Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

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

Example Bundle: bundle-oncology-diagnostic

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

ResourcePractitioner "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:

Generated Narrative: Specimen

ResourceSpecimen "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

ResourceObservation "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

-CodeValue[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

ResourceObservation "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

ResourceObservation "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: Associated 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)

SubjectNot done yet
When For2019-03-05

Report Details

CodeValue
Genetic variant assessmentPresent
Diagnostic Implication