Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, 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: 3.0.0-ballot
Active as of 2023-12-18 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..*ExtensionGenomic Study Analysis Metrics
... extension:read-depth 0..1ExtensionRead Depth
.... extension 0..0
.... url 1..1uri"read-depth"
.... value[x] 0..1SimpleQuantity30, 100
... extension:sequencing-coverage 0..1ExtensionSequencing Coverage
.... extension 0..0
.... url 1..1uri"sequencing-coverage"
.... value[x] 0..1SimpleQuantity95, 100
... extension:metrics-description 0..1ExtensionMetrics Description
.... extension 0..0
.... url 1..1uri"metrics-description"
.... value[x] 0..1stringValue of extension
... value[x] 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..*ExtensionGenomic Study Analysis Metrics
... id 0..1stringUnique id for inter-element referencing
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... extension:read-depth 0..1ExtensionRead Depth
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"read-depth"
.... value[x] C0..1SimpleQuantity30, 100
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"sequencing-coverage"
.... value[x] C0..1SimpleQuantity95, 100
... extension:metrics-description 0..1ExtensionMetrics Description
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"metrics-description"
.... value[x] 0..1stringValue of extension
... url 1..1uri"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..*ExtensionGenomic Study Analysis Metrics
... extension:read-depth 0..1ExtensionRead Depth
.... extension 0..0
.... url 1..1uri"read-depth"
.... value[x] 0..1SimpleQuantity30, 100
... extension:sequencing-coverage 0..1ExtensionSequencing Coverage
.... extension 0..0
.... url 1..1uri"sequencing-coverage"
.... value[x] 0..1SimpleQuantity95, 100
... extension:metrics-description 0..1ExtensionMetrics Description
.... extension 0..0
.... url 1..1uri"metrics-description"
.... value[x] 0..1stringValue of extension
... value[x] 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Extension 0..*ExtensionGenomic Study Analysis Metrics
... id 0..1stringUnique id for inter-element referencing
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... extension:read-depth 0..1ExtensionRead Depth
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"read-depth"
.... value[x] C0..1SimpleQuantity30, 100
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"sequencing-coverage"
.... value[x] C0..1SimpleQuantity95, 100
... extension:metrics-description 0..1ExtensionMetrics Description
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..0
.... url 1..1uri"metrics-description"
.... value[x] 0..1stringValue of extension
... url 1..1uri"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()