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.

A grouping of the Document Registry and Document Repository, indexing document metadata and serving document content to Document Consumers. Other names include Electronic Document Management Systems (EDMS) and IHE XDS. See Health Data API (HIE/EURIDICE) - Actors.

Queries the Document Registry to find documents and retrieves them from the Document Repository. See Health Data API (HIE/EURDICE) - Actors.

Transforms a laboratory report and pushes it to a Document Consumer or Document Access Provider, using IHE ITI-105 Simplified Publish or HL7 v2 MDM_T02. See Health Data API (HIE/EURIDICE) - Actors.

Analyses and interprets raw genomic data. Implemented by bioinformatics pipelines and Decision Support Systems (DSS), e.g. Omics DSS, or the Genomics England bioinformatics pipeline, interpretation services and Interpretation Portal.

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

Stores FHIR resources populated by a Resource Publisher and serves them to Resource/Data Consumers. See Health Data API (HIE/EURDICE) - Actors.

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.

FHIR Message equivalent of the HL7 v2 OML_O21 Laboratory Order. OMG_O19 General Clinical Order, which has the same segments including SPM, MAY be used instead of OML_O21 and converts to this same message.

For future use. FHIR Message equivalent of the IHE 360X HL7 v2.5.1 OMG^O19^OMG_O19 referral order - Referral Request [PCC-55]. The focus is the referral ServiceRequest.

For future use. FHIR Message equivalent of the IHE 360X HL7 v2.5.1 OSU^O51^OSU_O51 order status update for a referral or laboratory order - accept, decline, interim note, outcome, cancel request and cancel confirmation [PCC-55] to [PCC-59]. The focus is the Task.

Search parameter for searching resource identifier for assigning authority

For analysis purposes only - not an active or planned project. This referral is not expected to be implemented within this IG; it is expected to be implemented via a Genomics England Limited application, NHS England BaRS/eRS or the NHS England Genomic Order Management Service.

A closed-loop clinical referral into a genomics/clinical genetics service (see Genetic Referrals), modelled on the IHE 360X HL7 v2 referral order OMG^O19 with OSU^O51 status updates (see Referral Request [PCC-55]) - not a laboratory order. The referral itself stays small: clinical content travels as forms, clinical documents (pathology report, patient summary) and family history referenced from the referral.

This is a logical model - it is not exchanged as is. It breaks down into ServiceRequest, Patient, PractitionerRole, Organization, HealthcareService, QuestionnaireResponse, RelatedPerson, Observation and clinical documents (DocumentReference or a FHIR Document Bundle).

The common core of a Genomic Test Order: the Patient, Healthcare Professional, Test Request and Specimen shared by every order, regardless of test type. Ask At Order Entry questions, which vary by order/test type, are not part of this core - they are carried alongside it (see Order Entry Questions below).

This is a logical model - it is not exchanged as is. It breaks down into ServiceRequest, Patient, Encounter, PractitionerRole, Organization, Specimen, Observation and RelatedPerson for exchange via HL7 v2 OML_O21 or the FHIR Message O21.

The common core of a Genomic Test Report: the Patient, Hospital Spell, Diagnostic Workflow and Results shared by every report, regardless of test type. Individual test findings are carried as panel-specific results (see Report Panels below).

This is a logical model - it is not exchanged as is. It breaks down into DiagnosticReport, Patient, Encounter, ServiceRequest, PractitionerRole, Organization, Specimen, Observation and DocumentReference/Binary for exchange via HL7 v2 ORU_R01 or FHIR (Message R01 / RESTful API).

Result panel for BCR-ABL1 monitoring (chronic myeloid leukaemia), capturing a Cepheid-class ASTM-communicating analyser's result as a Laboratory Analyte Result Observation - see BCR-ABL Monitoring.

​item.definition and item.code are inferred directly from this IG's own example Observations - Observation-BCRABL-Valid, Observation-BCRABL-Invalid and Observation-LAR-BCRABL (input/fsh/Examples/BCRABL/) - not just the data mapping table: the local Cepheid CodeSystem component codes below (BCR-ABL&, ABL&Ct, etc.) are the exact codes those examples use, and the two examples together show both a normal result and the dataAbsentReason shape used when a value is invalid/out of range.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the R454 Mavacamten CYP2C19 Test Request Form (DOC6602), used alongside the common core order form - see Order Entry Questions. This is one of the leanest of the paper forms - the test itself (R454) is fixed by the choice of form, and there is no specimen-specific content beyond the common core's own Specimen group. Like several of the newer DOC-numbered forms, it captures Gender Identity separately from Biological Sex - see Genomic Test Order - Common Fields We May Have Missed for why that item is proposed as a common-core addition rather than repeated per Ask At Order Entry Questionnaire.

This Questionnaire is a proposal, not an active or planned project.

Test Specific Additional Ask At Order Entry Questions for Cancer orders - used alongside the common core order form and Ask At Order Entry Questions Common, the same "Test Specific" tier pattern WGS Test Additional Ask At Order Entry Questions already follows for WGS orders - see Order Entry Questions.

Its content is inferred, not yet confirmed against a live order-entry screen the way WGSTestAdditionalAskAtOrderQuestions was: each item below is a concept that recurs independently across the two Cancer-category NW GLH paper forms - HRD and Tumour BRCA (GB-27189) and GMS WGS Cancer (the national form) - see NW GLH Paper Test Request Forms. Neither of those two Questionnaires has been changed to actually use this one yet - both remain independent, standalone Questionnaires, each already carrying its own copy of the fields proposed here.

Test Specific Additional Ask At Order Entry Questions used alongside the common core order form for the "Chimerism Testing Blood (PB)" order screen within Histocompatibility and Immunogenetics orders (SNOMED CT 909871000000100) - the same "Test Specific" tier pattern WGS Test Additional Ask At Order Entry Questions follows for WGS orders - see Order Entry Questions and Histocompatibility and Immunogenetics. For the sibling HLA testing order screen, see HLA Tests - Transplant Ask At Order Entry.

Extracted from the NTE segments of a live Histotrac ORM^O01 order for a Chimerism Testing (Performable) test - see the worked example for the full message. The original order carried two NTE segments (Specimen Source, then Patient Test(s)); only Specimen Source is asked here - Specimen Identifier (a speculative future SPM-2 addition) and Patient Test(s) have both since been dropped as Ask At Order Entry questions. See also Chimerism Testing Result Panel for the (separate) structured result payload this order eventually produces.

Research summary: as with HLA Tests - Transplant, no NHS England or NHSBT-published order-comms/interoperability standard was found specifically for Chimerism testing order entry. NHSBT's INF136 "User Guide for Histocompatibility and Immunogenetics Diagnostics Services" defines FRM1010 "H&I Haematopoietic Stem Cell Transplantation (Recipients & Donors)" as the relevant national request form for post-transplant chimerism monitoring, but does not publish a FHIR/LOINC/SNOMED binding for the specific test-panel or specimen-source values Hive uses. See each item below for candidate LOINC/SNOMED codes.

Result panel for STR-based chimerism testing (Clatterbridge post-transplant monitoring) - see Histocompatibility and Immunogenetics - Chimerism Testing Result Panel (Future?) for the source data table this Questionnaire structures.

The payload described there is currently unstructured NTE/OBX text, with no FHIR mapping yet - item.definition values here are the same candidate mappings recorded in that table's "FHIR Genomic Report Field" column, most inferred by analogy with HL7's Genomics Reporting IG - Histocompatibility and Immunogenetic Reporting (a dependency of this IG, though it profiles HLA allele genotyping, not STR chimerism) rather than confirmed against a real example, unlike BCRABLResultPanel which is inferred from real Observation examples. Several rows have no direct FHIR fit and are marked as such rather than forced onto one.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Request for Genetic Cystic Fibrosis (CF) Carrier Testing (CFTR Gene) form, used alongside the common core order form - see Order Entry Questions. Unlike the other paper forms, this one is specifically for use by General Practitioners rather than hospital clinicians, and structures one of two mutually exclusive referral scenarios: a family history of CF, or a partner who is affected/a carrier.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the Deafness Testing Proforma (R67 Non-Syndromic Hearing Loss), used alongside the common core order form - see Order Entry Questions. The test code (R67) is fixed by the choice of form rather than entered - the proforma instead exists to capture the clinical detail (audiogram, syndromic features, risk factors) that supports the R67 eligibility criteria.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NHS Genomic Medicine Service (GMS) Whole Genome Sequencing (WGS) Test Request - Cancer form (the national GMS-branded form, not NW GLH-specific), used alongside the common core order form - see Order Entry Questions. Like GMS WGS Rare Disease, this form has no Whole Genome Sequencing Test Category in the common core's Test Code branches, so its own Test Directory Clinical Indication item fills that gap directly.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NHS Genomic Medicine Service (GMS) Whole Genome Sequencing (WGS) Test Request - Rare Disease form (the national GMS-branded form, not NW GLH-specific), used alongside the common core order form - see Order Entry Questions. This form has no Whole Genome Sequencing Test Category in the common core's Test Code branches, so its own Test Directory Clinical Indication item fills that gap directly. HPO (Human Phenotype Ontology) terms are mandatory on this form - WGS analysis cannot start without at least one - see Genomic Test Order - Common Fields We May Have Missed.

For analysis purposes only - not an active or planned project. See Genetic Referrals for the narrative use case this Questionnaire sketches a computable data model for, and Genetic Clinical Referral - Differences from Genomic Test Order for how this compares to Genomic Test Order.

This is a closed-loop clinical referral into a genomics/clinical genetics service (see Genetic Referrals), modelled on HL7 v2 OMG^O19 (IHE 360X referral order, for future use) - not a laboratory order. Where a data item is genuinely the same one Genomic Test Order already captures (e.g. patient demographics), this Questionnaire reuses the same item, per the "check for existing patterns" principle in How To Engineer (scale and deliver) Interoperability.

For analysis purposes only - not an active or planned project. See Genetic Clinical Referral for the common core this extends.

Structured detail for a named consultand - an at-risk relative of the proband (the patient on the referral itself) being referred for genetic counselling and/or cascade testing - see Genetic Referrals for the Proband/Consultand distinction. This represents HL7 v2 NK1 (Next of Kin/Associated Parties), converted to FHIR RelatedPerson.

This is the same NK1-shaped RelatedPerson group as WGS Test Additional Ask At Order Entry Questions - Related Individual (NK1) (NOS/RelatedIndividual), generalised from this Questionnaire's own original Consultand-only shape - a Role item now states whether this entry is a Consultand (the usual case here) or a Proband (the reverse direction, used when the referral's own Patient is itself a family member rather than the proband - see WGS Local Test Order's NOS/Proband for the same pattern applied to a lab order rather than a referral).

Scope note: general family history (who else is affected, the wider pedigree) remains in the unstructured family letter referenced from Genetic Clinical Referral

• this Questionnaire only structures the part of that information that identifies a named consultand who is themselves being referred, following the same shape as an NK1 segment.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Genomic Variant Review Request Form (R442.1) - Rare Disease (DOC6004), used alongside the common core order form - see Order Entry Questions. This form does not request a new test on a new specimen - it asks the laboratory to re-review a variant already reported, so its distinctive content is a reference back to that prior report rather than specimen detail.

Ask At Order Entry Questions for NHS Blood and Transplant's (NHSBT) national H&I Haematopoietic Stem Cell Transplantation (Recipients & Donors) request form (FRM1010, form "3C" in NHSBT's own numbering) - see NHSBT's published form and Histocompatibility and Immunogenetics.

Unlike the sibling HLA Tests - Transplant and Chimerism Test Additional Ask At Order Entry Questions - both extracted from a live Hive/Histotrac ORM^O01 order - this Questionnaire is modelled directly from NHSBT's own paper request form, since no live system message for it has been sourced. It is not derivedFrom/extends Genomic Test Order: this form is submitted directly to NHSBT (a national body, not NW GLH/MFT), so its own Patient/Requester fields are restored here rather than assumed available from the common core order form - the same reason HRD and Tumour BRCA restores its own Patient/ Healthcare Professional groups.

A separate form must be completed for each individual - the same physical form is used both for the patient being transplanted and for each family member/potential donor being tested, distinguished only by which "Complete for…" section is filled in. This is modelled below as a Role choice with enableWhen-conditioned items, since FHIR Questionnaire has no native "delete as applicable" concept.

The HLA Typing, Chimerism Analysis and HLA Specific Antibody Testing checkboxes on this form overlap with (but are not identical to) the test-selection lists already modelled as Patient Test(s) on the sibling HLA/Chimerism Questionnaires above - this form uses NHSBT's own coarser Class I/Class I+II and Total/Lineage-specific categories rather than Hive's finer-grained checklist, so they are modelled here as their own items rather than reusing those answerOption lists.

No NHSBT-published FHIR/LOINC/SNOMED binding was found for any of this form's own fields (Role, CMV Status, Time to transplant, HLA Typing scope, Chimerism Analysis type) - all coded locally against the NWGMSA CodeSystem, the same approach taken for the sibling H&I Questionnaires above. Field mappings below are this IG's own best-effort candidates, not confirmed against a live order message.

Ask At Order Entry Questions for NHS Blood and Transplant's (NHSBT) national H&I Organ Transplant (Patients and Donors) request form (FRM1008, form "3B" in NHSBT's own numbering) - see NHSBT's published form and Histocompatibility and Immunogenetics.

