - Genomic Order Reply fatal Acknowledgement
.... 38.230 Message Header - Genomic Order Reply Transient
.... 38.231 Message Header - Genomic Report
.... 38.232 Message Header - Patient
.... 38.233 Molecular Consequence - Loss of Heterozygosity (BRCA1)
.... 38.234 Observation - Lynch Syndrome Mutation Finding
.... 38.235 Order Tracking Number (type=ST)
.... 38.236 Organization MANCHESTER UNIVERSITY NHS FOUNDATION TRUST
.... 38.237 Organization North West GMSA
.... 38.238 Output from a FHIR Validation
.... 38.239 Parameters Expansion Profile
.... 38.240 Patient - Birmingham
.... 38.241 Patient - Bolton
.... 38.242 Patient - Congleton
.... 38.243 Patient - Fetus London
.... 38.244 Patient - Lancaster
.... 38.245 Patient - London
.... 38.246 Patient - Ned Liverpool NHS Number: 9737383206
.... 38.247 Patient - Northwich
.... 38.248 Patient - Nottingham
.... 38.249 Patient - Rob Leeds NHS Number: 9737383222
.... 38.250 Patient - Sansa Manchester NHS Number: 9737383192
.... 38.251 Patient - Theon Sheffield NHS Number: 9737873858
.... 38.252 Patient - Warrington
.... 38.253 Patient - Wrexham
.... 38.254 PractitionerRole C9999998 Example
.... 38.255 PractitionerRole Result INTERPRETER
.... 38.256 Pregnancy Expected Delivery Date (type=DT)
.... 38.257 Procedure - Liver Biopsy
.... 38.258 Region Studied - ctDNA
.... 38.259 RelatedPerson Birmingham-Lancaster
.... 38.260 RelatedPerson Birmingham-London
.... 38.261 RelatedPerson Lancaster-London
.... 38.262 RelatedPerson London-Lancaster
.... 38.263 RelatedPerson Mother Cersei London
.... 38.264 RelatedPerson Wrexham-Lancaster
.... 38.265 RelatedPerson Wrexham-London
.... 38.266 ServiceRequest ctDNA Example
.... 38.267 Shire Cytogenetics Report R01 - Future Structured Example
.... 38.268 Shire Cytogenetics Report R01 - Future Structured Example (FISH)
.... 38.269 Specimen ctDNA Example
.... 38.270 Task Genomic Test Completed
.... 38.271 Task Genomic Test Requested
.... 38.272 Variant - ctDNA
.... 38.273 Variant - ctDNA Intragenic Copy Number Variant (FBN1)
.... 38.274 Variant - ctDNA Multigenic Copy Number Variant
.... 38.275 Variant - ctDNA Small Variant (BRCA1)
.... 38.276 Variant - ctDNA Structural Variant
.... 38.277 Bundle 'Message' - Filler Order Message
.... 38.278 Bundle 'Message' - Filler Order Message
.... 38.279 Bundle 'Message' - Genomics Order Reply
.... 38.280 Bundle 'Message' - Genomics Order with Attachment
.... 38.281 Bundle 'Message' - Genomics Order with Coded Entries
.... 38.282 Bundle 'SearchSet' - Genomics Order
.... 38.283 Document Reference Laboratory Order
.... 38.284 Encounter 'episode/stay' Example
.... 38.285 Message Header - Genomic Order
.... 38.286 Message Header - Genomic Order Reply ok
.... 38.287 Patient - OctaviaCHISLETT NHS Number: 9449305552
.... 38.288 PractitionerRole C3456789 Example
.... 38.289 ServiceRequest Attachment Example
.... 38.290 ServiceRequest Coded Entries Example
.... 38.291 Specimen Example
.... 38.292 Bundle 'Message' - Genomics Report
.... 38.293 Diagnostic Report Example.
