Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
DiagnosticReport
DiagnosticReport-AnitaLamberts-Example
Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning unstructured reports back to a requester (NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For Structured Reports, users SHOULD follow guidance provided within the HL7 Genomic Reporting Implementation Guide.
| DiagnosticReport |
| id : DiagnosticReport-AnitaLamberts-Example |
| identifier |
| system : https://www.guysandstthomas.nhs.uk/SEGLH/lims |
| value : FHGenomicReport |
| assigner |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : RJ1 |
| basedOn |
| reference : ServiceRequest/ServiceRequest-NonWGSTestOrderForm-NewFollowupTest-Example |
| status : final |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : GE |
| category |
| coding |
| system : http://snomed.info/sct |
| code : 1236877003 |
| display : Genetic pathology |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 1054161000000101 |
| display : Genetic report |
| subject |
| reference : Patient/Patient-AnitaLamberts-Example |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 8449303649 |
| issued : 2023-11-24T09:45:00+00:00 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : RJ1 |
| specimen |
| reference : Specimen/Specimen-BloodEDTA-Example |
| presentedForm |
| url : DocumentReference/DocumentReference-AnitaLamberts-Example |
{
{
}
}
],
],
{
},
{
]
}
],
]
},
}
},
],
],
]
}
</identifier>
</assigner>
</identifier>
</basedOn>
</coding>
</category>
</coding>
</category>
</coding>
</code>
</identifier>
</subject>
</identifier>
</performer>
</specimen>
</presentedForm>
</DiagnosticReport>
DiagnosticReport-ExtensionMediaLink-Example
Example of a DiagnosticReport, with minimal information, demonstrating usage of the R4 DiagnosticReport.media.link with an alternate-reference extension to point to a DocumentReference resource, which can be used to directly reference data associated with the report, e.g. Genomic Data Files.
| DiagnosticReport |
| id : DiagnosticReport-ExtensionMediaLink-Example |
| text |
| status : additional |
| status : preliminary |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 1129261000000102 |
| display : Cardiac electrophysiology report |
| media |
| link |
| extension |
| url : http://hl7.org/fhir/StructureDefinition/alternate-reference |
| value |
| reference : DocumentReference/UKCore-DocumentReference-ECG-Example |
| display : ECG PDF (DocumentReference via backported extension) |
{
--- We have skipped the narrative for better readability of the resource ---
},
{
}
]
},
{
{
}
}
],
}
}
]
}
--- We have skipped the narrative for better readability of the resource ---
</text>
</coding>
</code>
</valueReference>
</extension>
</link>
</media>
</DiagnosticReport>
DiagnosticReport-FayMutlowGeneticReport-Example
Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning unstructured reports back to a requester (NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For Structured Reports, users SHOULD follow guidance provided within the HL7 Genomic Reporting Implementation Guide.
| DiagnosticReport |
| id : DiagnosticReport-FayMutlowGeneticReport-Example |
| identifier |
| system : https://newcastle-hospitsls.nhs.uk/nwglh/lims |
| value : FHGenomicReport |
| assigner |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : RTD |
| basedOn |
| reference : ServiceRequest/ServiceRequest-SavedTestOrderUpdated-CascadeTesting-Example |
| status : final |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : GE |
| category |
| coding |
| system : http://snomed.info/sct |
| code : 1236877003 |
| display : Genetic pathology |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 1054161000000101 |
| display : Genetic report |
| subject |
| reference : Patient/Patient-FayMutlow-Example |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 9449307806 |
| issued : 2023-10-09T09:45:00+00:00 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : RTD |
| specimen |
| reference : Specimen/Specimen-FayMutlowBloodEDTA-Example |
| conclusionCode |
| coding |
| system : http://snomed.info/sct |
| code : 398036000 |
| display : Familial hypercholesterolemia |
| presentedForm |
| url : DocumentReference/DocumentReference-FayMutlowGeneticReport-Example |
{
{
}
}
],
],
{
},
{
]
}
],
]
},
}
},
],
],
{
{
}
]
}
],
]
}
</identifier>
</assigner>
</identifier>
</basedOn>
</coding>
</category>
</coding>
</category>
</coding>
</code>
</identifier>
</subject>
</identifier>
</performer>
</specimen>
</coding>
</conclusionCode>
</presentedForm>
</DiagnosticReport>
DiagnosticReport-GenomicVariantAssessment-Example
Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning structured reports back to a requester.
(NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For more information about this sample structured report, see, Duo/Trio scenario-wireframe.
Additional guidance on Structured Reports is available on the HL7 Genomic Reporting Implementation Guide.
| DiagnosticReport |
| id : DiagnosticReport-GenomicVariantAssessment-Example |
| extension |
| url : http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition |
| value |
| reference : Composition/Composition-EULabGenomicReport-Example |
| extension |
| url : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action |
| value |
| reference : Task/Task-FollowupRecommendationReport-Example |
| display : Confirmatory testing recommended |
| extension |
| url : http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact |
| value |
| type : citation |
| display : Johnson et al 2012 (PMID22740598) |
| extension |
| url : http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact |
| value |
| type : citation |
| display : Foley et al 2014 (PMID22740598) |
| extension |
| url : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note |
| value |
| extension |
| url : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code |
| value |
| coding |
| system : http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs |
| code : test-disclaimer |
| text : Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868). |
| basedOn |
| reference : ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example |
| status : final |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : GE |
| category |
| coding |
| system : http://snomed.info/sct |
| code : 1236877003 |
| display : Genetic pathology |
| code |
| coding |
| system : http://loinc.org |
| code : 51969-4 |
| display : Genetic analysis report |
| coding |
| system : http://snomed.info/sct |
| code : 1054161000000101 |
| display : Genetic report |
| subject |
| reference : Patient/Patient-PheobeSmitham-Example |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 9449307539 |
| effective : 2023-10-16T00:00:00-05:00 |
| issued : 2023-09-16T00:00:00-05:00 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : R0A |
| specimen |
| reference : Specimen/Specimen-PheobeSmitham-Example |
| result |
| reference : Observation/Observation-GenomicsVariantSLC52A2-Example |
| display : Brown-Vialetto-Van Laere syndrome type 2 |
| result |
| reference : Observation/Observation-GenomicTherapeuticImplication-Example |
| media |
| link |
| extension |
| url : http://hl7.org/fhir/StructureDefinition/alternate-reference |
| value |
| reference : DocumentReference/DocumentReference-StructureReporting-Example |
| display : DocumentReference via backported extension |
| conclusion : Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707). |
| conclusionCode |
| coding |
| system : http://loinc.org |
| code : LA6576-8 |
| display : Positive |
| coding |
| system : http://snomed.info/sct |
| code : 10828004 |
| display : Positive |
| conclusionCode |
| coding |
| system : http://snomed.info/sct |
| code : 699866005 |
| display : Brown-Vialetto-Van Laere syndrome |
| presentedForm |
| url : DocumentReference/DocumentReference-GenomicVariantAssessment-Example |
{
{
}
},
{
}
},
{
}
},
{
}
},
{
{
{
}
]
}
}
],
"text": "Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)."
