Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "Bundle",
"id" : "diagnosticreport-pgxexample",
"type" : "transaction",
"entry" : [
{
"fullUrl" : "http://example.org/fhir/DiagnosticReport/pgx-report",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "pgx-report",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>Recommended Action</b>: <a href=\"#Task_med-usage-impact-task-pgx-example\">See above (Task/med-usage-impact-task-pgx-example)</a></p><p><b>basedOn</b>: <a href=\"#ServiceRequest_pgx-request\">See above (ServiceRequest/pgx-request)</a></p><p><b>status</b>: final</p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 81247-9}\">Master HL7 genetic variant reporting panel</span></p><p><b>subject</b>: <a href=\"#Patient_patient\">See above (Patient/patient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_lab\">See above (Organization/lab)</a></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_med-impact-pgx-example\">genetics impact for medication metabolism accessment. Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes therapeutic-implication}\">Therapeutic Implication</span>; effective: 2018; issued: Mar 6, 2018 5:00:00 AM</a></li><li><a href=\"#Observation_genotype-pgx-example\">See above (Observation/genotype-pgx-example)</a></li><li><a href=\"#Observation_haplotype-1-pgx-example\">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href=\"#Observation_haplotype-2-pgx-example\">See above (Observation/haplotype-2-pgx-example)</a></li><li><a href=\"#Observation_variant-1-pgx-example\">See above (Observation/variant-1-pgx-example)</a></li><li><a href=\"#Observation_variant-2-pgx-example\">See above (Observation/variant-2-pgx-example)</a></li></ul></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction",
"valueReference" : {
"reference" : "Task/med-usage-impact-task-pgx-example"
}
}
],
"basedOn" : [
{
"reference" : "ServiceRequest/pgx-request"
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE",
"display" : "Genetics"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2016",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"result" : [
{
"reference" : "Observation/med-impact-pgx-example",
"display" : "genetics impact for medication metabolism accessment"
},
{
"reference" : "Observation/genotype-pgx-example"
},
{
"reference" : "Observation/haplotype-1-pgx-example"
},
{
"reference" : "Observation/haplotype-2-pgx-example"
},
{
"reference" : "Observation/variant-1-pgx-example"
},
{
"reference" : "Observation/variant-2-pgx-example"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
},
{
"fullUrl" : "http://example.org/fhir/Patient/patient",
"resource" : {
"resourceType" : "Patient",
"id" : "patient",
"text" : {
"status" : "additional",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">This would contain patient identifiers, demographics, etc.</div>"
}
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "http://example.org/fhir/Specimen/specimen",
"resource" : {
"resourceType" : "Specimen",
"id" : "specimen",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"subject" : {
"reference" : "Patient/patient"
}
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "http://example.org/fhir/Organization/lab",
"resource" : {
"resourceType" : "Organization",
"id" : "lab",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"name" : "Some lab"
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "http://example.org/fhir/ServiceRequest/pgx-request",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "pgx-request",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
},
"status" : "active",
"intent" : "original-order",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81247-9"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"reasonCode" : [
{
"text" : "Worried about family planning"
}
]
},
"request" : {
"method" : "POST",
"url" : "ServiceRequest"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/med-impact-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "med-impact-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes therapeutic-implication}\">Therapeutic Implication</span></p><p><b>subject</b>: <a href=\"#Patient_patient\">See above (Patient/patient)</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_lab\">See above (Organization/lab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype-pgx-example\">See above (Observation/genotype-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 53040-2}\">Genetic variation's effect on drug metabolism</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA25390-8}\">Rapid metabolizer</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 51963-7}\">Medication assessed</span></p><p><b>value</b>: <span title=\"Codes: {http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
"code" : "therapeutic-implication",
"display" : "Therapeutic Implication"
}
]
},
"subject" : {
"reference" : "Patient/patient"
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"performer" : [
{
"reference" : "Organization/lab"
}
],
"derivedFrom" : [
{
"reference" : "Observation/genotype-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53040-2",
"display" : "Genetic variation's effect on drug metabolism"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA25390-8",
"display" : "Rapid metabolizer"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51963-7",
