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-sequence-phase-relation-CYP2C19

Bundle bundle-sequence-phase-relation-CYP2C19 of type transaction


Entry 1 - fullUrl = urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfe60

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "dv-5c7e9e1ca8252"

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: Human reference sequence assembly version (LOINC#62374-4)

value: GRCh37 (LOINC#LA14029-5)

component

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

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

component

code: Allelic state (LOINC#53034-5)

value: heterozygous (LOINC#LA6706-1)

component

code: Ref nucleotide (LOINC#69547-8)

value: C

component

code: Alt allele (LOINC#69551-0)

value: A

component

code: Genomic coord system (LOINC#92822-6)

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

component

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

value: 96527334-?


Entry 2 - fullUrl = urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe01

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "dv-5c7e9e1ca82e4"

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: Human reference sequence assembly version (LOINC#62374-4)

value: GRCh37 (LOINC#LA14029-5)

component

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

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

component

code: Allelic state (LOINC#53034-5)

value: heterozygous (LOINC#LA6706-1)

component

code: Ref nucleotide (LOINC#69547-8)

value: C

component

code: Alt allele (LOINC#69551-0)

value: G

component

code: Genomic coord system (LOINC#92822-6)

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

component

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

value: 96527722-?


Entry 3 - fullUrl = urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe02

Request:

POST Observation

Resource Observation:

Generated Narrative: Observation

ResourceObservation "sid-5c7e9e1ca8a29"

Profile: Sequence Phase Relationship

status: FINAL

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

code: Allelic phase (LOINC#82120-7)

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: Cis (Sequence Phase Relationship Codes#Cis)

derivedFrom:


Entry 4 - fullUrl = urn:uuid:20ac0aeb-6bd4-4e92-a891-d44a807bfe03

Request:

POST DiagnosticReport

Resource DiagnosticReport:

Genetic analysis report (Genetics)

Report Details

CodeValueWhen ForReported
Genetic variant assessmentPresent2019-03-052019-03-05 16:04:44+0000
Genetic variant assessmentPresent2019-03-052019-03-05 16:04:44+0000
Allelic phaseCis2019-03-052019-03-05 16:04:44+0000


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

Request:

POST Patient

Resource Patient:

Anonymous Patient Male, DoB: 1986-12-31