This is the national form the existing HLA Tests - Transplant Ask At Order Entry Questionnaire's own design notes already identify as FRM1008 - but that Questionnaire was extracted from Hive/Histotrac's own order-entry UI, which offers a narrower Patient Type (Stem cell/Renal/Thoracic) and Organ (Kidney/Pancreas/Islets/Simultaneous Pancreas-Kidney/Simultaneous Islet-Kidney) picker than this form's own Category (Patient - Renal/Patient - Non-Renal/Donor) and Request details checkboxes. As with HSCT Recipients and Donors, this Questionnaire is modelled directly from NHSBT's own paper request form rather than the live Hive UI, and is not derivedFrom/extends Genomic Test Order for the same reason - this form is submitted directly to NHSBT, so its own Patient/Requester fields are restored here.

A separate form must be completed for each individual - the same physical form is used both for the patient and for each family member/potential donor being tested, distinguished by which "Complete for…" section is filled in. Modelled below as a Role choice with enableWhen-conditioned items, the same pattern used on HSCT Recipients and Donors (and reusing its Patient/Family Member - Potential Donor NWGMSA codes).

The form's Category section (a further three-way choice - Patient - Renal, Patient - Non-Renal, or Donor, each with its own sub-checklist) is a related but separate concept from Role above: a person whose Role is Patient will pick a Patient - Renal or Patient - Non-Renal Category, while a person whose Role is Family Member/Potential Donor will pick the Donor Category - the form itself does not state this relationship explicitly, so it is not enforced here with enableWhen.

No NHSBT-published FHIR/LOINC/SNOMED binding was found for any of this form's own fields (Category, Request details, Previous transfusion(s)/Pregnancies/Previous transplant(s)) - all coded locally against the NWGMSA CodeSystem, the same approach taken for the sibling H&I Questionnaires above. Field mappings below are this IG's own best-effort candidates, not confirmed against a live order message.

Ask At Order Entry Questions used alongside the common core order form for the "HLA Tests - Transplant" order screen within Histocompatibility and Immunogenetics orders (SNOMED CT 909871000000100) - see Order Entry Questions and Histocompatibility and Immunogenetics. For the sibling Chimerism testing order screen, see Chimerism Test Additional Ask At Order Entry Questions.

Extracted from the NTE segments (each carrying HL7 v2 Table 0105-style comment type OSQ) of a live Histotrac ORM^O01 order - see the worked example for the full message. Each NTE-3 value uses a local Label:->Value convention (e.g. HLA Type:->Patient), split below into a question/answer pair.

Research summary (no NHS England-published order-comms/interoperability standard was found for these fields): NHS England's published pathology standards (Pathology Test and Results Standard, SNOMED CT for pathology reporting) do not cover Histocompatibility and Immunogenetics (H&I) order entry specifically. The relevant national body is NHS Blood and Transplant (NHSBT), not NHS England: its INF136 "User Guide for Histocompatibility and Immunogenetics Diagnostics Services" defines six national H&I request forms (Table 2) including FRM1008 "H&I Organ Transplant (Patients and Donors)" and FRM1010 "H&I Haematopoietic Stem Cell Transplantation (Recipients & Donors)", plus a sample-requirements table listing "HLA type of patient, donors or family members" for Solid Organ Transplantation - confirming HLA Type is a fixed national list, not free text, even though NHSBT does not publish a FHIR/LOINC/SNOMED binding for it. NHSBT's Solid Organ Transplantation section (4.5.1) also describes 24-hour on-call cover for "renal and, where appropriate, cardiothoracic transplantation", with liver/other transplant types noted separately as not having HLA match as a primary factor - consistent with Patient Type being a small, fixed list. The professional bodies BSHI (British Society for Histocompatibility and Immunogenetics) and BTS (British Transplantation Society) jointly publish clinical guidelines (e.g. the 2015 BTS/BSHI antibody characterisation guideline) but not data/interoperability standards. This IG's own dependency, HL7's Genomics Reporting IG - Histocompatibility and Immunogenetic Reporting, profiles structured HLA genotype/haplotype results (LOINC 84413-4 Genotype display name, 48018-6 Gene studied, 13298-5 HLA-A [Type], the GL String and HGNC systems) but does not address order-entry "ask at order" questions like these. See each item below for LOINC panels and UK code lists relevant to that specific question.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper HRD and Tumour BRCA Test Request Form (GB-27189), used alongside the common core order form - see Order Entry Questions. This form is specific to newly-diagnosed advanced high-grade epithelial ovarian, fallopian tube or primary peritoneal cancer (HRD test, performed by Myriad Genetics Inc. in the United States) and its relapsed-disease tumour BRCA-only pathway.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Molecular Genomic Testing Request Form - Haemato-Oncology (DOC5775), used alongside the common core order form - see Order Entry Questions. Unlike the Genomic Test Directory R-code panels used elsewhere, this form selects a named laboratory test panel directly (e.g. Myeloid NGS panel, BCR::ABL, MRD panels) rather than a coded test-directory indication.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Request for Genetic Testing for Haemoglobinopathies form (DOC4544), used alongside the common core order form - see Order Entry Questions. Two things are distinctive here: prior full blood count/HPLC laboratory results are submitted with the request (used to interpret the genetic result, not produced by it), and a relative/partner's own affected/carrier status can be referenced to give a couple-specific pregnancy risk.

Ask At Order Entry Questions Common - the default set used alongside the common core order form for order/test types that do not have their own dedicated Ask At Order Entry Questionnaire - see Order Entry Questions. These questions were originally part of GenomicTestOrder and have been extracted here so the core form stays generic to every order/test type.

​Covers Cancer, Whole Genome Sequencing (WGS) and Rare and Inherited Disease orders generally - see Guidance by Order Type below for which questions actually apply to which. Questions only relevant to WGS specifically (Related Individual (NK1), Record of Discussion attached or to follow) have moved to WGS Test Additional Ask At Order Entry Questions, used alongside this Questionnaire for WGS orders, not instead of it.

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).

For analysis purposes only - not an active or planned project.

