Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: John Storm(official) Male, DoB: 1986-12-31

> effective: 2019-03-05

> issued: 2019-03-05 16:04:44+0000

> performer: Organization aTypingLab Inc

> value: Present

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: Genomic reference sequence ID

> > value: NC_000010.10

> > component

> > code: Allelic state

> > value: heterozygous

> > component

> > code: Ref nucleotide

> > value: C

> > component

> > code: Alt allele

> > value: A

> > component

> > code: Genomic coord system

> > value: 1-based character counting

> > component

> > code: Genomic allele start-end

> > value: 96527334-?

Request:

    POST Observation

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

Resource Observation:

> Profile: Variant

> status: Final

> category: Laboratory, Genetics

> code: Genetic variant assessment

> subject: John Storm(official) Male, DoB: 1986-12-31

> effective: 2019-03-05

> issued: 2019-03-05 16:04:44+0000

> performer: Organization aTypingLab Inc

> value: Present

> > component

> > code: Human reference sequence assembly version

> > value: GRCh37

> > component

> > code: Genomic reference sequence ID

> > value: NC_000010.10

> > component

> > code: Allelic state

> > value: heterozygous

> > component

> > code: Ref nucleotide

> > value: C

> > component

> > code: Alt allele

> > value: G

> > component

> > code: Genomic coord system

> > value: 1-based character counting

> > component

> > code: Genomic allele start-end

> > value: 96527722-?

Request:

    POST Observation

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

Resource Observation:

> Profile: Sequence Phase Relationship

> status: Final

> category: Laboratory, Genetics

> code: Allelic phase

> subject: John Storm(official) Male, DoB: 1986-12-31

> effective: 2019-03-05

> issued: 2019-03-05 16:04:44+0000

> performer: Organization aTypingLab Inc

> value: Cis

> derivedFrom:

> - Observation Genetic variant assessment
> - Observation Genetic variant assessment

Request:

    POST Observation

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

Resource DiagnosticReport:

> Profile: Genomic Report

> ## Genetic analysis report (Genetics)

> Report Details

> Code | Value | Flags | When For | Reported
> Genetic variant assessment | Present | Final | 2019-03-05 | 2019-03-05 16:04:44+0000
> Genetic variant assessment | Present | Final | 2019-03-05 | 2019-03-05 16:04:44+0000
> Allelic phase | Cis | Final | 2019-03-05 | 2019-03-05 16:04:44+0000

Request:

    POST DiagnosticReport

Entry 5 - fullUrl = urn:uuid:19ac0aeb-6bd4-4e92-a891-d44a807bfeab

Resource Organization:

> name: aTypingLab Inc

> alias: aTL

> ### Contacts

> - | Telecom | Address
> * | ph: 1-800-555-1234(Work) | 123 Main St, Sometown, ND 99999(work)

Request:

    POST Organization

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

Resource Patient:

> John Storm(official) Male, DoB: 1986-12-31

> Contact Detail | ph: 1-800-555-1234(Work) 123 Main St, Sometown, ND 99999(work)

Request:

    POST Patient