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-complexVariant-nonHGVS

Bundle bundle-complexVariant-nonHGVS of type transaction


Entry 1 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "Inline-Instance-for-complexVariant-nonHGVS-1"

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:19ac0aeb-6bd4-4e92-a891-d44a807bfeac

effective: 2019-03-05

issued: Mar 5, 2019, 4:04:44 PM

performer: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab

value: Present (LOINC#LA9633-4)

component

code: Transcript ref sequence ID (LOINC#51958-7)

value: NM_022787.3 (Gene Reference Sequence Collection#NM_022787.3)

component

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

value: 769-769

component

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

value: G

component

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

value: A

component

code: Allelic state (LOINC#53034-5)

value: Heterozygous (LOINC#LA6706-1)


Entry 2 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "Inline-Instance-for-complexVariant-nonHGVS-2"

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:19ac0aeb-6bd4-4e92-a891-d44a807bfeac

effective: 2019-03-05

issued: Mar 5, 2019, 4:04:44 PM

performer: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab

value: Present (LOINC#LA9633-4)

component

code: Transcript ref sequence ID (LOINC#51958-7)

value: NM_022787.3 (Gene Reference Sequence Collection#NM_022787.3)

component

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

value: 53-53

component

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

value: A

component

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

value: G

component

code: Allelic state (LOINC#53034-5)

value: Heterozygous (LOINC#LA6706-1)


Entry 3 - fullUrl = urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "Inline-Instance-for-complexVariant-nonHGVS-3"

Profile: Genotype

status: FINAL

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

code: Genotype display name (LOINC#84413-4)

subject: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac

effective: 2019-03-05

issued: Mar 5, 2019, 4:04:44 PM

performer: See on this page: urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab

value: NM_022787.3(NMNAT1):c.[53A>G];[769G>A] AND Cone-rod dystrophy (ClinVar Variant ID#RCV000664188.1)

hasMember:


Entry 4 - fullUrl = urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab

Request:

POST Organization

Resource Organization:

Generated Narrative: Organization

ResourceOrganization "performingLab"

name: aTypingLab Inc

alias: aTL

Contacts

-TelecomAddress
*ph: 1-800-555-1234(WORK)123 Main St, Sometown, ND 99999(work)


Entry 5 - fullUrl = urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeac

Request:

POST Patient

Resource Patient:

Anonymous Patient Male, DoB: 1986-12-31