CSV manifest description, not an Ask At Order Entry Questionnaire - this Questionnaire documents the complete digital manifest for a distributed WGS (dWGS) sub-contracted order (IHE LTW LAB-35), sent by a Requesting Genomic Laboratory (RGL) to North West Genomics acting as Sequencing Genomic Laboratory (SGL): the 37 national digital manifest fields (NHS England RGL to SGL SOP Appendix 3) plus 7 NW GMS local extension fields, with item.definition mappings to FHIR where a confirmed mapping exists - see dWGS. It deliberately carries every manifest field, including several also asked by Genomic Test Order (Patient name/DOB/NHS number/Hospital Number, Specimen Type, Specimen Collection Date) - because it describes the full CSV structure a Requesting Genomic Laboratory actually sends, not an incremental set of order-entry questions. For the genuinely additional Ask At Order Entry content - the manifest fields not already covered by the common core - see dWGS Ask At Order Entry Questions, which derivedFrom/ extends Genomic Test Order in the usual way.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Request for Prenatal Diagnosis of Haemoglobinopathies form (DOC4544), used alongside the common core order form - see Order Entry Questions. This form is unusual among the paper forms in naming two patients (maternal and paternal) rather than one - the common core's own Patient group is completed for the mother (the referral's own registered patient - not a "proband" in the classical sense, since prenatal carrier testing doesn't imply an already-affected index case), and this Questionnaire adds a reference to the father via the same NK1-shaped RelatedPerson group as WGS Test Additional Ask At Order Entry Questions - Related Individual (NK1).

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Genomic Testing Request Form - Rare Disease (DOC4900), the generic Rare Disease paper order form, used alongside the common core order form - see Order Entry Questions. This form's own Test Request Details section (R code, clinical details) already maps directly onto the common core's Test Request group, so this Questionnaire only carries the additional Clinical Utility and targeted familial testing detail the paper form asks for.

Result panel for a Variant (Reportable Variant) Observation, structured around the HL7 v2 Lab Results Interface (LRI)'s own Discrete Variant Panel (LOINC 81250-3, LRI Chapter 5 Table 5-2, plus the Structural Variant Addenda in Table 5-3) - the same panel the NTHL1 and CFTR examples are based on. LRI already defines this as a single panel covering both simple and structural variants; this Questionnaire follows that same single-panel structure rather than iGene's separate per-variant-type field sets, mapping each item to both its LRI OBX row and its corresponding component in the HL7 Genomics Reporting IG's Variant profile. See OMICS DSS Result Integration for the full LRI/FHIR/iGene three-way mapping table.

item.definition/item.code are cross-checked against this IG's current Variant examples: Variant - NTHL1 and Variant - CFTR (both based on LRI examples), Observation-EGFR-Variant-ctDNA, Observation-BRCA1, and the four Variant Observations (a small variant, an intragenic CNV, a multi-gene CNV and a structural variant) in Bundle-ctdna9737383222-testresults, plus iGene's own custom field spec for variants (NotGit/iGene Custom Fields Master Dataset - Updated 13-Aug-26.xlsx, "Variant Level Data" sheet) - only elements genuinely populated by at least one of these is modelled, since these are the only elements needed for the iGene feed. See OMICS DSS Result Integration - Result Panel: Elements Not Included for the LRI/FHIR elements deliberately left out because no current example populates them.

Known gaps between iGene, LRI and the FHIR profile, not yet resolved:

• Loss of Heterozygosity is one of iGene's five variant types, but has no corresponding row anywhere in LRI's Discrete Variant Panel - LRI's closest concept, Allelic State (53034-5, row B.23), does not offer an LOH answer option. No current FHIR example produces LOH data either.
• Coordinate System [Type] (92822-6) and Origin of Germline Genetic Variant [Type] (94186-4), both used by the ctDNA Bundle examples, have no row in LRI's Discrete Variant Panel - LRI's closest concept to the latter is Allelic Phase (82120-7, row B.26), a different LOINC code whose answer list happens to include Maternal/Paternal as two of several "sets of variants in cis" options, not a dedicated parent-of-origin field.
• Structural Variant: iGene expects a single Complex variant HGVS name field (LOINC 81262-8 - itself an LRI Complex Variant Panel code, row C.2, not part of the Discrete Variant Panel at all), but the ctDNA Bundle's structural-variant Observation does not populate 81262-8 - it uses several Discrete Variant Panel components instead (Genomic Reference Sequence, Coordinate System, Genomic Ref/Alt Allele, DNA Change Type, Genomic DNA Change).

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for the NW GLH paper Genetic Testing Request Form - Whole Genome Sequencing (WGS) form, which accompanies samples sent directly to a NW GLH site, used alongside the common core order form - see Order Entry Questions.

Not to be confused with dWGS Sub-Order Manifest - that Questionnaire is the digital manifest for a distributed WGS sub-contracted order between GLHs (see dWGS); this one is the plain paper form used for a local WGS request, and does not by itself imply any sub-contracting.

Test Specific Additional Ask At Order Entry Questions for Whole Genome Sequencing (WGS) orders - used alongside the common core order form and Ask At Order Entry Questions Common, rather than instead of it - see Order Entry Questions. A WGS order therefore combines three Questionnaires, not the usual two.

Split out of Genomic General Ask At Order Entry: Related Individual (NK1) and Record of Discussion attached or to follow are only genuinely relevant to WGS orders, not every order/test type that Questionnaire covers (Cancer, WGS and Rare and Inherited Disease generally) - see that Questionnaire's own Guidance by Order Type section. WGS participant type is new here, surfaced by a real NHS Trust WGS order-entry screen with no prior equivalent anywhere in this IG.

For analysis purposes only - not an active or planned project.

Ask At Order Entry Questions for a distributed WGS (dWGS) sub-contracted order (IHE LTW LAB-35), used alongside the common core order form - see Order Entry Questions. This Questionnaire carries only the fields from the dWGS digital manifest (NHS England RGL to SGL SOP Appendix 3, plus 7 NW GMS local extension fields) that are not already asked by the common core - see dWGS Sub-Order Manifest for the full 44-field manifest description, including the fields this Questionnaire deliberately omits because the common core already asks them.

Represents the flat-file shape of NEYctDNA.csv, iGene's daily CSV export of ctDNA orders and reports copied to NE&Y Genomics for regional management information - see ctDNA Management Information (NW to NE&Y Genomics). One row per test; a report row carries both order fields and report/result fields together, so this Questionnaire models the full row - the order-only columns populate the FHIR Message O21 Laboratory Order (Bundle-GenomicsOrderMessage-ctDNA), while the report/result columns (ReportStatusDateTime, ReportIdentifier, ObservationResultStatus, ObservationDateTime, ObservationIdentifierCode, ObservationIdentifierDescription) instead populate the separate FHIR Message R01 Laboratory Report (Bundle-GenomicsReportMessage-ctDNA, itself based on an HL7 v2 ORU^R01, not O21). See ctDNA Management Information - Laboratory Order O21 Mapping for the O21-only columns and Laboratory Report R01 Mapping for the report/result columns - the two markdown tables split this Questionnaire's items by which FHIR Message actually carries them, even though all items live on this one Questionnaire. Named for iGene (the common source) rather than NE&Y/ctDNA specifically, since the shape isn't NE&Y- or ctDNA-specific - it's the same LAB-2 CSV re-export pattern iGene Work Order Export documents for StarLIMS/DLIMS work orders, just with ctDNA report/result columns added.

