Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Extension: Genomic Study Analysis Regions

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions Version: 3.0.0-ballot
Active as of 2023-12-18 Computable Name: GenomicStudyAnalysisRegions

Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

Context of Use

This extension may be used on the following element(s):

  • Element ID Procedure

Usage info

Usage:

Formal Views of Extension Content

Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

This structure is derived from Extension

Summary

Complex Extension: Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

  • description: string: Freetext description of the regions studied for the sequencing test
  • studied: CodeableConcept, Reference: The genes or regions that were studied in the analysis.
  • called: CodeableConcept, Reference: The genes or regions that were studied for the analysis with sufficient coverage and quality to be called.
  • uncalled: CodeableConcept, Reference: The genes or regions that were studied for the analysis but were deemed uncallable.

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..*ExtensionGenomic Study Analysis Regions
... extension:description 0..1ExtensionRegions Studied Description
.... extension 0..0
.... url 1..1uri"description"
.... value[x] 0..1stringValue of extension
... extension:studied 0..*ExtensionGenes or Regions Studied (GenomicStudy.analysis.regionsStudied)
.... extension 0..0
.... url 1..1uri"studied"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... extension:called 0..*ExtensionGenes or Regions Called (GenomicStudy.analysis.regionsCalled)
.... extension 0..0
.... url 1..1uri"called"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
.... extension 0..0
.... url 1..1uri"uncalled"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... url 1..1uri"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
... value[x] 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..*ExtensionGenomic Study Analysis Regions
... id 0..1stringUnique id for inter-element referencing
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... extension:description 0..1ExtensionRegions Studied Description
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"description"
.... value[x] 0..1stringValue of extension
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"studied"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... extension:called 0..*ExtensionGenes or Regions Called (GenomicStudy.analysis.regionsCalled)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"called"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... extension:uncalled 0..*ExtensionGenes or Regions Uncalled
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"uncalled"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... url 1..1uri"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"

doco Documentation for this format

This structure is derived from Extension

Summary

Complex Extension: Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

  • description: string: Freetext description of the regions studied for the sequencing test
  • studied: CodeableConcept, Reference: The genes or regions that were studied in the analysis.
  • called: CodeableConcept, Reference: The genes or regions that were studied for the analysis with sufficient coverage and quality to be called.
  • uncalled: CodeableConcept, Reference: The genes or regions that were studied for the analysis but were deemed uncallable.

Differential View

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..*ExtensionGenomic Study Analysis Regions
... extension:description 0..1ExtensionRegions Studied Description
.... extension 0..0
.... url 1..1uri"description"
.... value[x] 0..1stringValue of extension
... extension:studied 0..*ExtensionGenes or Regions Studied (GenomicStudy.analysis.regionsStudied)
.... extension 0..0
.... url 1..1uri"studied"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... extension:called 0..*ExtensionGenes or Regions Called (GenomicStudy.analysis.regionsCalled)
.... extension 0..0
.... url 1..1uri"called"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
.... extension 0..0
.... url 1..1uri"uncalled"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... url 1..1uri"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
... value[x] 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..*ExtensionGenomic Study Analysis Regions
... id 0..1stringUnique id for inter-element referencing
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... extension:description 0..1ExtensionRegions Studied Description
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"description"
.... value[x] 0..1stringValue of extension
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"studied"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... extension:called 0..*ExtensionGenes or Regions Called (GenomicStudy.analysis.regionsCalled)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"called"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... extension:uncalled 0..*ExtensionGenes or Regions Uncalled
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"uncalled"
.... value[x] 1..1Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... valueCodeableConceptCodeableConcept
..... valueReferenceReference(Genomic Data File)
... url 1..1uri"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSet
Extension.extension:studied.value[x]extensibleHGNCVS
Extension.extension:called.value[x]extensibleHGNCVS
Extension.extension:uncalled.value[x]extensibleHGNCVS

Constraints

IdGradePath(s)DetailsRequirements
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()