Clinical Genomics Resource Incubator
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Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions

Example GenomicStudy: Genomic Study Lung Mass Example

Page standards status: Informative

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1112 (use: temp, )

status: Registered

type: Sequencing of entire coding region of gene (procedure)

subject: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))

encounter: Encounter: status = in-progress; class = inpatient encounter

startDate: 2019-03-01

basedOn: ServiceRequest Carrier detection, molecular genetics (procedure)

referrer: Practitioner John Doel

interpreter: Practitioner Jane Doel

Reasons

-Concept
*Lung mass (finding)

note:

For technical reasons, PIK3CA was deemed uncallable.

description:

Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable.

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1112 (use: official, )

methodType: Nucleic acid sequencing (procedure)

changeType: SNV, MNV, delins

genomeBuild: GRCh38

title: Simple variant analysis

specimen: Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000

date: 2019-03-01 01:01:10-0600

note:

For technical reasons, PIK3CA was deemed uncallable using this method.

Outputs

-Type
*VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer

Devices

-DeviceFunction
*Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)Sequencing

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1115 (use: official, )

methodType: Nucleic acid sequencing (procedure)

changeType: CNV

genomeBuild: GRCh38

title: CNV analysis

specimen: Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000

date: 2019-03-01 01:01:10-0600

Outputs

-Type
*VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer