Genomicstudy-example-trio2 - FHIR v6.0.0-ballot2

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Example GenomicStudy/example-trio2 (Narrative)

Clinical Genomics Work Group

Maturity Level: N/A

Standards Status: Informative

Compartments: Group, Patient

This is the narrative for the resource. See also the XML, JSON or Turtle format. This example conforms to the profile GenomicStudy.

Generated Narrative: GenomicStudy example-trio2

identifier: http://www.somesystemabc.net/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1113 (use: temp, )

status: available

type: Trio-analysis

subject: Anonymous Patient female, DoB: 1966-04-04 ( Computer-Stored Abulatory Records (COSTAR): 999999999 (use: usual, ))

encounter: Encounter/denovoEncounter

startDate: 2022-05-01

basedOn:

referrer: Practitioner/practitioner01

interpreter: Practitioner/practitioner02

Reasons

Concept

Cystic fibrosis, prenatal detection (procedure)

note: 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: http://www.somesystemabc.net/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1112 (use: temp, )
instantiatesUri: https://pubmed.ncbi.nlm.nih.gov/33927380/
title: Maternal Sequence Variation Detection Using Next Generation Sequencing
focus: Patient/mother
specimen: Specimen/specimenMother
date: 2022-07-01T01:01:10-06:00
note: This is a next generation sequencing analysis of a mother of a proband.
Performers

- Actor Role

* Practitioner/practitioner02 Performer
Devices

- Device

* Device/NGS-device

analysis
identifier: http://www.somesystemabc.net/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1113 (use: temp, )
instantiatesUri: https://pubmed.ncbi.nlm.nih.gov/33927380/
title: Paternal Sequence Variation Detection Using Next Generation Sequencing
focus: Patient/father
specimen: Specimen/specimenFather
date: 2022-07-01T01:01:10-06:00
note: This is a next generation sequencing analysis of a father of a proband.
Performers

- Actor Role

* Practitioner/practitioner02 Performer
Devices

- Device

* Device/NGS-device

analysis
identifier: http://www.somesystemabc.net/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1114 (use: temp, )
instantiatesUri: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/
title: De Novo Mutation Detection and Interpretation
focus:

Patient/denovoChild

RelatedPerson/relatedPersonDenovoFather

RelatedPerson/relatedPersonDenovoMother
date: 2022-07-01T03:01:10-06:00
note: This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences.
input
file: DocumentReference/genomicFileProband
type: BAM
input
file: DocumentReference/genomicFileMother
type: BAM
input
file: DocumentReference/genomicFileFather
type: BAM
Outputs

- File Type

* DocumentReference/genomicFileGroupAsSubject VCF
Performers

- Actor Role

* Practitioner/practitioner02 Performer
Devices

- Device

* Device/Triodenovo-SW

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.