.... 38.294 Document Reference Laboratory Report
.... 38.295 Message Header - Genomic Report
.... 38.296 Bundle 'Message' - Genomics Order ctDNA O21
.... 38.297 Bundle 'Message' - Genomics Report ctDNA R01
.... 38.298 Bundle `Document` - Genomics Report ctDNA
.... 38.299 Bundle `Document` - Genomics Report Inherited MMR deficiency (Lynch syndrome)
.... 38.300 Bundle `Document` - Genomics Report Targeted Variant
.... 38.301 Composition - Genomics Report LynchSyndrome
.... 38.302 Composition - Genomics Report Octavia CHISLETT
.... 38.303 DiagnosticImplication - Cystic Fibrosis Carrier
.... 38.304 DiagnosticImplication - Lynch Syndrome
.... 38.305 Genomic Study - Cystic Fibrosis
.... 38.306 Genomic Study - Lynch Syndrome
.... 38.307 Variant - CFTR
.... 38.308 Variant - NTHL1
.... 38.309 748683741
.... 38.310 EPIC-OBR-1 Example
.... 38.311 EPIC-OBX-10 Example
.... 38.312 EPIC-OBX-11 Example
.... 38.313 EPIC-OBX-2 Example
.... 38.314 EPIC-OBX-4 Example
.... 38.315 EPIC-OBX-6 Example
.... 38.316 EPIC-OBX-7 Example
.... 38.317 EPIC-OBX-8 Example
.... 38.318 Genomic General Ask At Order Entry Response - Octavia CHISLETT
.... 38.319 Genomic Referral Category
.... 38.320 High infection risk sample
.... 38.321 Informed Consent
.... 38.322 North West Genomics Test Order Response - Octavia CHISLETT
.... 38.323 North West Genomics Test Order Response - Theon SHEFFIELD
.... 38.324 OBX Pregnancy
.... 38.325 Supervising Clinician
.... 38.326 Bundle-Bundle-NonWGSTestOrderForm-Reanalysis-Example
.... 38.327 Bundle-NonWGSScenario3-FetusAsProband-Example-FetusA
.... 38.328 Bundle-NonWGSScenario4-ProbandWithMultipleFetus-Example-FetusA
.... 38.329 Bundle-NonWGSScenario4-ProbandWithMultipleFetus-Example-FetusB
.... 38.330 Bundle-NonWGSScenario5-ProductsofConception-Example
.... 38.331 Bundle-NonWGSTestOrderForm-CancerSolidTumor-Example
.... 38.332 Bundle-NonWGSTestOrderForm-Example
.... 38.333 Bundle-NonWGSTestOrderForm-FetalScenario-Example
.... 38.334 Bundle-NonWGSTestOrderFormQRPatientExtensions-Example
.... 38.335 Bundle-WGSTestOrderForm-Example
.... 38.336 UKCore-Bundle-MichaelJonesRequest-Example (minimal)
.... 38.337 UKCore-Bundle-MichaelJonesRequest-Example (v3 message)
.... 38.338 NRL Genomic Report for Cersei LONDON (Test NHS Number 9737383230). Original order electronic from EPIC system
.... 38.339 NRL Genomic Report for Tommen BIRMINGHAM (Test NHS Number 9737383249). Original order not electronic
.... 38.340 dWGS Manifest Response - Duo (Family Member)
.... 38.341 dWGS Manifest Response - Duo (Proband)
.... 38.342 dWGS Manifest Response - Singleton
.... 38.343 dWGS Manifest Response - Trio (Family Member 1)
.... 38.344 dWGS Manifest Response - Trio (Family Member 2)
.... 38.345 dWGS Manifest Response - Trio (Proband)
.... 38.346 dWGS Sub-order - Duo (Family Member)
.... 38.347 dWGS Sub-order - Duo (Proband)
.... 38.348 dWGS Sub-order - Singleton
.... 38.349 dWGS Sub-order - Trio (Family Member 1)
.... 38.350 dWGS Sub-order - Trio (Family Member 2)
.... 38.351 dWGS Sub-order - Trio (Proband)
.... 38.352 HLA Tests - Transplant Ask At Order Entry Response - HLA Antibody Screening
.... 38.353 Chimerism Test Additional Ask At Order Entry Questions Response
.... 38.354 OMICS DSS ctDNA Test Results (R01)
.... 38.355 ctDNA UGR Phase 2 - EU Laboratory Report FHIR Document
.... 38.356 Example Document and Document Notification Message
.... 38.357 Variant DSS BRCA1