"display" : "Medication assessed"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "103",
"display" : "mercaptopurine"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/genotype-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "genotype-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 84413-4}\">genotype display name</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title=\"Codes: {http://www.pharmvar.org CYP2C9 *4/*35B}\">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href=\"#Specimen_specimen\">See above (Specimen/specimen)</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"#Observation_haplotype-1-pgx-example\">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href=\"#Observation_haplotype-2-pgx-example\">See above (Observation/haplotype-2-pgx-example)</a></li></ul><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td><span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes: {http://www.genenames.org/geneId 2623}\">CYP2C9</span></td></tr></table></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84413-4",
"display" : "genotype display name"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9 *4/*35B",
"display" : "CYP2C9 *4/*35B"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "Observation/haplotype-1-pgx-example"
},
{
"reference" : "Observation/haplotype-2-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/haplotype-1-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "haplotype-1-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 84414-2}\">Haplotype Name</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title=\"Codes: {http://www.pharmvar.org CYP2C9 *35B}\">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href=\"#Specimen_specimen\">See above (Specimen/specimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_variant-1-pgx-example\">See above (Observation/variant-1-pgx-example)</a></p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td><span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes: {http://www.genenames.org/geneId 2623}\">CYP2C9</span></td></tr></table></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84414-2",
"display" : "Haplotype Name"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9 *35B",
"display" : "CYP2C9 *35B"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "Observation/variant-1-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/haplotype-2-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "haplotype-2-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 84414-2}\">Haplotype Name</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title=\"Codes: {http://www.pharmvar.org CYP2C9 *4}\">CYP2C9 *4</span></p><p><b>specimen</b>: <a href=\"#Specimen_specimen\">See above (Specimen/specimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_variant-2-pgx-example\">See above (Observation/variant-2-pgx-example)</a></p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td><span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes: {http://www.genenames.org/geneId 2623}\">CYP2C9</span></td></tr></table></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84414-2",
"display" : "Haplotype Name"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.pharmvar.org",
"code" : "CYP2C9 *4",
"display" : "CYP2C9 *4"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "Observation/variant-2-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/variant-1-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "variant-1-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"#Specimen_specimen\">See above (Specimen/specimen)</a></p><p><b>derivedFrom</b>: <a href=\"#MolecularSequence_sequence-1-pgx-example\">See above (MolecularSequence/sequence-1-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes: {http://www.genenames.org/geneId 2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 81255-2}\">dbSNP ID</span></p><p><b>value</b>: <span title=\"Codes: {http://www.ncbi.nlm.nih.gov/SNP rs12345}\">rs12345</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes exact-start-end}\">Variant exact start and end</span></p><p><b>value</b>: 55227976-55227977</p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "MolecularSequence/sequence-1-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81255-2",
"display" : "dbSNP ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/SNP",
"code" : "rs12345"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69547-8",
"display" : "Ref nucleotide"
}
]
},
"valueString" : "T"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69551-0",
"display" : "Alt allele"
}
]
},
"valueString" : "G"
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
"code" : "exact-start-end",
"display" : "Variant exact start and end"
}
]
},
"valueRange" : {
"low" : {
"value" : 55227976
},
"high" : {
"value" : 55227977
}
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/Observation/variant-2-pgx-example",
"resource" : {
"resourceType" : "Observation",
