Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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-cibuild 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-cibuild
Standards status: Trial-use | Maturity Level: 2 | 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:

- Use this Extension: Genomic Study Analysis
- Examples for this Extension: Procedure/PGXGenomicStudyAnalysis, Procedure/analysisTumorNormalDNA, Procedure/analysisTumorRNA, Procedure/lungMass-analysis1 and Procedure/lungMass-analysis2

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.

- Differential Table
- Snapshot Table
- Statistics/References
- All

This structure is derived from Extension

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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 |  | Extension
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 |  | Extension
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 |  | Extension
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 |  | Extension
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 |  | Value of extension
Documentation for this format

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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 |  | Extension Slice: Unordered, Open by value:url
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 |  | Extension Slice: Unordered, Open by value:url
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 |  | Extension Slice: Unordered, Open by value:url
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 |  | Extension Slice: Unordered, Open by value:url
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"
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: 2

Differential View

This structure is derived from Extension

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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 |  | Extension
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 |  | Extension
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 |  | Extension
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 |  | Extension
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 |  | Value of extension
Documentation for this format

Snapshot View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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 |  | Extension Slice: Unordered, Open by value:url
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 |  | Extension Slice: Unordered, Open by value:url
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 |  | Extension Slice: Unordered, Open by value:url
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 |  | Extension Slice: Unordered, Open by value:url
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"
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: 2

Other representations of profile: CSV, Excel, Schematron

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
Extension.extension:studied.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG
Extension.extension:called.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG
Extension.extension:uncalled.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG

#### Constraints

Id | Grade | Path(s) | Description | Expression
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`