Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. 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: 4.0.0-ballot
Standards status: Trial-use Maturity Level: 1 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

Usages:

You can also check for usages in the FHIR IG Statistics

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.

Maturity: 1

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Genomic Study Analysis Regions
... Slices for extension Content/Rules for all slices
.... extension:description 0..1 Extension Regions Studied Description
..... extension 0..0
..... url 1..1 uri "description"
..... value[x] 0..1 string Value of extension
.... extension:studied 0..* Extension Genes or Regions Studied (GenomicStudy.analysis.regionsStudied)
..... extension 0..0
..... url 1..1 uri "studied"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:called 0..* Extension Genes or Regions Called (GenomicStudy.analysis.regionsCalled)
..... extension 0..0
..... url 1..1 uri "called"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:uncalled 0..* Extension Genes or Regions Uncalled
..... extension 0..0
..... url 1..1 uri "uncalled"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
... url 1..1 uri "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
... value[x] 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Genomic Study Analysis Regions
... id 0..1 string Unique id for inter-element referencing
... Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... extension:description 0..1 Extension Regions Studied Description
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "description"
..... value[x] 0..1 string Value of extension
.... extension:studied 0..* Extension Genes or Regions Studied (GenomicStudy.analysis.regionsStudied)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "studied"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:called 0..* Extension Genes or Regions Called (GenomicStudy.analysis.regionsCalled)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "called"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:uncalled 0..* Extension Genes or Regions Uncalled
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "uncalled"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
... url 1..1 uri "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.

Maturity: 1

Differential View

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Genomic Study Analysis Regions
... Slices for extension Content/Rules for all slices
.... extension:description 0..1 Extension Regions Studied Description
..... extension 0..0
..... url 1..1 uri "description"
..... value[x] 0..1 string Value of extension
.... extension:studied 0..* Extension Genes or Regions Studied (GenomicStudy.analysis.regionsStudied)
..... extension 0..0
..... url 1..1 uri "studied"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:called 0..* Extension Genes or Regions Called (GenomicStudy.analysis.regionsCalled)
..... extension 0..0
..... url 1..1 uri "called"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:uncalled 0..* Extension Genes or Regions Uncalled
..... extension 0..0
..... url 1..1 uri "uncalled"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
... url 1..1 uri "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 & Constraints    Filter: Filtersdoco
.. Extension 0..* Extension Genomic Study Analysis Regions
... id 0..1 string Unique id for inter-element referencing
... Slices for extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... extension:description 0..1 Extension Regions Studied Description
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "description"
..... value[x] 0..1 string Value of extension
.... extension:studied 0..* Extension Genes or Regions Studied (GenomicStudy.analysis.regionsStudied)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "studied"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:called 0..* Extension Genes or Regions Called (GenomicStudy.analysis.regionsCalled)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "called"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
.... extension:uncalled 0..* Extension Genes or Regions Uncalled
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "uncalled"
..... value[x] 1..1 Gene codes or BED file
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
...... valueCodeableConcept CodeableConcept
...... valueReference Reference(Genomic Data File)
... url 1..1 uri "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

PathConformanceValueSetURI
Extension.extension:studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
From this IG
Extension.extension:called.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
From this IG
Extension.extension:uncalled.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
From this IG

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()