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: GenomicStudyAnalysisRegions - Detailed Descriptions

Active as of 2024-07-08

Definitions for the genomic-study-analysis-regions extension.

Guidance on how to interpret the contents of this table can be found here

0. Extension
Definition

Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

ShortGenomic Study Analysis Regions
2. Extension.extension:description
Slice Namedescription
Definition

Freetext description of the regions studied for the sequencing test

ShortRegions Studied Description
Control0..1
4. Extension.extension:description.extension
Control0..0
6. Extension.extension:description.url
Fixed Valuedescription
8. Extension.extension:description.value[x]
Typestring
[x] NoteSeeChoice of Data Typesfor further information about how to use [x]
Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
10. Extension.extension:studied
Slice Namestudied
Definition

The genes or regions that were studied in the analysis.

ShortGenes or Regions Studied (GenomicStudy.analysis.regionsStudied)
Control0..*
Requirements

Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions studied in the analysis.

12. Extension.extension:studied.extension
Control0..0
14. Extension.extension:studied.url
Fixed Valuestudied
16. Extension.extension:studied.value[x]
ShortGene codes or BED file
Control1..?
BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
(extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
TypeChoice of: CodeableConcept, Reference(Genomic Data File)
[x] NoteSeeChoice of Data Typesfor further information about how to use [x]
18. Extension.extension:called
Slice Namecalled
Definition

The genes or regions that were studied for the analysis with sufficient coverage and quality to be called.

ShortGenes or Regions Called (GenomicStudy.analysis.regionsCalled)
Control0..*
Requirements

Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions deemed callable.

20. Extension.extension:called.extension
Control0..0
22. Extension.extension:called.url
Fixed Valuecalled
24. Extension.extension:called.value[x]
ShortGene codes or BED file
Control1..?
BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
(extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
TypeChoice of: CodeableConcept, Reference(Genomic Data File)
[x] NoteSeeChoice of Data Typesfor further information about how to use [x]
26. Extension.extension:uncalled
Slice Nameuncalled
Definition

The genes or regions that were studied for the analysis but were deemed uncallable.

ShortGenes or Regions Uncalled
Control0..*
Requirements

Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions deemed uncallable.

28. Extension.extension:uncalled.extension
Control0..0
30. Extension.extension:uncalled.url
Fixed Valueuncalled
32. Extension.extension:uncalled.value[x]
ShortGene codes or BED file
Control1..?
BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
(extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
TypeChoice of: CodeableConcept, Reference(Genomic Data File)
[x] NoteSeeChoice of Data Typesfor further information about how to use [x]
34. Extension.url
Fixed Valuehttp://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions
36. Extension.value[x]
Control0..0

Guidance on how to interpret the contents of this table can be found here

0. Extension
Definition

Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)


Optional Extension Element - found in all resources.

ShortGenomic Study Analysis RegionsOptional Extensions Element
Control0..*
This element is affected by the following invariants: ele-1
Is Modifierfalse
Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
2. Extension.extension:description
Slice Namedescription
Definition

Freetext description of the regions studied for the sequencing test

ShortRegions Studied DescriptionAdditional content defined by implementations
Control0..1*
TypeExtension
Is Modifierfalse
Summaryfalse
Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
4. Extension.extension:description.extension
Definition

An Extension


May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

ShortExtensionAdditional content defined by implementations
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

Control0..0*
TypeExtension
Is Modifierfalse
Summaryfalse
Alternate Namesextensions, user content
Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
  • value @ url
  • 6. Extension.extension:description.url
    Definition

    Source of the definition for the extension code - a logical name or a URL.

    Shortidentifies the meaning of the extension
    Comments

    The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

    Control1..1
    Typeuri
    Is Modifierfalse
    XML FormatIn the XML format, this property is represented as an attribute.
    Summaryfalse
    Fixed Valuedescription
    8. Extension.extension:description.value[x]
    Definition

    Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

    ShortValue of extension
    Control0..1
    Typestring, date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, CodeableConcept, ParameterDefinition, dateTime, code, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, Reference, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
    Is Modifierfalse
    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
    Summaryfalse
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    10. Extension.extension:studied
    Slice Namestudied
    Definition

    The genes or regions that were studied in the analysis.

    ShortGenes or Regions Studied (GenomicStudy.analysis.regionsStudied)Additional content defined by implementations
    Control0..*
    TypeExtension
    Is Modifierfalse
    Summaryfalse
    Requirements

    Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions studied in the analysis.

