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 Observation: Pgx-var-1018

Generated Narrative: Observation

ResourceObservation "Pgx-var-1018"

Profile: Variant

status: final

category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/CGPatientExample01 " EVERYMAN"

effective: 2019-04-01

performer: Organization/ExampleOrg "some lab"

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)

component

code: Genomic reference sequence [ID] (LOINC#48013-7)

value: b37 Chr10 (Gene Reference Sequence Collection#NC_000010.10)

component

code: Genomic coordinate system [Type] (LOINC#92822-6)

value: 1-based character counting (LOINC#LA30102-0)

component

code: Genomic allele start-end (LOINC#81254-5)

value: 96612495-96612495

component

code: Genomic ref allele [ID] (LOINC#69547-8)

value: C

component

code: Genomic alt allele [ID] (LOINC#69551-0)

value: C

component

code: Genomic source class [Type] (LOINC#48002-0)

value: Germline (LOINC#LA6683-2)

component

code: Allelic state (LOINC#53034-5)

value: homozygous (LOINC#LA6705-3)

component

code: Gene studied [ID] (LOINC#48018-6)

value: CYP2C19 (HUGO Gene Nomenclature Committee Genes#HGNC:2621)

component

code: DNA change type (LOINC#48019-4)

value: wild type (sequenceontology.org#SO:1000002)

component

code: Allelic read depth (LOINC#82121-5)

value: >20

component

code: Variant Confidence Status (To Be Determined Codes#variant-confidence-status)

value: High (Variant Confidence Status Codes#high)