{ "resourceType" : "GenomicStudy", "resourceDefinition" : "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build", "id" : "example", "language" : "en", "text" : { "status" : "generated", "div" : "

Generated Narrative: GenomicStudy example

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1111\u00a0(use:\u00a0temp,\u00a0)

status: Unknown

type: Familial variant segregation

subject: Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (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.

\n

description:

De novo mutation study of the patient.

\n

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1111\u00a0(use:\u00a0temp,\u00a0)

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.

\n

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\u00a0(use:\u00a0temp,\u00a0)

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\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (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.

\n

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\u00a0(use:\u00a0temp,\u00a0)

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\u00a0(use:\u00a0temp,\u00a0period:\u00a02021-01-01 --> (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.

\n

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\u00a0(use:\u00a0temp,\u00a0)

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.

\n

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)
" }, "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicstudies", "value" : "urn:uuid:1111-1111-1111-1111" }], "status" : "unknown", "type" : [{ "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type", "code" : "fam-var-segr", "display" : "Familial variant segregation" }] }], "subject" : { "reference" : "Patient/denovoChild" }, "encounter" : { "reference" : "Encounter/denovoEncounter" }, "startDate" : "2021-01-01", "basedOn" : [{ "reference" : "ServiceRequest/genomicServiceRequest" }], "referrer" : { "reference" : "Practitioner/practitioner01" }, "interpreter" : [{ "reference" : "Practitioner/practitioner02" }], "reason" : [{ "concept" : { "coding" : [{ "system" : "http://snomed.info/sct", "code" : "267431006", "display" : "Disorder of lipid metabolism (disorder)" }] } }], "note" : [{ "text" : "This de novo mutation is urgent and important for establishing the treatment plan." }], "description" : "De novo mutation study of the patient.", "analysis" : [{ "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicAnalyses", "value" : "urn:uuid:1111-1111-1111-1111" }], "genomicSourceClass" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA6683-2", "display" : "Germline" }] }, "title" : "Proband Sequence Variation Detection Using Next Generation Sequencing", "specimen" : [{ "reference" : "Specimen/denovo-1" }], "date" : "2021-01-01T01:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of a proband." }], "input" : [{ "file" : { "reference" : "DocumentReference/genomicFile1" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }], "performer" : [{ "actor" : { "reference" : "Practitioner/practitioner02" }, "role" : { "coding" : [{ "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", "code" : "PRF", "display" : "Performer" }] } }], "device" : [{ "device" : { "reference" : "Device/NGS-device" }, "function" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA26398-0", "display" : "Sequencing" }] } }] }, { "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicAnalyses", "value" : "urn:uuid:1111-1111-1111-1112" }], "genomicSourceClass" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA6683-2", "display" : "Germline" }] }, "title" : "Maternal Sequence Variation Detection Using Next Generation Sequencing", "focus" : [{ "reference" : "Patient/denovoMother" }], "specimen" : [{ "reference" : "Specimen/denovo-2" }], "date" : "2021-01-01T01:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of a mother of a proband." }], "input" : [{ "file" : { "reference" : "DocumentReference/genomicFile2" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }], "performer" : [{ "actor" : { "reference" : "Practitioner/practitioner02" }, "role" : { "coding" : [{ "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", "code" : "PRF", "display" : "Performer" }] } }], "device" : [{ "device" : { "reference" : "Device/NGS-device" } }] }, { "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicAnalyses", "value" : "urn:uuid:1111-1111-1111-1113" }], "genomicSourceClass" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA6683-2", "display" : "Germline" }] }, "title" : "Paternal Sequence Variation Detection Using Next Generation Sequencing", "focus" : [{ "reference" : "Patient/denovoFather" }], "specimen" : [{ "reference" : "Specimen/denovo-3" }], "date" : "2021-01-01T01:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of a father of a proband." }], "input" : [{ "file" : { "reference" : "DocumentReference/genomicFile3" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }], "performer" : [{ "actor" : { "reference" : "Practitioner/practitioner02" }, "role" : { "coding" : [{ "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", "code" : "PRF", "display" : "Performer" }] } }], "device" : [{ "device" : { "reference" : "Device/NGS-device" } }] }, { "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicAnalyses", "value" : "urn:uuid:1111-1111-1111-1114" }], "title" : "De Novo Mutation Detection and Interpretation", "date" : "2021-01-01T03:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences." }], "input" : [{ "file" : { "reference" : "DocumentReference/genomicFile1" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }, { "file" : { "reference" : "DocumentReference/genomicFile2" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }, { "file" : { "reference" : "DocumentReference/genomicFile3" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "vcf", "display" : "VCF" }] } }], "performer" : [{ "actor" : { "reference" : "Practitioner/practitioner02" }, "role" : { "coding" : [{ "system" : "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", "code" : "PRF", "display" : "Performer" }] } }], "device" : [{ "device" : { "reference" : "Device/Triodenovo-SW" } }] }] }