Each item's linkId is the literal CSV column header, type the FHIR datatype the column's values coerce to, and definition the FHIR field the column populates once converted into the relevant FHIR Message - many of these reuse the exact same field as the equivalent item already defined on Genomic Test Order or iGene Work Order Export, since this is the same underlying order data plus report/result-specific columns those don't carry. See NEYctDNA.csv for the source file this was extracted from.

Unlike the Ask At Order Entry Questionnaires elsewhere in this IG, this is not a derivedFrom/extends Questionnaire - it documents an existing system-to-system CSV export shape, not a human-facing order-entry form.

Represents the flat-file shape of StarLIMSSampleData.csv, iGene's daily CSV export of work orders sub-contracted to StarLIMS (the Liverpool GLH satellite LIMS) - see StarLIMS / iGene Integration. The same export shape/pattern is reused by the OMICS DSS Result Integration use case for DLIMS work order metadata (see that page's Future Process) - one row per sub-contracted test, named for iGene (the common source) rather than StarLIMS specifically, since it isn't StarLIMS-specific.

Each item's linkId is the literal CSV column header, type the FHIR datatype the column's values coerce to, and definition the FHIR field the column populates once imported - many of these reuse the exact same field as the equivalent item already defined on Genomic Test Order, since a sub-contracted work order carries the same underlying data as any other order. See StarLIMS / iGene Integration - Work Order CSV Export from iGene for a simple description of each column plus its FHIR mapping (also reused, unchanged, by OMICS DSS Result Integration), and StarLIMSSampleData.csv for the source file this was extracted from.

Unlike the Ask At Order Entry Questionnaires elsewhere in this IG, this is not a derivedFrom/extends Questionnaire - it documents an existing system-to-system CSV export shape, not a human-facing order-entry form, so items aren't nested under the same Patient/HealthcareProfessional/TestRequest/Specimen groups derivedFrom would imply; they're grouped the same way only because that's how the source CSV's columns naturally cluster.

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

A family (pedigree) tested together, e.g. a Distributed WGS (dWGS) Singleton, Duo or Trio. The group is identified by its Pedigree Number (also known as Family Id) and/or, for dWGS, the NGIS referral_id from TOMS. Either can be carried on each family member's order as its Order Group Number (ServiceRequest.requisition, HL7 v2 ORC-4 Placer Group Number). Neither is a patient identifier.

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 - Genomics Reporting Molecular Consequence

Communicates the calculated or observed effect of a DNA variant, generally on its downstream transcript/protein, or a broader functional effect such as loss of heterozygosity. Follows the HL7 Genomics Reporting IG's Molecular Consequence profile: a separate Observation from the Variant it describes the consequence of, referenced via derivedFrom - not a component on the Variant itself.

This is this IG's preferred pattern for representing Loss of Heterozygosity (LOH) - see OMICS DSS Result Integration for the decision and the tradeoff against modelling LOH as a bare component/extension on Variant instead.

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

Pedigree Number (Family Id). Identifies a family tested together and is used as the Order Group Number (ServiceRequest.requisition, HL7 v2 ORC-4 Placer Group Number) - not a patient identifier.

The referral_id returned by TOMS (Test Order Management System, Genomics England) for a Distributed WGS (dWGS) referral. It identifies the family tested together (Family Genetic Group) and can be used as the Order Group Number (ServiceRequest.requisition, HL7 v2 ORC-4 Placer Group Number). Assigned by Genomics England Limited (ODS 8J834).

Only traced NHS Number SHOULD be used, un-traced NHS Numbers MUST be clearly indicated.

Not applicable per the NHS England Canonical Data Model - use Medical Record Number instead.

Uniquely identifies a Specimen across multiple laboratory systems.

(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 )

The FamilyMemberHistory recorded for this family member, in relation to the proband. Sits alongside the Family Member Relationship extension.

The role of the patient in the family group - their relationship to the proband, e.g. mother, father, son, daughter. The proband is ONESELF.

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

How many family members are tested together: Singleton, Duo or Trio. See dWGS - Singleton, Duo and Trio testing.

The Genomic Test Code ($GTD, England-GenomicTestDirectory) M* codes whose display text names Whole Genome Sequencing (WGS) specifically - 214 codes, all Cancer. Same relationship as GMS WGS Guide Test Codes has to GMS WGS Rare Disease: a candidate guide list for GMS WGS Cancer's own Test Directory Clinical Indication item, which is currently bound to the full GenomicTestCodes ValueSet (every test family, not just WGS).

Every code follows one of three patterns per cancer type - WGS Germline and Tumour/Tumor (both spellings appear in NHS England's own source spreadsheet, carried through unchanged), WGS Tumour First, or WGS Follow-up Germline - reflecting the three-sample-timing WGS pathway (paired germline+tumour together, tumour-first, or a later germline follow-up) rather than three different tests.

The 38 example HPO (Human Phenotype Ontology) terms shown as a guide (rendered as an image, not selectable text, so no codes were available directly from the form itself) on page 2 of the [GMS WGS Test Request Form

• Rare Disease](https://mft.nhs.uk/app/uploads/2026/05/GMS-WGS-Test-Order-Form-Rare-Disease.pdf).

Unlike the CodeSystem this ValueSet previously drew from, these are real HPO codes (http://purl.obolibrary.org/obo/hp.owl, release 20191108) - confirmed against the Genomics England terminology server (https://ontoserver.aws.gel.ac/fhir) via CodeSystem/$lookup, not guessed. See GMSWGSGuideHPOTermsToSCT ConceptMap for the SNOMED CT mapping built from the same verification pass (27 of these 38 resolved; the rest have no entry in that server's own sct-to-hpo map).

Bound as #open-choice on Questionnaire-GMSWGSRareDisease's NOS/HPOTerm item, so these 38 terms are offered as quick picks without preventing free-text/other-code entry of any other HPO term, consistent with the source form's own "guide … not an exhaustive list" wording.

The Genomic Test Code ($GTD, England-GenomicTestDirectory) R* codes whose display text names Whole Genome Sequencing (WGS) specifically - 37 codes, all Rare & Inherited Disease. A candidate guide list for GMS WGS Rare Disease's Test Directory Clinical Indication item, which is currently bound to the full GenomicTestCodes ValueSet (every test family, not just WGS) - the same relationship GMS WGS Guide HPO Terms has to that Questionnaire's HPO Terms item: a curated, form-specific subset of a much larger external code list, not a replacement for it.

Excludes R447.1 "Validation of WGS Diagnostic discovery (Targeted variant testing)" - its display text names WGS, but it's a targeted follow-up/confirmation test of a WGS finding, not itself an order for WGS.

