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 Example

Page standards status: Informative

Language: en

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

status: Unknown

type: Familial variant segregation

subject: Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111 (use: temp, period: 2021-01-01 --> (ongoing)))

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

startDate: 2021-01-01

basedOn: ServiceRequest Carrier detection, molecular genetics (procedure)

referrer: Practitioner John Doel

interpreter: Practitioner Jane Doel

Reasons

-Concept
*Disorder of lipid metabolism (disorder)

note:

This de novo mutation is urgent and important for establishing the treatment plan.

description:

De novo mutation study of the patient.

analysis

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

genomicSourceClass: Germline

title: Proband Sequence Variation Detection Using Next Generation Sequencing

specimen: Specimen: identifier = http://example.org/identifiers/specimens#1; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000

date: 2021-01-01 01:01:10-0600

note:

This is a next generation sequencing analysis of a proband.

Inputs

-FileType
*DocumentReference: identifier = http://example.org/identifiers/files#11111; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.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:1111-1111-1111-1112 (use: temp, )

genomicSourceClass: Germline

title: Maternal Sequence Variation Detection Using Next Generation Sequencing

focus: Jane Mother Doe (official) Female, DoB: 2000-01-01 ( Medical record number: 11112 (use: temp, period: 2021-01-01 --> (ongoing)))

specimen: Specimen: identifier = http://example.org/identifiers/specimens#2; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000

date: 2021-01-01 01:01:10-0600

note:

This is a next generation sequencing analysis of a mother of a proband.

Inputs

-FileType
*DocumentReference: identifier = http://example.org/identifiers/files#11112; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer

Devices

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

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1113 (use: temp, )

genomicSourceClass: Germline

title: Paternal Sequence Variation Detection Using Next Generation Sequencing

focus: John Father Doe (official) Male, DoB: 2000-01-01 ( Medical record number: 11113 (use: temp, period: 2021-01-01 --> (ongoing)))

specimen: Specimen: identifier = http://example.org/identifiers/specimens#3; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000

date: 2021-01-01 01:01:10-0600

note:

This is a next generation sequencing analysis of a father of a proband.

Inputs

-FileType
*DocumentReference: identifier = http://example.org/identifiers/files#11113; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer

Devices

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

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1114 (use: temp, )

title: De Novo Mutation Detection and Interpretation

date: 2021-01-01 03:01:10-0600

note:

This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences.

input

file: DocumentReference: identifier = http://example.org/identifiers/files#11111; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

type: VCF

input

file: DocumentReference: identifier = http://example.org/identifiers/files#11112; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

type: VCF

input

file: DocumentReference: identifier = http://example.org/identifiers/files#11113; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.

type: VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer

Devices

-Device
*Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)