}
}
],
],
{
},
{
]
}
],
{
},
{
}
]
},
}
},
],
],
{
},
{
}
],
{
{
}
}
],
}
}
],
"conclusion": "Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707).",
{
{
},
{
}
]
},
{
{
}
]
}
],
]
}
<extension url="http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.composition">
</valueReference>
</extension>
</valueReference>
</extension>
</valueRelatedArtifact>
</extension>
</valueRelatedArtifact>
</extension>
</coding>
</valueCodeableConcept>
</extension>
<text value="Proband whole genome sequencing by the 100,000 Genomics Project with analysis of the PanelApp Paediatric motor neuronopathies (version 1.6) gene panel followed by in-house Sanger sequencing confirmation. Please note that the sensitivity of this test is limited by the types of detectable pathogenic variants, regions of low read depth coverage and incomplete ascertainment of disease-gene associations. Further information including read depth coverage is available on request. *Variants are classified using the ACMG/AMP guidelines (Richards et al 2015 PMID25741868)." />
</valueAnnotation>
</extension>
</basedOn>
</coding>
</category>
</coding>
</category>
</coding>
</coding>
</code>
</identifier>
</subject>
</identifier>
</performer>
</specimen>
</result>
</result>
</valueReference>
</extension>
</link>
</media>
<conclusion value="Pheobe is homozygous for a pathogenic SLC52A2 missense variant (details below) previously reported by Johnson et al 2012 (PMID22740598). Biallelic pathogenic SLC52A2 variants cause autosomal recessive Brown-Vialetto-Van Laere syndrome type 2 (MIM614707)." />
</coding>
</coding>
</conclusionCode>
</coding>
</conclusionCode>
</presentedForm>
</DiagnosticReport>
DiagnosticReport-JamesMetcalfeGeneticReport-Example
Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning unstructured reports back to a requester (NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For Structured Reports, users SHOULD follow guidance provided within the HL7 Genomic Reporting Implementation Guide.
| DiagnosticReport |
| id : DiagnosticReport-JamesMetcalfeGeneticReport-Example |
| identifier |
| system : https://royaldevon.nhs.uk//nwglh/lims |
| value : MD_GenomicReport |
| assigner |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : RH8 |
| basedOn |
| reference : ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-DirectToLab-Example |
| status : final |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : GE |
| category |
| coding |
| system : http://snomed.info/sct |
| code : 1236877003 |
| display : Genetic pathology |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 1054161000000101 |
| display : Genetic report |
| subject |
| reference : Patient/Patient-JamesMetcalfe-Example |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 7449306524 |
| issued : 2023-10-18T11:10:00+00:00 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : RH8 |
| specimen |
| reference : Specimen/Specimen-JamesMetcalfeBloodEDTA-Example |
| presentedForm |
| url : DocumentReference/DocumentReference-JamesMetcalfeGeneticReport-Example |
{
{
}
}
],
],
{
},
{
]
}
],
]
},
}
},
],
],
]
}
</identifier>
</assigner>
</identifier>
</basedOn>
</coding>
</category>
</coding>
</category>
</coding>
</code>
</identifier>
</subject>
</identifier>
</performer>
</specimen>
</presentedForm>
</DiagnosticReport>
DiagnosticReport-PhoebeSmithGeneticReport-Example
Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning unstructured reports back to a requester (NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For Structured Reports, users SHOULD follow guidance provided within the HL7 Genomic Reporting Implementation Guide.
| DiagnosticReport |
| id : DiagnosticReport-PhoebeSmithGeneticReport-Example |
| identifier |
| system : https://mft.nhs.uk//nwglh/lims |
| value : SLC52A2_GenomicReport |
| assigner |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : R0A |
| basedOn |
| reference : ServiceRequest-WGSTestOrderForm-TrioTestingProband-Example |
| status : final |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : GE |
| category |
| coding |
| system : http://snomed.info/sct |
| code : 1236877003 |
| display : Genetic pathology |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 1054161000000101 |
| display : Genetic report |
| subject |
| reference : Patient/Patient-PheobeSmitham-Example |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 9449307539 |
| issued : 2023-10-16T15:50:00+00:00 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : R0A |
| specimen |
| reference : Specimen/Specimen-PheobeSmitham-Example |
| specimen |
| reference : Specimen/Specimen-PheobeSmithamFather-Example |
| specimen |
| reference : Specimen/Specimen-PheobeSmithamMother-Example |
| conclusionCode |
| coding |
| system : http://snomed.info/sct |
| code : 699866005 |
| display : Brown-Vialetto-Van Laere syndrome |
| text : Brown-Vialetto-Van Laere syndrome 2 |
| presentedForm |
| url : DocumentReference/DocumentReference-PhoebeSmithGeneticReport-Example |
{
{
}
}
],
],
{
},
{
]
}
],
]
},
}
},
],
{
},
{
},
{
}
],
{
{
}
],
}
],
]
}
</identifier>
</assigner>
</identifier>
</basedOn>
</coding>
</category>
</coding>
</category>
</coding>
</code>
</identifier>
</subject>
</identifier>
</performer>
</specimen>
</specimen>
</specimen>
</coding>
</conclusionCode>
</presentedForm>
</DiagnosticReport>
DiagnosticReport-MichaelJonesReport
For Information Only. Example of a DiagnosticReport for DPYD indicating a patient is a poor metaboliser for Dihydropyrimidine dehydrogenase. Diagnostic reports from genomic services are expected to either attach the PDF report through the presentedForm element (either as a base64 encoded attachment or URL reference to the location where the PDF can be retrieved), or follow guidance provided within the HL7 Genomic Reporting Implementation Guide for structured reporting.