"id" : "variant-2-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"#Specimen_specimen\">See above (Specimen/specimen)</a></p><p><b>derivedFrom</b>: <a href=\"#MolecularSequence_sequence-2-pgx-example\">See above (MolecularSequence/sequence-2-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes: {http://www.genenames.org/geneId 2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes: {http://www.ncbi.nlm.nih.gov/nuccore NG_007726.3}\">NG_007726.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 81255-2}\">dbSNP ID</span></p><p><b>value</b>: <span title=\"Codes: {http://www.ncbi.nlm.nih.gov/SNP rs233455}\">rs233455</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes exact-start-end}\">Variant exact start and end</span></p><p><b>value</b>: 55227978-55227979</p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"effectiveDateTime" : "2018",
"issued" : "2018-03-06T00:00:00-05:00",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"specimen" : {
"reference" : "Specimen/specimen"
},
"derivedFrom" : [
{
"reference" : "MolecularSequence/sequence-2-pgx-example"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48018-6",
"display" : "Gene studied ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.genenames.org/geneId",
"code" : "2623",
"display" : "CYP2C9"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48013-7",
"display" : "Genomic reference sequence ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/nuccore",
"code" : "NG_007726.3"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81255-2",
"display" : "dbSNP ID"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/SNP",
"code" : "rs233455"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69547-8",
"display" : "Ref nucleotide"
}
]
},
"valueString" : "T"
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69551-0",
"display" : "Alt allele"
}
]
},
"valueString" : "G"
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
"code" : "exact-start-end",
"display" : "Variant exact start and end"
}
]
},
"valueRange" : {
"low" : {
"value" : 55227978
},
"high" : {
"value" : 55227979
}
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "http://example.org/fhir/MolecularSequence/sequence-1-pgx-example",
"resource" : {
"resourceType" : "MolecularSequence",
"id" : "sequence-1-pgx-example",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td><span title=\"Codes: {http://www.ncbi.nlm.nih.gov/nuccore NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>"
},
"type" : "dna",
"coordinateSystem" : 0,
"referenceSeq" : {
"orientation" : "sense",
"referenceSeqId" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/nuccore",
"code" : "NG-007726.3"
}
]
},
"windowStart" : 55227970,
"windowEnd" : 55227980
}
},
"request" : {
"method" : "POST",
"url" : "MolecularSequence"
}
},
{
"fullUrl" : "http://example.org/fhir/MolecularSequence/sequence-2-pgx-example",
"resource" : {
"resourceType" : "MolecularSequence",
"id" : "sequence-2-pgx-example",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td><span title=\"Codes: {http://www.ncbi.nlm.nih.gov/nuccore NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>"
},
"type" : "dna",
"coordinateSystem" : 0,
"referenceSeq" : {
"orientation" : "sense",
"referenceSeqId" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/nuccore",
"code" : "NG-007726.3"
}
]
},
"windowStart" : 55227970,
"windowEnd" : 55227980
}
},
"request" : {
"method" : "POST",
"url" : "MolecularSequence"
}
},
{
"fullUrl" : "http://example.org/fhir/Task/med-usage-impact-task-pgx-example",
"resource" : {
"resourceType" : "Task",
"id" : "med-usage-impact-task-pgx-example",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/task-med-chg"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>status</b>: requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: <span title=\"Codes: {http://loinc.org LA26423-6}\">Any Increase does Recommendation Text from the provider</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"#MedicationStatement_current-med-example\">See above (MedicationStatement/current-med-example)</a></p><p><b>for</b>: <a href=\"#Patient_patient\">See above (Patient/patient)</a></p><p><b>reasonReference</b>: <a href=\"#Observation_med-impact-pgx-example\">See above (Observation/med-impact-pgx-example)</a></p></div>"
},
"status" : "requested",
"intent" : "proposal",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA26423-6",
"display" : "Increase dose"
}
],
"text" : "Any Increase does Recommendation Text from the provider"
},
"description" : "Any Increase does Recommendation Text from the provider",
"focus" : {
"reference" : "MedicationStatement/current-med-example"
},
"for" : {
"reference" : "Patient/patient"
},
"reasonReference" : {
"reference" : "Observation/med-impact-pgx-example"
}
},
"request" : {
"method" : "POST",
"url" : "Task"
}
},
{
"fullUrl" : "http://example.org/fhir/MedicationStatement/current-med-example",
"resource" : {
"resourceType" : "MedicationStatement",
"id" : "current-med-example",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p><b>status</b>: unknown</p><p><b>medication</b>: <span title=\"Codes: {http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</span></p><p><b>subject</b>: <a href=\"#Patient_patient\">See above (Patient/patient)</a></p></div>"
},
"status" : "unknown",
"medicationCodeableConcept" : {
"coding" : [
{
"system" : "http://www.nlm.nih.gov/research/umls/rxnorm",
"code" : "103",
"display" : "mercaptopurine"
}
]
},
"subject" : {
"reference" : "Patient/patient"
}
},
"request" : {
"method" : "POST",
"url" : "MedicationStatement"
}
}
]
}
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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