{ "resourceType" : "GenomicStudy", "resourceDefinition" : "http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build", "id" : "example-trio2", "language" : "en", "text" : { "status" : "generated", "div" : "

Generated Narrative: GenomicStudy example-trio2

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1113\u00a0(use:\u00a0temp,\u00a0)

status: Available

type: Trio analysis

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: 2022-05-01

basedOn:

referrer: Practitioner John Doel

interpreter: Practitioner Jane Doel

Reasons

-Concept
*Cystic fibrosis, prenatal detection (procedure)

note:

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

\n

description:

De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.

\n

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#6; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000

date: 2022-07-01 01:01:10-0600

note:

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

\n

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#7; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000

date: 2022-07-01 01:01:10-0600

note:

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

\n

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

focus:

date: 2022-07-01 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#11118; 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: BAM

input

file: DocumentReference: identifier = http://example.org/identifiers/files#11119; 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: BAM

input

file: DocumentReference: identifier = http://example.org/identifiers/files#111110; 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: BAM

Outputs

-FileType
*DocumentReference: identifier = http://example.org/identifiers/files#11115; status = current; docStatus = preliminary; description = Combined VCF file of a Proband and Parents that may be 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#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)
" }, "identifier" : [{ "use" : "temp", "system" : "http://example.org/identifiers/genomicstudies", "value" : "urn:uuid:1111-1111-1111-1113" }], "status" : "available", "type" : [{ "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type", "code" : "trio", "display" : "Trio analysis" }] }], "subject" : { "reference" : "Patient/proband" }, "encounter" : { "reference" : "Encounter/denovoEncounter" }, "startDate" : "2022-05-01", "basedOn" : [{ "reference" : "ServiceRequest/genomicSRProband" }, { "reference" : "ServiceRequest/genomicSRMother" }, { "reference" : "ServiceRequest/genomicSRFather" }], "referrer" : { "reference" : "Practitioner/practitioner01" }, "interpreter" : [{ "reference" : "Practitioner/practitioner02" }], "reason" : [{ "concept" : { "coding" : [{ "system" : "http://snomed.info/sct", "code" : "67799006", "display" : "Cystic fibrosis, prenatal detection (procedure)" }] } }], "note" : [{ "text" : "This de novo mutation is urgent and important for establishing the treatment plan." }], "description" : "De novo mutation study of the patient. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic.", "analysis" : [{ "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/mother" }], "specimen" : [{ "reference" : "Specimen/specimenMother" }], "date" : "2022-07-01T01:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of a mother of a proband." }], "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/father" }], "specimen" : [{ "reference" : "Specimen/specimenFather" }], "date" : "2022-07-01T01:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of a father of a proband." }], "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", "focus" : [{ "reference" : "Patient/denovoChild" }, { "reference" : "RelatedPerson/relatedPersonDenovoFather" }, { "reference" : "RelatedPerson/relatedPersonDenovoMother" }], "date" : "2022-07-01T03:01:10-06:00", "note" : [{ "text" : "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences." }], "input" : [{ "file" : { "reference" : "DocumentReference/genomicFileProband" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "bam", "display" : "BAM" }] } }, { "file" : { "reference" : "DocumentReference/genomicFileMother" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "bam", "display" : "BAM" }] } }, { "file" : { "reference" : "DocumentReference/genomicFileFather" }, "type" : { "coding" : [{ "system" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat", "code" : "bam", "display" : "BAM" }] } }], "output" : [{ "file" : { "reference" : "DocumentReference/genomicFileGroupAsSubject" }, "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" } }] }] }