Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
{
"resourceType" : "Bundle",
"id" : "bundle-compound-heterozygote",
"type" : "transaction",
"entry" : [
{
"fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-compound-heterozygote-1",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-compound-heterozygote-1\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-compound-heterozygote-1</b></p><a name=\"Inline-Instance-for-compound-heterozygote-1\"> </a><a name=\"hcInline-Instance-for-compound-heterozygote-1\"> </a><a name=\"Inline-Instance-for-compound-heterozygote-1-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_022787.3:c.769G>A}\">NM_022787.3:c.769G>A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
"reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"
},
"effectiveDateTime" : "2019-03-05",
"issued" : "2019-03-05T16:04:44+00:00",
"performer" : [
{
"reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6",
"display" : "DNA change (c.HGVS)"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_022787.3:c.769G>A",
"display" : "NM_022787.3:c.769G>A"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53034-5",
"display" : "Allelic state"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6706-1",
"display" : "Heterozygous"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-compound-heterozygote-2",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-compound-heterozygote-2\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-compound-heterozygote-2</b></p><a name=\"Inline-Instance-for-compound-heterozygote-2\"> </a><a name=\"hcInline-Instance-for-compound-heterozygote-2\"> </a><a name=\"Inline-Instance-for-compound-heterozygote-2-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_022787.3:c.53A>G}\">NM_022787.3:c.53A>G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6706-1}\">Heterozygous</span></p></blockquote></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
"reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"
},
"effectiveDateTime" : "2019-03-05",
"issued" : "2019-03-05T16:04:44+00:00",
"performer" : [
{
"reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48004-6",
"display" : "DNA change (c.HGVS)"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://varnomen.hgvs.org",
"code" : "NM_022787.3:c.53A>G",
"display" : "NM_022787.3:c.53A>G"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53034-5",
"display" : "Allelic state"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6706-1",
"display" : "Heterozygous"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a",
"resource" : {
"resourceType" : "Observation",
"id" : "Inline-Instance-for-compound-heterozygote-3",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-compound-heterozygote-3\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-compound-heterozygote-3</b></p><a name=\"Inline-Instance-for-compound-heterozygote-3\"> </a><a name=\"hcInline-Instance-for-compound-heterozygote-3\"> </a><a name=\"Inline-Instance-for-compound-heterozygote-3-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84413-4}\">Genotype display name</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeac\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>issued</b>: 2019-03-05 16:04:44+0000</p><p><b>performer</b>: <a href=\"Bundle-bundle-CYP2C19.html#urn-uuid-19ac0aeb-6bd4-4e92-a891-d44a807bfeab\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/clinvar RCV000664188.1}\">NM_022787.3(NMNAT1):c.[53A>G];[769G>A] AND Cone-rod dystrophy</span></p><p><b>hasMember</b>: </p><ul><li><a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12e\">NM_022787.3:c.53A>G</a></li><li><a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d\">NM_022787.3:c.769G>A</a></li></ul></div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "84413-4"
}
]
},
"subject" : {
"reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac"
},
"effectiveDateTime" : "2019-03-05",
"issued" : "2019-03-05T16:04:44+00:00",
"performer" : [
{
"reference" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab"
}
],
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/clinvar",
"code" : "RCV000664188.1",
"display" : "NM_022787.3(NMNAT1):c.[53A>G];[769G>A] AND Cone-rod dystrophy"
}
]
},
"hasMember" : [
{
"reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e",
"display" : "NM_022787.3:c.53A>G"
},
{
"reference" : "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d",
"display" : "NM_022787.3:c.769G>A"
}
]
},
"request" : {
"method" : "POST",
"url" : "Observation"
}
},
{
"fullUrl" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab",
"resource" : {
"resourceType" : "Organization",
"id" : "performingLab",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_performingLab\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization performingLab</b></p><a name=\"performingLab\"> </a><a name=\"hcperformingLab\"> </a><a name=\"performingLab-en-US\"> </a><p><b>name</b>: aTypingLab Inc</p><p><b>alias</b>: aTL</p><p><b>telecom</b>: ph: 1-800-555-1234(Work)</p><p><b>address</b>: 123 Main St, Sometown, ND 99999(work)</p></div>"
},
"name" : "aTypingLab Inc",
"alias" : [
"aTL"
],
"telecom" : [
{
"system" : "phone",
"value" : "1-800-555-1234",
"use" : "work",
"rank" : 1
}
],
"address" : [
{
"use" : "work",
"type" : "both",
"text" : "123 Main St, Sometown, ND 99999",
"line" : [
"123 Main St"
],
"city" : "Sometown",
"state" : "ND",
"postalCode" : "99999",
"country" : "USA"
}
]
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac",
"resource" : {
"resourceType" : "Patient",
"id" : "patient",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Patient_patient\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Patient patient</b></p><a name=\"patient\"> </a><a name=\"hcpatient\"> </a><a name=\"patient-en-US\"> </a><p style=\"border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;\">John Storm(official) Male, DoB: 1986-12-31</p><hr/></div>"
},
"name" : [
{
"use" : "official",
"text" : "John Storm",
"family" : "Storm",
"given" : [
"John"
]
},
{
"use" : "nickname",
"text" : "Johnny Storm",
"family" : "Storm",
"given" : [
"Johnny"
]
},
{
"use" : "nickname",
"text" : "The Human Torch"
}
],
"gender" : "male",
"birthDate" : "1986-12-31"
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change