FHIR IG analytics| Package | pc.ig |
| Resource Type | Basic |
| Id | Basic-genomic-test-example-1.json |
| FHIR Version | R4 |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Basic genomic-test-example-1
Profile: Genomic Test
Reference Genome ID relationship: Basic GRCh38
Genomic Test Name: ExomeSeq v1
Genomic Test Version: 1.2.3
Sequencing device: Illumina NovaSeq 6000
Target capture: Exome capture kit XYZ v5
Read type: Paired-end
Read length: 150
Mean target coverage: 120.5
Per target base cover x100: 95.3
Alignment tools: BWA-MEM 0.7.17
Variant calling tools: GATK HaplotypeCaller 4.2.0
Chromosome coordinate: GRCh38 (1-based, inclusive)
Annotation tools: VEP 104
Annotation databases: gnomAD v3.1, ClinVar 2025-01, dbNSFP 4.3
identifier: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id/GT0001
code: Exome sequencing
FHIR
FHIRsmith{
"resourceType": "Basic",
"id": "genomic-test-example-1",
"meta": {
"profile": [
"https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test"
]
},
"text": {
"status": "extensions",
"div": "<!-- snip (see above) -->"
},
"extension": [
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-reference-genome",
"valueReference": {
"reference": "Basic/reference-genome-grch38"
}
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-name",
"valueString": "ExomeSeq v1"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-version",
"valueString": "1.2.3"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-sequencing-device",
"valueString": "Illumina NovaSeq 6000"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-target-capture",
"valueString": "Exome capture kit XYZ v5"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-type",
"valueString": "Paired-end"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-length",
"valueInteger": 150
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-mean-target-coverage",
"valueDecimal": 120.5
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-per-target-base-cover-100x",
"valueDecimal": 95.3
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-alignment-tools",
"valueString": "BWA-MEM 0.7.17"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-variant-calling-tools",
"valueString": "GATK HaplotypeCaller 4.2.0"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-chromosome-corrdinate",
"valueString": "GRCh38 (1-based, inclusive)"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-tools",
"valueString": "VEP 104"
},
{
"url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-databases",
"valueString": "gnomAD v3.1, ClinVar 2025-01, dbNSFP 4.3"
}
],
"identifier": [
{
"system": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id",
"value": "GT0001"
}
],
"code": {
"coding": [
{
"system": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/genomic-test-type",
"code": "exome",
"display": "Exome sequencing"
}
]
}
}