    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    12. Extension.extension:studied.extension
    Definition

    An Extension


    May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

    ShortExtensionAdditional content defined by implementations
    Comments

    There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

    Control0..0*
    TypeExtension
    Is Modifierfalse
    Summaryfalse
    Alternate Namesextensions, user content
    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
    ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
    SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
    • value @ url
    • 14. Extension.extension:studied.url
      Definition

      Source of the definition for the extension code - a logical name or a URL.

      Shortidentifies the meaning of the extension
      Comments

      The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

      Control1..1
      Typeuri
      Is Modifierfalse
      XML FormatIn the XML format, this property is represented as an attribute.
      Summaryfalse
      Fixed Valuestudied
      16. Extension.extension:studied.value[x]
      Definition

      Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

      ShortGene codes or BED fileValue of extension
      Control10..1
      BindingUnless not suitable, these codes SHALL be taken from For codes, see HUGO Gene Nomenclature Committee Gene Names (HGNC)
      (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
      TypeChoice of: CodeableConcept, Reference(Genomic Data File), date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ParameterDefinition, dateTime, code, string, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
      [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
      Is Modifierfalse
      Summaryfalse
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      18. Extension.extension:called
      Slice Namecalled
      Definition

      The genes or regions that were studied for the analysis with sufficient coverage and quality to be called.

      ShortGenes or Regions Called (GenomicStudy.analysis.regionsCalled)Additional content defined by implementations
      Control0..*
      TypeExtension
      Is Modifierfalse
      Summaryfalse
      Requirements

      Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions deemed callable.

      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      20. Extension.extension:called.extension
      Definition

      An Extension


      May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

      ShortExtensionAdditional content defined by implementations
      Comments

      There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

      Control0..0*
      TypeExtension
      Is Modifierfalse
      Summaryfalse
      Alternate Namesextensions, user content
      Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
      ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
      SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
      • value @ url
      • 22. Extension.extension:called.url
        Definition

        Source of the definition for the extension code - a logical name or a URL.

        Shortidentifies the meaning of the extension
        Comments

        The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

        Control1..1
        Typeuri
        Is Modifierfalse
        XML FormatIn the XML format, this property is represented as an attribute.
        Summaryfalse
        Fixed Valuecalled
        24. Extension.extension:called.value[x]
        Definition

        Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

        ShortGene codes or BED fileValue of extension
        Control10..1
        BindingUnless not suitable, these codes SHALL be taken from For codes, see HUGO Gene Nomenclature Committee Gene Names (HGNC)
        (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
        TypeChoice of: CodeableConcept, Reference(Genomic Data File), date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ParameterDefinition, dateTime, code, string, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
        [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
        Is Modifierfalse
        Summaryfalse
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        26. Extension.extension:uncalled
        Slice Nameuncalled
        Definition

        The genes or regions that were studied for the analysis but were deemed uncallable.

        ShortGenes or Regions UncalledAdditional content defined by implementations
        Control0..*
        TypeExtension
        Is Modifierfalse
        Summaryfalse
        Requirements

        Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions deemed uncallable.

        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        28. Extension.extension:uncalled.extension
        Definition

        An Extension


        May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

        ShortExtensionAdditional content defined by implementations
        Comments

        There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

        Control0..0*
        TypeExtension
        Is Modifierfalse
        Summaryfalse
        Alternate Namesextensions, user content
        Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
        ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
        SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
        • value @ url
        • 30. Extension.extension:uncalled.url
          Definition

          Source of the definition for the extension code - a logical name or a URL.

          Shortidentifies the meaning of the extension
          Comments

          The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

          Control1..1
          Typeuri
          Is Modifierfalse
          XML FormatIn the XML format, this property is represented as an attribute.
          Summaryfalse
          Fixed Valueuncalled
          32. Extension.extension:uncalled.value[x]
          Definition

          Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

          ShortGene codes or BED fileValue of extension
          Control10..1
          BindingUnless not suitable, these codes SHALL be taken from For codes, see HUGO Gene Nomenclature Committee Gene Names (HGNC)
          (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
          TypeChoice of: CodeableConcept, Reference(Genomic Data File), date, Meta, Address, Attachment, integer, Count, DataRequirement, Dosage, uuid, Identifier, Coding, SampledData, id, positiveInt, Distance, Period, Duration, canonical, Range, RelatedArtifact, base64Binary, UsageContext, Timing, decimal, ParameterDefinition, dateTime, code, string, Contributor, oid, instant, ContactPoint, HumanName, Money, markdown, Ratio, Age, TriggerDefinition, Quantity, uri, url, Annotation, ContactDetail, boolean, Expression, Signature, unsignedInt, time
          [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
          Is Modifierfalse
          Summaryfalse
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          34. Extension.url
          Definition

          Source of the definition for the extension code - a logical name or a URL.