• See National genomic test directory for cancer (non-CNS v16) on Genomic Test Directory
• Includes CNS cancer (and one solid-tumour outlier, Fibrolamellar Hepatocellular Carcinoma) from the M* Haematological Oncology/Cancer CNS block that predates the digital TP/GT scheme - see CodeSystem-GenomicTestCode for detail. Haematological Oncology codes from that same block are instead in ValueSet-HaematologicalOncologyTestCodes, not here.
• All category = cancer codes from EnglandTestCode (CodeSystem-GenomicTestCode), checked/refreshed 2026-09-05.

1st level classification of NHS England Genomic Test Directory codes

Genomic Disorder Carrier

Genomic Finding

Genomic Finding Detected

• Haematological Oncology test codes from the M* Haematological Oncology/Cancer CNS block that predates the digital TP/GT scheme - see CodeSystem-GenomicTestCode for detail and the DGTS GT-code replacements (ConceptMap-GenomicTestCodeToDigitalGenomicTestServices).
• CNS cancer codes from that same block are instead in ValueSet-CancerTestCode, not here.
• All category = haematological-oncology codes from EnglandTestCode (CodeSystem-GenomicTestCode), checked/refreshed 2026-09-05.

• See National genomic test directory for rare and inherited disease (v9) on Genomic Test Directory
• All category = rare-and-inherited-disease codes from EnglandTestCode (CodeSystem-GenomicTestCode), checked/refreshed 2026-09-05.

• See NHS England Genomic Test Directory

Test Outcome Codes from NHS England Genomic Test Outcome Codes

All codes from the Histotrac CodeSystem - the Patient Test(s) order-detail restatement codes Histotrac itself uses alongside its Test Code (OBR-4). Bound to ServiceRequest.orderDetail - see Histocompatibility and Immunogenetics for the worked examples this covers.

All codes from the NHS England Genomic Test Code CodeSystem (the National Genomic Informatics System (NGIS) test directory) - used to answer the NGIS Test Code question on WGS Local Test Order Ask At Order Entry. Unlike GenomicTestCodes, this does not also pull in the Digital Genomic Test Services, NW-local, or Histotrac CodeSystems, since NGIS Test Code is specifically the national test directory code.

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

Example only, for future use. Reasons a referral is declined or cancelled.

For future use. Business status of a referral, from the IHE 360X state transitions.

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
  • OID 2.16.840.1.113883.2.1.6.8
• 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

iGene's five variant-type categories - see the IGeneVariantCategory CodeSystem.

TODO

Local OBX-3 sub-identifier codes used by the Clatterbridge chimerism testing payload - see Histocompatibility and Immunogenetics - Chimerism Testing Result Panel (Future?).

TODO

Section codes for the Composition Genomic Report where no LOINC document section code was found. Draft - see Document Layout.

Local order-detail codes from Histotrac, the Histocompatibility and Immunogenetics LIMS - see Histocompatibility and Immunogenetics, HLA Tests - Transplant Ask At Order Entry and Chimerism Test Additional Ask At Order Entry Questions.

Unlike the Test Code carried in OBR-4/ServiceRequest.code (a $DGTS Genomic/Genetic Test (GT) code, or a local NWTestCode code for test families with no national code), these concepts model the Patient Test(s) order-detail restatement seen in the live Histotrac ORM^O01/OML^O21 orders - the value Histotrac itself carries alongside the Test Code to say which specific lineage/panel or transplant test was ordered. Bound to ServiceRequest.orderDetail via HistotracOrderDetail - see GenomicTestCodes for the separate ServiceRequest.code binding these relate to via the relatedTestCode property below.

Sourced as HL7 v2 CE (coded element)-style code^text^codingSystem strings from the HISTOTRACEAP coding system - see each concept's worked example (HLA Tests - Transplant, Chimerism Testing). These are distinct from the local NWGMSA answer options (e.g. HLAAntibodyScreening, ChimerismPeripheralBlood) used on the Ask At Order Entry Questionnaires' own order-entry choice items - those model the order-entry UI selection, these are what Histotrac itself calls the resulting order.

Bucket for local codes

The digital National Genomic Test Directory codes, rolled out as the Test Directory itself went digital - replacing the legacy R-code/M-code style codes in NHS England Genomic Test Code ($GTD, England-GenomicTestDirectory) for new/migrated indications. Two code types share this one system, distinguished by prefix:

• TP (Test Package) codes replace the old clinical-indication concept - a package of related genomic tests grouped by clinical condition.
• GT (Genomic/Genetic Test) codes identify a single specific laboratory investigation.

Refreshed from the Haematological Oncology (v1.1) and Cancer CNS (v2) national genomic test directories on 2026-09-08 - see ConceptMap-GenomicTestCodeToDigitalGenomicTestServices and ConceptMap-GenomicClinicalIndicationToDigitalGenomicTestServices for how these relate to the legacy codes they replace.

category is mostly file-derived (haem-onc v1.1 -> haematological-oncology, CNS v2 -> cancer) but not entirely - a handful of codes are curated by hand outside this notebook (e.g. TP401 "Chimerism Testing" -> chimerism) and preserved across reruns rather than re-derived; see notebook 14's own note on this for the full reasoning. test-method (GT codes only) comes straight from each source row's own "Test Method" column, refreshed fresh every run. No specialist-test-group here - neither source directory has an equivalent column.

1st level Genomic Test Directory Codes - completed from the same master spreadsheets as GenomicTestCode (EnglandTestCode.fsh); see that CodeSystem's own Description for the legacy-versus-current distinction, which applies the same way here.

• Source: National genomic test directories - Rare & Inherited Disease v9 and Cancer (non-CNS) v16 checked/refreshed on 2026-09-08.
• The M* codes for Haematological Oncology and Cancer CNS below predate those two directories' move to the digital TP/GT scheme and no longer appear in any live M*-coded master spreadsheet - preserved for backwards compatibility, not refreshable from a current source. See ConceptMap-GenomicTestCodeToDigitalGenomicTestServices for their DGTS GT-code replacements.
• specialist-test-group is populated for R* codes only, from the Rare & Inherited Disease spreadsheet's own "Specialist test group" column - the Cancer directories have no equivalent column, so M* codes don't carry it.
• test-method is populated for R* codes from that same spreadsheet's "Test Method" column, and for current (non-legacy) M* codes from the Cancer directory's "Technology" column (the same concept, differently named) - not populated for legacy M* codes, or the small number of current M* codes (M4.14, M119.5) whose source cell had no clean single value.

