Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
| Page standards status: Informative |
{
"resourceType" : "GenomicStudy",
"resourceDefinition" : "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build",
"id" : "example-pgx",
"language" : "en",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><p class=\"res-header-id\"><b>Generated Narrative: GenomicStudy example-pgx</b></p><a name=\"example-pgx\"> </a><a name=\"hcexample-pgx\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Language: en</p></div><p><b>identifier</b>: <code>http://example.org/identifiers/genomicstudies</code>/urn:uuid:pgx-study-0001\u00a0(use:\u00a0temp,\u00a0)</p><p><b>status</b>: Available</p><p><b>type</b>: <span title=\"Codes:{http://snomed.info/sct 405825005}\">Molecular genetic test (procedure)</span></p><p><b>subject</b>: <a href=\"Patient-pgxPatient.html\">Adam B. Everyman (official) Male, DoB: 1951-01-20 ( Medical record number: m123\u00a0(use:\u00a0usual,\u00a0period:\u00a02021-01-01 --> (ongoing)))</a></p><p><b>startDate</b>: 2021-01-01</p><p><b>basedOn</b>: <a href=\"ServiceRequest-pgxServiceRequest.html\">ServiceRequest </a></p><p><b>interpreter</b>: <a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://snomed.info/sct 182992009}\">Treatment completed (situation)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype.</p>\n</div></blockquote><p><b>description</b>: </p><div><p>Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing.</p>\n</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:pgx-analysis-0001\u00a0(use:\u00a0temp,\u00a0)</p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">copy_number_variation</span></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: PGX Targeted Gene Panel - Sequencing Analysis</p><p><b>specimen</b>: <a href=\"Specimen-pgxSpecimen.html\">Specimen: identifier = http://example.org/identifiers/specimens#pgx-spec-001; status = available; type = Blood specimen (specimen); receivedTime = 2020-12-20 10:00:00+0000</a></p><p><b>date</b>: 2021-01-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>Sequencing coverage of 100% achieved across all targeted regions.</p>\n</div></blockquote><h3>Metrics</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>SequencingCoverage</b></td><td><b>Description</b></td></tr><tr><td style=\"display: none\">*</td><td>100 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code% = '%')</span></td><td>100% coverage of protein-coding and exon-splicing regions for all three genes.</td></tr></table><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype studied}\">Studied</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:2621}\">protein-coding and exon-splicing regions of CYP2C19</span></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">protein-coding and exon-splicing regions of CYP2C9</span></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:23663}\">protein-coding and exon-splicing regions of VKORC1</span></td></tr></table></blockquote><blockquote><p><b>genomicRegion</b></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype called}\">Called</span></p><h3>Locus</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:2621}\">CYP2C19</span></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://www.genenames.org HGNC:23663}\">VKORC1</span></td></tr></table></blockquote><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-pgxVCFfile.html\">DocumentReference: identifier = http://example.org/identifiers/files#pgx-vcf-001; status = current; docStatus = final; description = VCF file containing PGX variant calls for CYP2C19, CYP2C9, and VKORC1; securityLabel = Restricted</a></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td><td><b>Function</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td><td><span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></td></tr></table></blockquote></div>"
},
"identifier" : [
//
Pharmacogenomics (PGX) targeted gene panel study.
Germline sequencing of CYP2C19, CYP2C9, and VKORC1 protein-coding and
exon-splicing regions to guide drug dosing decisions.
Demonstrates: coded gene genomicRegion.studied (HGNC), genomicRegion.called, metrics (sequencing coverage),
germline genomicSourceClass.
