Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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
Bundle bundle-oncology-diagnostic of type transaction
Entry 1 - fullUrl = urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
Request:
POST Patient
Resource Patient:
Anonymous Patient Male, DoB: 1962-12-31 ( 1007)
Entry 2 - fullUrl = urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
Request:
POST Practitioner
Resource Practitioner:
Generated Narrative: Practitioner
Resource Practitioner "Inline-Instance-for-oncology-diagnostic-2"
identifier: 4654765876
name: Akerman Philip Prof
address: Castro Valley CA
Entry 3 - fullUrl = urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
Request:
POST Specimen
Resource Specimen:
Resource Specimen "Inline-Instance-for-oncology-diagnostic-3"
identifier: 076e1948-2217-11e9-94d8-12e241dc1f66
status: AVAILABLE
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
Collections
Collector See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
Entry 4 - fullUrl = urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-diagnostic-4"
Profile: Molecular Biomarker
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), A characterization of a given biomarker observation. (To Be Determined Codes#biomarker-category), Genetics (diagnosticServiceSectionId#GE)
code: Mutations/Megabase [# Ratio] in Tumor (LOINC#94076-7)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2019-03-05
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: 25 Mutations/Megabase (Details: UCUM code 1/1000000 = '1/1000000')
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
Components
Code Value[x] A characterization of a given biomarker observation. (To Be Determined Codes#biomarker-category) molecular sequence adjacent category (Molecular Biomarker Ontology Codes#molgen)
Entry 5 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-diagnostic-5"
Profile: Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Genetic variant assessment (LOINC#69548-6)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2019-03-05
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
value: Present (LOINC#LA9633-4)
method: Sequencing (LOINC#LA26398-0)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
component
code: Human reference sequence assembly version (LOINC#62374-4)
value: GRCh37 (LOINC#LA14029-5)
component
code: Genomic DNA change (gHGVS) (LOINC#81290-9)
value: NC_000007.13:g.140453136A>T (Human Genome Variation Society nomenclature#NC_000007.13:g.140453136A>T)
component
code: Discrete genetic variant (LOINC#81252-9)
value: Clinvar ID 13961 (ClinVar Variant ID#13961)
component
code: Amino acid change (pHGVS) (LOINC#48005-3)
value: NP_004324.2:p.Val600Glu (Human Genome Variation Society nomenclature#NP_004324.2:p.Val600Glu)
component
code: Gene studied ID (LOINC#48018-6)
value: BRAF (HUGO Gene Nomenclature Committee Genes#HGNC:1097)
Entry 6 - fullUrl = urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524
Request:
POST Observation
Resource Observation:
Generated Narrative: Observation
Resource Observation "Inline-Instance-for-oncology-diagnostic-6"
Profile: Diagnostic Implication
Related Artifact:
status: FINAL
category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)
code: Diagnostic Implication (To Be Determined Codes#diagnostic-implication)
subject: See on this page: urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d
effective: 2019-03-05
performer: See on this page: urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef
method: Computational analysis (LOINC#LA26811-2)
specimen: See on this page: urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d
derivedFrom: See on this page: urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d
component
code: Genetic variation clinical significance [Imp] (LOINC#53037-8)
value: Pathogenic (LOINC#LA6668-3)
component
code: Level of Evidence (LOINC#93044-6)
value: Very strong evidence pathogenic (LOINC#LA30200-2)
component
code: Prob assoc phenotype (LOINC#81259-4)
value: melanoma ()
Entry 7 - fullUrl = urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5
Request:
POST DiagnosticReport
Resource DiagnosticReport:
Genetic analysis report (Genetics)
Subject Not done yet When For 2019-03-05 Report Details
Code Value Genetic variant assessment Present Diagnostic Implication
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
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