Genomic Study Analysis Metrics - Genomics Reporting Implementation Guide v3.0.0

Genomics Reporting Implementation Guide
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Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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: 3.0.0
Active as of 2024-12-12				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:

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

Formal Views of Extension Content

Description of Profiles, Differentials, Snapshots, and how the XML and JSON presentations work.

Text Summary
Differential Table
Snapshot Table
All

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

Name	Card.	Type	Description & Constraints
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
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
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"
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

Name	Card.	Type	Description & Constraints
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
Documentation for this format

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
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"
Documentation for this format

Other representations of profile: CSV, Excel, Schematron

Constraints

Id	Grade	Path(s)	Details	Requirements
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()
qty-3	error	Extension.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-1	error	ALL extensions	The comparator is not used on a SimpleQuantity : comparator.empty()

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IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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