HL7 v2 CodeSystem : England-GenomicTestDirectory

Test Outcome Code from NHS England Genomics Test Reporting Specification

Bucket for local codes

HL7 v2 CodeSystem : NWTestCode

Example only, for future use. Reasons a referral or laboratory order is declined [PCC-55, PCC-56] or cancelled [PCC-58] (HL7 v2 ORC-16). 360X only requires free text (ORC-16.2). NHS England eRS, BaRS and the Genomic Order Management Service may have their own reasons - To confirm whether one of those should replace this list.

For future use. Business status of a Genetic Clinical Referral or a laboratory order (Genomic Test Order), from the IHE 360X state transitions (PCC TF-1 X.4.1). Carried in Task.businessStatus, with the matching HL7 v2 OSU^O51 ORC-1 / ORC-5 values - see Referral Request [PCC-55]. information-requested is not in 360X; it covers the eRS "return to referrer" step.

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

iGene's five variant-type categories, each with its own repeating set of custom fields in iGene's "Variant Level Data" spec (SEQV1-SEQV10, ICNV1-ICNV3, MCNV1-MCNV3, SV1-SV3, LOH1-LOH2) - see OMICS DSS Result Integration for the decision this codifies: making "which iGene slot type is this" an explicit, coded Variant.component:variant-category value instead of an inferred classification.

This extends LRI's own "Variant category" (LOINC 83005-9), whose answer list (LL4165-8) only distinguishes Simple Variant vs Structural Variant - not granular enough to route a reported variant to the correct iGene slot type.

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).

HPO (Human Phenotype Ontology) to SNOMED CT mapping for the 38 terms in GMSWGSGuideHPOTermsVS - see Questionnaire-GMSWGSRareDisease's NOS/HPOTerm item.

Built against the Genomics England terminology server (https://re-docs.genomicsengland.co.uk/terminology_server/, https://ontoserver.aws.gel.ac/fhir), HPO release 20191108. That server only publishes a SNOMED CT to HPO ConceptMap (sct-to-hpo) by name, but does support querying it in the HPO-to-SNOMED direction directly via ConceptMap/sct-to-hpo/$translate?...&reverse=true - see nw-gmsa/Testing notebook 13, which uses the same server and surfaced this parameter. An initial pass of this ConceptMap missed that: it instead found a candidate SNOMED CT concept for each HPO term (ValueSet/$expand free-text search under the Clinical finding (404684003) subtree) and forward-verified it through ConceptMap/sct-to-hpo/$translate in the SNOMED-to-HPO direction - which undercounted, since a genuinely-mapped HPO term can have a mapped SNOMED code that isn't the one a text search happens to surface (e.g. Cataract is mapped, to SNOMED 128306009, not the 193570009 a plain text search returns first). This version instead queries reverse=true directly for every HPO code, with the equivalence value taken directly from that server response (equivalent in every case found).

27 of the 38 terms resolved this way; the remaining 11 do not appear in the server's sct-to-hpo map even via reverse=true - so these are genuinely absent from the server's curated map, not an artefact of the search methodology. Rather than assert an unverified equivalence, unresolved terms are recorded below with equivalence = unmatched and no target code.

Legacy 1st-level clinical-indication numbers (GenomicClinicalIndication) for Haematological Oncology and Cancer CNS, mapped to the TP* codes that replace them - derived from the same Legacy 'M' codes column used for the GT* map above (each legacy code's leading number, cross-referenced against which TP its row belongs to), since NHS England's spreadsheets don't name the old CI number directly. Genuinely many-to-many for a large share of these: the old haem-onc CI grouping was organised around a shared assay/test method, not disease, so one old CI number routinely feeds several disease-specific TPs - recorded as multiple targets with equivalence = #relatedto, not forced to one.

Display text for the old CI numbers has no live source any more (see notebook 14's own note on this) - taken from the current EnglandTestCode.fsh's own M*.* entries for that number.

Built by nw-gmsa/Testing notebook 14, checked against v1.1/v2 on 2026-09-08.

Every GenomicTestCode (England-GenomicTestDirectory) entry belongs to exactly one GenomicClinicalIndication entry, by construction (<CI>.<n> under <CI>) - not an empirical mapping like the legacy/digital ConceptMaps below, so every element uses equivalence = #narrower (the target, a specific test, is always narrower in scope than the source, the clinical indication it sits under), regardless of how many tests a given indication has.

Built by nw-gmsa/Testing notebook 14, checked against v9/v16 on 2026-09-08.

Legacy M* test codes (GenomicTestCode/England-GenomicTestDirectory) for Haematological Oncology and Cancer CNS, mapped to the GT* codes that replace them - taken directly from the Legacy 'M' codes column in NHS England's Haematological Oncology (v1.1) and Cancer CNS (v2) national genomic test directories, not inferred. Not 1:1 throughout: several old M* tests were consolidated into one GT code (equivalence = #equivalent), and a smaller number split or shared across more than one GT code, recorded as multiple targets with equivalence = #relatedto rather than an arbitrary pick.

Built by nw-gmsa/Testing notebook 14, checked against v1.1/v2 on 2026-09-08.

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

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

Example of a Message Acknowledgement

Example of a Message Search

FHIR RESTful POST ServiceRequest

Family Genetic Group for the London family: the fetus (proband) and mother, both Patients

Family Genetic Group for a Trio: the fetus (proband), mother Cersei London and father Jaime Lancaster, all Patients

Family Genetic Group for the dWGS Trio referral r26000000203, identified by its NGIS referral_id. Members are referenced by NHS Number, as the participants are only held in the dWGS example Bundles.

FamilyMemberHistory for Cersei London, mother of the proband Baby London. Referenced from the London Family Genetic Groups.

FamilyMemberHistory for Jaime Lancaster, father of the proband Baby London. Referenced from the London Trio Family Genetic Group.

FamilyMemberHistory - Lyarra Nottingham

FamilyMemberHistory - Rob LEEDS

FamilyMemberHistory for Six Editestpatient, family member of the dWGS Trio r26000000203 proband Gilly Brough.

FamilyMemberHistory for Thirteen Editestpatient, family member of the dWGS Trio r26000000203 proband Gilly Brough.

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 3 (Ref 5.9.1.3)

The EGFR region studied by the ctDNA digital PCR assay, using the Genomics Reporting genomic-study-analysis-regions extension

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

Worked example of this IG's preferred pattern for Loss of Heterozygosity: a separate MolecularConsequence Observation, derivedFrom the Variant it is the consequence of, rather than a component on the Variant itself. Represents the classic germline-mutation-plus-somatic-LOH "two-hit" finding at the same locus as Variant - ctDNA Small Variant (BRCA1) - see OMICS DSS Result Integration for the decision this grounds.