          Shortidentifies the meaning of the extension
          Comments

          The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

          Control1..1
          Typeuri
          Is Modifierfalse
          XML FormatIn the XML format, this property is represented as an attribute.
          Summaryfalse
          Fixed Valuehttp://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions
          36. Extension.value[x]
          Definition

          Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

          ShortValue of extension
          Control0..01
          TypeChoice of: base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, Reference, SampledData, Signature, Timing, ContactDetail, Contributor, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Dosage, Meta
          Is Modifierfalse
          Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
          Summaryfalse
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))

          Guidance on how to interpret the contents of this table can be found here

          0. Extension
          Definition

          Defines the regions studied, regions called, and regions deemed uncallable (generally due to low coverage)

          ShortGenomic Study Analysis Regions
          Control0..*
          This element is affected by the following invariants: ele-1
          Is Modifierfalse
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
          2. Extension.id
          Definition

          Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

          ShortUnique id for inter-element referencing
          Control0..1
          Typestring
          Is Modifierfalse
          XML FormatIn the XML format, this property is represented as an attribute.
          Summaryfalse
          4. Extension.extension
          Definition

          May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

          ShortAdditional content defined by implementations
          Comments

          There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

          Control0..*
          TypeExtension
          Is Modifierfalse
          Summaryfalse
          Alternate Namesextensions, user content
          Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
          ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
          SlicingThis element introduces a set of slices on Extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
          • value @ url
          • 6. Extension.extension:description
            Slice Namedescription
            Definition

            Freetext description of the regions studied for the sequencing test

            ShortRegions Studied Description
            Control0..1
            TypeExtension
            Is Modifierfalse
            Summaryfalse
            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
            ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
            8. Extension.extension:description.id
            Definition

            Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

            ShortUnique id for inter-element referencing
            Control0..1
            Typestring
            Is Modifierfalse
            XML FormatIn the XML format, this property is represented as an attribute.
            Summaryfalse
            10. Extension.extension:description.extension
            Definition

            An Extension

            ShortExtension
            Control0..0
            TypeExtension
            Is Modifierfalse
            Summaryfalse
            Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
            ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
            SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
            • value @ url
            • 12. Extension.extension:description.url
              Definition

              Source of the definition for the extension code - a logical name or a URL.

              Shortidentifies the meaning of the extension
              Comments

              The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

              Control1..1
              Typeuri
              Is Modifierfalse
              XML FormatIn the XML format, this property is represented as an attribute.
              Summaryfalse
              Fixed Valuedescription
              14. Extension.extension:description.value[x]
              Definition

              Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

              ShortValue of extension
              Control0..1
              Typestring
              [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
              Is Modifierfalse
              Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
              Summaryfalse
              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              16. Extension.extension:studied
              Slice Namestudied
              Definition

              The genes or regions that were studied in the analysis.

              ShortGenes or Regions Studied (GenomicStudy.analysis.regionsStudied)
              Control0..*
              TypeExtension
              Is Modifierfalse
              Summaryfalse
              Requirements

              Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions studied in the analysis.

              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
              18. Extension.extension:studied.id
              Definition

              Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

              ShortUnique id for inter-element referencing
              Control0..1
              Typestring
              Is Modifierfalse
              XML FormatIn the XML format, this property is represented as an attribute.
              Summaryfalse
              20. Extension.extension:studied.extension
              Definition

              An Extension

              ShortExtension
              Control0..0
              TypeExtension
              Is Modifierfalse
              Summaryfalse
              Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
              ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
              SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
              • value @ url
              • 22. Extension.extension:studied.url
                Definition

                Source of the definition for the extension code - a logical name or a URL.

                Shortidentifies the meaning of the extension
                Comments

                The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

                Control1..1
                Typeuri
                Is Modifierfalse
                XML FormatIn the XML format, this property is represented as an attribute.
                Summaryfalse
                Fixed Valuestudied
                24. Extension.extension:studied.value[x]
                Definition

                Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

                ShortGene codes or BED file
                Control1..1
                BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
                (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
                TypeChoice of: CodeableConcept, Reference(Genomic Data File)
                [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                Is Modifierfalse
                Summaryfalse
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                26. Extension.extension:called
                Slice Namecalled
                Definition

                The genes or regions that were studied for the analysis with sufficient coverage and quality to be called.

                ShortGenes or Regions Called (GenomicStudy.analysis.regionsCalled)
                Control0..*
                TypeExtension
                Is Modifierfalse
                Summaryfalse
                Requirements

                Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions deemed callable.

