Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - 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 3.0.1-SNAPSHOT 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: 3.0.1-SNAPSHOT
Active as of 2024-05-15 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..* 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 & Constraintsdoco
.. 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.

Differential View

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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 & Constraintsdoco
.. 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()