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 Metrics

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics | Version: 4.0.0-cibuild
Standards status: Trial-use | Maturity Level: 2 | Computable Name: GenomicStudyAnalysisMetrics

Metrics about the sequencing analysis that was performed

Context of Use

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

- Element ID: `Procedure`

This extension is used for overall, analysis level metrics. These metrics are not specific to a region that is studied in the analysis. The metrics here are specific to sequencing analysis, but others could be added if they make sense to the use case.

Usage info

Usages:

- Use this Extension: Genomic Study Analysis
- Examples for this Extension: Procedure/PGXGenomicStudyAnalysis

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 Metrics
Slices for extension |  |  |  | Content/Rules for all slices
extension:read-depth |  | 0..1 | Extension | Read Depth
extension |  | 0..0 |  | Extension
url |  | 1..1 | uri | "read-depth"
value[x] |  | 0..1 | SimpleQuantity | 30, 100
extension:sequencing-coverage |  | 0..1 | Extension | Sequencing Coverage
extension |  | 0..0 |  | Extension
url |  | 1..1 | uri | "sequencing-coverage"
value[x] |  | 0..1 | SimpleQuantity | 95, 100
extension:metrics-description |  | 0..1 | Extension | Metrics Description
extension |  | 0..0 |  | Extension
url |  | 1..1 | uri | "metrics-description"
value[x] |  | 0..1 | string | Value of extension
url |  | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
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 Metrics
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:read-depth |  | 0..1 | Extension | Read Depth
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..0 |  | Extension Slice: Unordered, Open by value:url
url |  | 1..1 | uri | "read-depth"
value[x] |  | 0..1 | SimpleQuantity | 30, 100
extension:sequencing-coverage |  | 0..1 | Extension | Sequencing Coverage
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..0 |  | Extension Slice: Unordered, Open by value:url
url |  | 1..1 | uri | "sequencing-coverage"
value[x] |  | 0..1 | SimpleQuantity | 95, 100
extension:metrics-description |  | 0..1 | Extension | Metrics 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 | "metrics-description"
value[x] |  | 0..1 | string | Value of extension
url |  | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
Documentation for this format

This structure is derived from Extension

Summary

Complex Extension: Metrics about the sequencing analysis that was performed

- read-depth: Quantity: The average read depth (number of reads for a position) for the sequencing test
- sequencing-coverage: Quantity: The percentage of the studied regions that were sequenced
- metrics-description: string: Freetext description of the coverage metrics for the sequencing test

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 Metrics
Slices for extension |  |  |  | Content/Rules for all slices
extension:read-depth |  | 0..1 | Extension | Read Depth
extension |  | 0..0 |  | Extension
url |  | 1..1 | uri | "read-depth"
value[x] |  | 0..1 | SimpleQuantity | 30, 100
extension:sequencing-coverage |  | 0..1 | Extension | Sequencing Coverage
extension |  | 0..0 |  | Extension
url |  | 1..1 | uri | "sequencing-coverage"
value[x] |  | 0..1 | SimpleQuantity | 95, 100
extension:metrics-description |  | 0..1 | Extension | Metrics Description
extension |  | 0..0 |  | Extension
url |  | 1..1 | uri | "metrics-description"
value[x] |  | 0..1 | string | Value of extension
url |  | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
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 Metrics
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:read-depth |  | 0..1 | Extension | Read Depth
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..0 |  | Extension Slice: Unordered, Open by value:url
url |  | 1..1 | uri | "read-depth"
value[x] |  | 0..1 | SimpleQuantity | 30, 100
extension:sequencing-coverage |  | 0..1 | Extension | Sequencing Coverage
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..0 |  | Extension Slice: Unordered, Open by value:url
url |  | 1..1 | uri | "sequencing-coverage"
value[x] |  | 0..1 | SimpleQuantity | 95, 100
extension:metrics-description |  | 0..1 | Extension | Metrics 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 | "metrics-description"
value[x] |  | 0..1 | string | Value of extension
url |  | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
Documentation for this format

This structure is derived from Extension

Summary

Complex Extension: Metrics about the sequencing analysis that was performed

- read-depth: Quantity: The average read depth (number of reads for a position) for the sequencing test
- sequencing-coverage: Quantity: The percentage of the studied regions that were sequenced
- metrics-description: string: Freetext description of the coverage metrics for the sequencing test

Maturity: 2

Other representations of profile: CSV, Excel, Schematron

#### 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()`