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 Metrics

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics Version: 3.0.1-SNAPSHOT
Active as of 2024-07-08 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

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: 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

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
..... url 1..1 uri "read-depth"
..... value[x] 0..1 SimpleQuantity 30, 100
.... extension:sequencing-coverage 0..1 Extension Sequencing Coverage
..... extension 0..0
..... url 1..1 uri "sequencing-coverage"
..... value[x] 0..1 SimpleQuantity 95, 100
.... extension:metrics-description 0..1 Extension Metrics Description
..... extension 0..0
..... 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

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
..... url 1..1 uri "read-depth"
..... value[x] C 0..1 SimpleQuantity 30, 100
qty-3: If a code for the unit is present, the system SHALL also be present
.... extension:sequencing-coverage 0..1 Extension Sequencing Coverage
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "sequencing-coverage"
..... value[x] C 0..1 SimpleQuantity 95, 100
qty-3: If a code for the unit is present, the system SHALL also be present
.... extension:metrics-description 0..1 Extension Metrics Description
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... 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"

doco 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

Differential View

This structure is derived from Extension

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
..... url 1..1 uri "read-depth"
..... value[x] 0..1 SimpleQuantity 30, 100
.... extension:sequencing-coverage 0..1 Extension Sequencing Coverage
..... extension 0..0
..... url 1..1 uri "sequencing-coverage"
..... value[x] 0..1 SimpleQuantity 95, 100
.... extension:metrics-description 0..1 Extension Metrics Description
..... extension 0..0
..... 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

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
..... url 1..1 uri "read-depth"
..... value[x] C 0..1 SimpleQuantity 30, 100
qty-3: If a code for the unit is present, the system SHALL also be present
.... extension:sequencing-coverage 0..1 Extension Sequencing Coverage
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... url 1..1 uri "sequencing-coverage"
..... value[x] C 0..1 SimpleQuantity 95, 100
qty-3: If a code for the unit is present, the system SHALL also be present
.... extension:metrics-description 0..1 Extension Metrics Description
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..0
..... 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"

doco Documentation for this format

 

Other representations of profile: CSV, Excel, Schematron

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()
qty-3errorExtension.extension:read-depth.value[x], Extension.extension:sequencing-coverage.value[x]If a code for the unit is present, the system SHALL also be present
: code.empty() or system.exists()
sqty-1error**ALL** extensionsThe comparator is not used on a SimpleQuantity
: comparator.empty()