| DiagnosticReport |
| id : UKCore-DiagnosticReport-MichaelJonesReport-Example |
| identifier |
| system : https://mft.nhs.uk/nwglh/lims |
| value : DPYDGenomicReport |
| assigner |
| reference : Organization/1b81b2e9-d428-4cf6-8d9f-b3f3e3833430 |
| basedOn |
| reference : ServiceRequest/7f70bb0c-5792-46d4-bbfd-c48cbcd3895b |
| status : final |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : LAB |
| display : Laboratory |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 4321000179101 |
| display : Hematology report |
| subject |
| reference : Patient/f52cae9c-81eb-422c-be58-8363e72144aa |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 9999999999 |
| issued : 2022-07-15T09:00:00+00:00 |
| performer |
| reference : Organization/1b81b2e9-d428-4cf6-8d9f-b3f3e3833430 |
| resultsInterpreter |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : REP |
| specimen |
| reference : Specimen/e64a0757-f092-47ff-ad36-e8ff0c3b6fa1 |
| conclusionCode |
| coding |
| system : http://snomed.info/sct |
| code : 738542003 |
| display : Dihydropyrimidine dehydrogenase poor metabolizer |
| presentedForm |
| url : DocumentReference/DocumentReference-MichaelJonesReport-Example |
{
{
}
}
],
],
{
{
}
]
}
],
]
},
}
},
],
],
],
{
{
}
]
}
],
]
}
</assigner>
</identifier>
</basedOn>
</coding>
</category>
</coding>
</code>
</identifier>
</subject>
</performer>
</identifier>
</resultsInterpreter>
</specimen>
</coding>
</conclusionCode>
</presentedForm>
</DiagnosticReport>
DiagnosticReport-MichaelJonesReport-Minimal
For Information Only. Example of a DiagnosticReport with the minimal amount of information expected by the Genomic Medicine Service when returning unstructured reports back to a requester (NOTE: basedOn SHALL reference a ServiceRequest resource within the central broker). For Structured Reports, users SHOULD follow guidance provided within the HL7 Genomic Reporting Implementation Guide.
| DiagnosticReport |
| id : UKCore-DiagnosticReport-MichaelJonesReport-Example-Minimal |
| basedOn |
| identifier |
| system : https://www.christie.nhs.uk/ehr |
| value : LabOrder123456 |
| status : final |
| code |
| coding |
| system : http://snomed.info/sct |
| code : 1054161000000101 |
| display : Genetic report |
| subject |
| identifier |
| system : https://fhir.nhs.uk/Id/nhs-number |
| value : 9999999999 |
| issued : 2022-07-15T09:00:00+00:00 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : 699X0 |
| resultsInterpreter |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : REP |
| specimen |
| identifier |
| system : https://www.christie.nhs.uk/path |
| value : Spec123456 |
| presentedForm |
| url : DocumentReference/DocumentReference-MichaelJonesReport-Example-Minimal |
{
],
]
},
},
],
],
],
]
}
</identifier>
</basedOn>
</coding>
</code>
</identifier>
</subject>
</identifier>
</performer>
</identifier>
</resultsInterpreter>
</identifier>
</specimen>
</presentedForm>
</DiagnosticReport>