References

• A. HL7 Lab Results Interface (LRI), Release 1 from May 2017 (HL7 v2,5,1)
• B. HL7 International Genomics Reporting Implementation Guide (HL7 FHIR)
  • HL7 USA minimal Common Oncology Data Elements (mCODE) Implementation Guide - Genomics
• C. openEHR Genomics Project
• D. NHS England FHIR Genomics Implementation Guide—Clinical Headings

Domain Archetype

Laboratory Report - MindMap

Diagnostic Report

Metadata is data that applies to the patient's entire clinical pathway and so it extends beyond diagnostic tests. Test detail tends to be common across all diagnostic tests in a patient's pathway, not just genomics.

Name	LOINC	Value Set / Data Type	Cardinality	HL7 v2 ORU_RO1 Message	HL7 FHIR DiagnosticReport	HL7 FHIR Resource (RESTful)
Patient			1..1	PID	subject	Patient
Case Identification or Visit/Stay Number	56797-4	HospitalProviderSpellIdentifier	0..1	PV1-19	encounter	Encounter
Order Number		Placer Order Number	1..1	ORC-2	basedOn	ServiceRequest
Report Number		Report Number	1..1	OBR-3	identifier[ReportNumber]
Genomic Test Code		Genomic Test Code	1..1	OBR-4	code
Report date			1..1	OBR-7	effectiveDateTime
Results Interpreter		England Practitioner Identifier	0..*	OBR-32 and OBR-33	resultsInterpreter	Practitioner
Performer (operator)		England Practitioner Identifier	1..*	OBR-34	performer[operator]	Practitioner
Performer (organisation)		Organisation Code	1..*		performer[organisation]	​Organizaton
Specimen	80398-1		0..1	SPM	specimen	Specimen

Results Mapping

Results section is specific to genomics and is focused on the requirements of general clinicians, not genomic specialists. For this reason this section will tend to be an extract of the wider genomics reporting specifications.

classDiagram
    class GenomicReport["Genomic Laboratory Report (result)"]
    class Variant
    class GenomicStudy["Genomic Study"]
    class DiagnosticImplication["Diagnostic Implication"]
    class TherapeuticImplication["Therapeutic Implication"]
    class GenomicStudyAnalysis["Genomic Study Analysis"]

    Variant --|> GenomicReport 
    GenomicStudy --|> GenomicReport
    GenomicStudyAnalysis --|> GenomicReport
    DiagnosticImplication --|> GenomicReport
    TherapeuticImplication ..|> GenomicReport
    Variant <|--|> DiagnosticImplication
    Variant <|..|> TherapeuticImplication

A more detailed mapping of the results section of the laboratory report, see Genomics Reporting Implementation Guide

Name	LOINC	Value Set / Data Type	Example	Cardinality	HL7 v2 ORU_RO1 Message	HL7 v2 OBX-4	HL7 FHIR Resource (RESTful)
Narrative Report	51969-4			1..1	OBX (type=ED)	1	DiagnosticReport.presentedForm Attachment and Binary
Gene studied [ID]	48018-6		ACAD9	0..1	OBX	1.a	Observation Profile Variant.component:gene-studied

Genomic Study

Description: Genomic Study

Genomic Study

See also HL7 Genomic Reporting - Genomic Study

Name	LOINC	Value Set / Data Type	Example	Cardinality	HL7 v2 OBX-4	FHIR Profile
Analysis method [Type]	Might be 81304-8	Genomic Study Type ValueSet	SNP Array	0..1		Genomic Study.code
Gene disease assessed / Clinical Indication	51967-8			1..1	1.a	Genomic Study.reasonCode
Genomic Test Outcome	TESTCOME (NWGMSA)	Genomic Test Outcome Codes				Genomic Study.outcome

Genomic Study Analysis

TBC - This includes Gene studied [ID] (48018-6) and Gene mutations tested (36908-2). Maybe a requirement from oncology. This appears to be part of FHIR R6 GenomicStudy

Name	LOINC	Value Set / Data Type	Example	Cardinality	HL7 v2 OBX-4	FHIR Observation Profile
regions						Genomic Study Analysis .extension[regions]
Genomic source class [Type]	48002-0	Genetic variant source	Somatic	0..1		Genomic Study Analysis.extension[genomic-source-class]
specimen						Genomic Study Analysis.extension[specimen]

Findings / Observations

Description: Genomic Observations

Variant

Name	LOINC	Value Set / Data Type	Example	Cardinality	HL7 v2 OBX-4	FHIR Observation Profile
Gene studied [ID]	48018-6		ACAD9	0..1	2a	Variant.component[gene-studied]
Genomic DNA change g.HGVS	81290-9		NC_000003.11:g.128625063C>T	0..1	2a	Variant.component[genomic-hgvs]
Transcript reference sequence [Identifier]	51958-7		NM_014049.4	0..1	2a	Variant.component[representative-transcript-ref-seq]
Genetic variant Assessment	69548-6	Variant Assess	Present	0..1	2a	Variant.valueCodeableConcept
Variant analysis method [Type]	81304-8	Structural variant analysis method	SNP Array	0..1	2a	Variant.method
Genomic source class [Type]	48002-0	Genetic variant source	Somatic	0..1	2a	Variant.component[genomic-source-class]
DNA change type	48019-4	LOINC DNA change type or DNA Change Type	Substitution	0..1	2a	Variant.component[coding-change-type]
Allelic state	53034-5	Genetic variant allelic state	Heterozygous	0..1	2a	Variant.component[allelic-state]
Genomic ref allele [ID]	69547-8		C	0..1	2a	Variant.component[ref-allele]
Allelic phase	82120-7	Allelic phase	Maternal	0..1	2a	See 94186-4 below?
Origin of germline genetic variant [Type]	94186-4	Origin of Genetic Variance	Maternal	0..1	- n/a	Variant.component[variant-inheritance]

Implications

Description: Genomic Implications

Diagnostic Implication

Name	LOINC	Value Set / Data Type	Example	Cardinality	HL7 v2 OBX-4	FHIR Observation Profile
Genetic sequence variation clinical significance [Imp]	53037-8	ACMG_Clinical significance of genetic variation	Pathogenic	0..1	2a	Diagnostic Implication.component[clinical-significance]
Probable Associated Phenotype	81259-4		Lynch syndrome	0..1	2a	Diagnostic Implication.component[predicted-phenotype]

Examples

Inherited MMR deficiency (Lynch syndrome) - R210

HL7 LRI (Ref A) Example 2 (5.9.1.2) - FOUND DISCRETE – TARGETED MUTATIONS ANALYSIS THAT STUDIES MANY MUTATIONS (106)

• Patient Paul LIVERPOOL
• Genomic Study- Inherited MMR deficiency (Lynch syndrome)
• Diagnostic Implication - Lynch syndrome
• Variant NTHL1

Cystic fibrosis Carrier R184

HL7 LRI (Ref A) Example 3 (5.9.1.3) - SIMPLE VARIANT – MUTATION ANALYSIS WITH SEQUENCE PLUS DELETION-DUPLICATION STUDY

• Patient Liam MANCHESTER
• Genomic Study - Cystic fibrosis carrier testing
• Diagnostic Implication - Cystic Fibrosis Carrier
• Variant CFTR