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

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

Illustrative future-state structured FHIR equivalent of the Shire-1 LAB-36 cytogenetics R01 message (Haemato-Oncology Diagnostic Pathway), converted from the raw HL7 v2 sample

Illustrative future-state structured FHIR equivalent of the Shire-2 LAB-36 cytogenetics R01 message (Haemato-Oncology Diagnostic Pathway), including a FISH panel result, converted from the raw HL7 v2 sample

TODO

For future use. Referral Outcome [PCC-57]: the NW GLH has issued every report for the laboratory order, so the order is complete (HL7 v2 OSU^O51, ORC-1 SC, ORC-5 CM). The reports are external references to the NHS England Unified Genomic Record (UGR).

TODO

TODO

Standalone extraction of the intragenic-CNV Observation (FBN1 exon deletion) from Bundle-ctdna9737383222-testresults, for individual reference - see OMICS DSS Result Integration for the LRI/FHIR/iGene mapping this example grounds.

Standalone extraction of the multi-gene-CNV Observation (Xq22.1-q28 deletion) from Bundle-ctdna9737383222-testresults, for individual reference - see OMICS DSS Result Integration for the LRI/FHIR/iGene mapping this example grounds.

Standalone extraction of the small-variant Observation (BRCA1 deletion) from Bundle-ctdna9737383222-testresults, for individual reference - see OMICS DSS Result Integration for the LRI/FHIR/iGene mapping this example grounds.

Standalone extraction of the structural-variant Observation from Bundle-ctdna9737383222-testresults, for individual reference - see OMICS DSS Result Integration for the LRI/FHIR/iGene mapping this example grounds, including the open gap around iGene's own 81262-8 "Complex variant HGVS name" field, which this example does not populate.

For future use. FHIR Message equivalent of the HL7 v2 OSU^O51 accept (ORC-1 OK, ORC-5 IP) on Referral Request [PCC-55].

For future use. FHIR Message equivalent of the HL7 v2 OSU^O51 decline (ORC-1 UA, ORC-5 CA, reason in ORC-16) on Referral Request [PCC-55].

For future use. FHIR Message equivalent of the HL7 v2 OSU^O51 on Referral Decline [PCC-56].

For future use. FHIR Message equivalent of the HL7 v2 OSU^O51 outcome (ORC-1 SC, ORC-5 CM) on Referral Outcome [PCC-57]: the completed Task only. The genomic test reports are external references (with Report Identifiers) to the NHS England Unified Genomic Record.

For future use. Referral Accept [PCC-55].

For future use. Referral Decline [PCC-55].

For future use. Referral Decline [PCC-56].

For future use. Referral Outcome [PCC-57].

For future use. Referral Accept [PCC-55]: the NW GLH has accepted the laboratory order (HL7 v2 OSU^O51, ORC-1 OK, ORC-5 IP).

For future use. Referral Decline [PCC-55]: the alternative first response - the NW GLH declines the laboratory order because the patient does not meet the test directory eligibility criteria (HL7 v2 OSU^O51, ORC-1 UA, ORC-5 CA, reason in ORC-16).

For future use. Referral Decline [PCC-56]: the laboratory order was accepted, then the sample was found to be unsuitable, so the NW GLH declines the order (HL7 v2 OSU^O51, ORC-1 UA, ORC-5 CA, reason in ORC-16).

Example Filler Order Message for internal or external LIMS

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

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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)

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QuestionnaireResponse answering the default Genomic General Ask At Order Entry Questionnaire, sourced from the existing ServiceRequestGenomicsOrderCodedEntries order (test code R240.1) and its free-text note

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QuestionnaireResponse answering the common core North West Genomics Test Order form, sourced from the existing ServiceRequestGenomicsOrderCodedEntries order and its associated Patient, PractitionerRole and Specimen resources

QuestionnaireResponse answering the common core North West Genomics Test Order form, sourced from the existing ServiceRequest-ctDNA order (test code M4.14) and its associated Patient, PractitionerRole and Specimen resources

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See Bundle-Bundle-NonWGSTestOrderForm-Reanalysis-Example

See Bundle-NonWGSScenario3-FetusAsProband-Example

See Bundle-NonWGSScenario4-ProbandWithMultipleFetus-Example

See Bundle-NonWGSScenario4-ProbandWithMultipleFetus-Example

See Bundle-NonWGSScenario5-ProductsofConception-Example

See Bundle-NonWGSTestOrderForm-CancerSolidTumor-Example

See Bundle-NonWGSTestOrderForm-Example

See Bundle-NonWGSTestOrderForm-FetalScenario-Example

See Bundle-NonWGSTestOrderFormQRPatientExtensions-Example

See Bundle-WGSTestOrderForm-Example

See the FHIR Genomics Implementation Guide on Simplifier - a minimal-population variant of the MichaelJonesRequest example

See the FHIR Genomics Implementation Guide on Simplifier - the fully-populated FHIR message variant of the MichaelJonesRequest 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

Distributed WGS (dWGS) LAB-35 sub-order - the Family Member half of a Duo referral (see dWGS-Duo-r26000000202-p26000000102 for the Proband)

Distributed WGS (dWGS) LAB-35 sub-order - the Proband half of a Duo referral (see dWGS-Duo-r26000000202-p26000000103 for the Family Member)

Distributed WGS (dWGS) LAB-35 sub-order from NE&Y Genomics (RGL) to NW Genomics (SGL) - a Singleton (Proband only) referral

Distributed WGS (dWGS) LAB-35 sub-order - a Family Member of a Trio referral (see dWGS-Trio-r26000000203-p26000000104 for the Proband)

Distributed WGS (dWGS) LAB-35 sub-order - a Family Member of a Trio referral (see dWGS-Trio-r26000000203-p26000000104 for the Proband)

Distributed WGS (dWGS) LAB-35 sub-order - the Proband member of a Trio referral (see dWGS-Trio-r26000000203-p26000000105/106 for the two Family Members)

QuestionnaireResponse answering HLA Tests - Transplant Ask At Order Entry, sourced from a live Histotrac ORM^O01 HLA Antibody Screening (Transplant) order

QuestionnaireResponse answering Chimerism Test Additional Ask At Order Entry Questions, sourced from a live Histotrac ORM^O01 Chimerism Testing (Performable) order

NW-GMSA R01 Test Results message produced from a GA4GH VCF/Phenopacket by the "05 - Test Results - GA4GH VCF to FHIR Genomics Reporting" notebook, covering a ctDNA Non-Small Cell Lung Cancer multi-target panel (sequence variant, individual and multiple copy number variants, structural variant)

Example Document and Document Notification Message for GMCR

HL7 Europe Laboratory Report FHIR Document (Composition-led Bundle, type document) produced from the same ctDNA source data by the "06 - EU Laboratory Report - FHIR Messages to a FHIR Document" notebook, combining the Laboratory Report with its Reportable Variant Observations for the NHS England Unified Genomic Record (UGR) Phase 2

Variant DSS BRCA1