                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                28. Extension.extension:called.id
                Definition

                Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                ShortUnique id for inter-element referencing
                Control0..1
                Typestring
                Is Modifierfalse
                XML FormatIn the XML format, this property is represented as an attribute.
                Summaryfalse
                30. Extension.extension:called.extension
                Definition

                An Extension

                ShortExtension
                Control0..0
                TypeExtension
                Is Modifierfalse
                Summaryfalse
                Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                • value @ url
                • 32. Extension.extension:called.url
                  Definition

                  Source of the definition for the extension code - a logical name or a URL.

                  Shortidentifies the meaning of the extension
                  Comments

                  The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

                  Control1..1
                  Typeuri
                  Is Modifierfalse
                  XML FormatIn the XML format, this property is represented as an attribute.
                  Summaryfalse
                  Fixed Valuecalled
                  34. Extension.extension:called.value[x]
                  Definition

                  Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

                  ShortGene codes or BED file
                  Control1..1
                  BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
                  (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
                  TypeChoice of: CodeableConcept, Reference(Genomic Data File)
                  [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                  Is Modifierfalse
                  Summaryfalse
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  36. Extension.extension:uncalled
                  Slice Nameuncalled
                  Definition

                  The genes or regions that were studied for the analysis but were deemed uncallable.

                  ShortGenes or Regions Uncalled
                  Control0..*
                  TypeExtension
                  Is Modifierfalse
                  Summaryfalse
                  Requirements

                  Shared as a coded list of HGNC gene symbols or a BED file. For coded genes, the HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. If details beyond a coded list of genes are needed, a BED file SHALL be used to further describe the regions deemed uncallable.

                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                  38. Extension.extension:uncalled.id
                  Definition

                  Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

                  ShortUnique id for inter-element referencing
                  Control0..1
                  Typestring
                  Is Modifierfalse
                  XML FormatIn the XML format, this property is represented as an attribute.
                  Summaryfalse
                  40. Extension.extension:uncalled.extension
                  Definition

                  An Extension

                  ShortExtension
                  Control0..0
                  TypeExtension
                  Is Modifierfalse
                  Summaryfalse
                  Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                  ext-1: Must have either extensions or value[x], not both (extension.exists() != value.exists())
                  SlicingThis element introduces a set of slices on Extension.extension.extension. The slices areUnordered and Open, and can be differentiated using the following discriminators:
                  • value @ url
                  • 42. Extension.extension:uncalled.url
                    Definition

                    Source of the definition for the extension code - a logical name or a URL.

                    Shortidentifies the meaning of the extension
                    Comments

                    The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

                    Control1..1
                    Typeuri
                    Is Modifierfalse
                    XML FormatIn the XML format, this property is represented as an attribute.
                    Summaryfalse
                    Fixed Valueuncalled
                    44. Extension.extension:uncalled.value[x]
                    Definition

                    Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

                    ShortGene codes or BED file
                    Control1..1
                    BindingUnless not suitable, these codes SHALL be taken from HUGO Gene Nomenclature Committee Gene Names (HGNC)
                    (extensible to http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs)
                    TypeChoice of: CodeableConcept, Reference(Genomic Data File)
                    [x] NoteSeeChoice of Data Typesfor further information about how to use [x]
                    Is Modifierfalse
                    Summaryfalse
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))
                    46. Extension.url
                    Definition

                    Source of the definition for the extension code - a logical name or a URL.

                    Shortidentifies the meaning of the extension
                    Comments

                    The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.

                    Control1..1
                    Typeuri
                    Is Modifierfalse
                    XML FormatIn the XML format, this property is represented as an attribute.
                    Summaryfalse
                    Fixed Valuehttp://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions
                    48. Extension.value[x]
                    Definition

                    Value of extension - must be one of a constrained set of the data types (see Extensibility for a list).

                    ShortValue of extension
                    Control0..0
                    TypeChoice of: base64Binary, boolean, canonical, code, date, dateTime, decimal, id, instant, integer, markdown, oid, positiveInt, string, time, unsignedInt, uri, url, uuid, Address, Age, Annotation, Attachment, CodeableConcept, Coding, ContactPoint, Count, Distance, Duration, HumanName, Identifier, Money, Period, Quantity, Range, Ratio, Reference, SampledData, Signature, Timing, ContactDetail, Contributor, DataRequirement, Expression, ParameterDefinition, RelatedArtifact, TriggerDefinition, UsageContext, Dosage, Meta
                    Is Modifierfalse
                    Primitive ValueThis primitive element may be present, or absent, or replaced by an extension
                    Summaryfalse
                    Invariantsele-1: All FHIR elements must have a @value or children (hasValue() or (children().count() > id.count()))