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicstudies",
"value" : "urn:uuid:pgx-study-0001"
}
],
"status" : "available",
"type" : [
{
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "405825005",
"display" : "Molecular genetic test (procedure)"
}
]
}
],
"subject" : {
🔗 "reference" : "Patient/pgxPatient"
},
"startDate" : "2021-01-01",
"basedOn" : [
{
🔗 "reference" : "ServiceRequest/pgxServiceRequest"
}
],
"interpreter" : [
{
🔗 "reference" : "Practitioner/practitioner02"
}
],
"reason" : [
{
"concept" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "182992009",
"display" : "Treatment completed (situation)"
}
]
}
}
],
"note" : [
{
"text" : "PGX panel ordered prior to initiating warfarin therapy to guide dosing based on CYP2C9 and VKORC1 genotype."
}
],
"description" : "Pharmacogenomics sequencing panel targeting protein-coding and exon-splicing regions of CYP2C19, CYP2C9, and VKORC1 to inform drug selection and dosing.",
"analysis" : [
{
"identifier" : [
{
"use" : "temp",
"system" : "http://example.org/identifiers/genomicAnalyses",
"value" : "urn:uuid:pgx-analysis-0001"
}
],
"methodType" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-methodtype",
"code" : "sequence-analysis-of-the-entire-coding-region",
"display" : "Sequence analysis of the entire coding region"
}
]
}
],
"changeType" : [
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0001483",
"display" : "SNV"
}
]
},
{
"coding" : [
{
"system" : "http://www.sequenceontology.org",
"code" : "SO:0001019",
"display" : "copy_number_variation"
}
]
}
],
"genomeBuild" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26806-2",
"display" : "GRCh38"
}
]
},
"genomicSourceClass" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6683-2",
"display" : "Germline"
}
]
},
"title" : "PGX Targeted Gene Panel - Sequencing Analysis",
"specimen" : [
{
🔗 "reference" : "Specimen/pgxSpecimen"
}
],
"date" : "2021-01-01T01:01:10-06:00",
"note" : [
{
"text" : "Sequencing coverage of 100% achieved across all targeted regions."
}
],
"metrics" : {
"sequencingCoverage" : {
"value" : 100,
"unit" : "%",
"system" : "http://unitsofmeasure.org",
"code" : "%"
},
"description" : "100% coverage of protein-coding and exon-splicing regions for all three genes."
},
"genomicRegion" : [
// genomicRegion: studied = all three PGx gene targets (protein-coding and exon-splicing regions)
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "studied",
"display" : "Studied"
}
]
},
"locus" : [
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2621",
"display" : "CYP2C19"
}
],
"text" : "protein-coding and exon-splicing regions of CYP2C19"
}
},
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
],
"text" : "protein-coding and exon-splicing regions of CYP2C9"
}
},
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:23663",
"display" : "VKORC1"
}
],
"text" : "protein-coding and exon-splicing regions of VKORC1"
}
}
]
},
{
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype",
"code" : "called",
"display" : "Called"
}
]
},
"locus" : [
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2621",
"display" : "CYP2C19"
}
]
}
},
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:2623",
"display" : "CYP2C9"
}
]
}
},
{
"concept" : {
"coding" : [
{
"system" : "http://www.genenames.org",
"code" : "HGNC:23663",
"display" : "VKORC1"
}
]
}
}
]
}
],
"output" : [
// genomicRegion: called = same three genes, all achieved sufficient coverage to produce calls
{
"file" : {
🔗 "reference" : "DocumentReference/pgxVCFfile"
},
"type" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"code" : "vcf",
"display" : "VCF"
}
]
}
}
],
"performer" : [
{
"actor" : {
🔗 "reference" : "Practitioner/practitioner02"
},
"role" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
"code" : "PRF",
"display" : "Performer"
}
]
}
}
],
"device" : [
{
"device" : {
🔗 "reference" : "Device/NGS-device"
},
"function" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26398-0",
"display" : "Sequencing"
}
]
}
}
]
}
]
}
IG © 2026+ HL7 International / Clinical Genomics.
Package hl7.fhir.uv.cg-incubator#0.1.0-ci-build based on FHIR 6.0.0-ballot3.
Generated
2026-03-24
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