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-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 |
| meta |
| profile : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report |
| profile : https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport |
| profile : http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab |
| 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 |
| 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 |
| media |
| link |
| type : DocumentReference |
| display : Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition. |
| extension |
| url : http://hl7.org/fhir/StructureDefinition/data-absent-reason |
| value : unsupported |
| extension |
| url : http://hl7.org/fhir/5.0/StructureDefinition/extension-DiagnosticReport.media.link |
| value |
| reference : DocumentReference/DocumentReference-StructureReporting-Example |
| result |
| reference : Observation/Observation-GenomicsVariantSLC52A2-Example |
| display : Brown-Vialetto-Van Laere syndrome type 2 |
| result |
| reference : Observation/Observation-GenomicTherapeuticImplication-Example |
| 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 |
| contentType : application/pdf |
| language : en-GB |
| url : https://cts5j3.axshare.com/?id=mhxwul&p=final_report_issued_test_complete&g=1 |
| size : 43272 |
| title : Genomic Report for Pheobe Smitham |
| creation : 2023-10-16 |
{
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report",
"https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport",
"http://hl7.eu/fhir/laboratory/StructureDefinition/DiagnosticReport-eu-lab"
]
},
{
}
},
{
}
},
{
}
},
{
}
},
{
{
{
}
]
}
}
],
"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)."
}
}
],
],
{
},
{
]
}
],
{
},
{
}
]
},
},
],
],
{
"display": "Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition.",
]
},
{
}
}
]
}
],
{
},
{
}
],
"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).",
{
{
},
{
}
]
},
{
{
}
]
}
],
{
}
]
}
</meta>
<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>
</subject>
</identifier>
</performer>
</specimen>
</result>
</result>
</valueReference>
</extension>
</extension>
<display value="Reference to DocumentReferences are not supported within media.link in DiagnosticReport R4 StructureDefinition." />
</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>