DSTU2

This page is part of the FHIR Specification (v0.0.82: (v1.0.2: DSTU 1). 2). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions

Extension Extension: GenomicSource - Definition

URL for this extension: 


http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass

Status: draft. Extension maintained by: Health Level Seven, Intl - Clinical Genomics Seven International (Clinical Genomics)

The genomic Genomic source class means category of source of tissue sample used to determine the variant: Germline for inherited genome, somatic for cancer genome (e.g. DNA from tumor cells), and prenatal for fetal genome. Associated with LOINC sequence. Here is the loinc answer list: 48002-0. List for Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6.

Context of Use: Use on element: Observation

usage info: insert a list of places where this extension is used

Extension Content

Structure Summary

Name Flags Card. Type Description & Constraints doco
. . extension 0..1 CodeableConcept Extension URL = http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass
GenomicSource: The genomic Genomic source class means category of source of tissue sample used to determine the variant: Germline for inherited genome, somatic sequence. Here is the loinc answer List for cancer genome (e.g. DNA from tumor cells), and prenatal Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6.
Use on element: Observation

doco Documentation for fetal genome. Associated with LOINC this format

Fulle Structure

identifies the meaning of the extension Fixed Value:
Name Flags Card. Type Description & Constraints doco
.. extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass
GenomicSource: Genomic source class means category of source of tissue sample used to determine the sequence. Here is the loinc answer list: 48002-0. List for Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6.
Use on element: Observation
. . . extension 0..* Extension 0 .. 0 Additional Content defined by implementations
. . . url 1..1 uri http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass "http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass"
. . valueCode . valueCodeableConcept 0..1 1..1 code CodeableConcept Value of extension

doco Documentation for this format

XML Template 

<!-- GenomicSource -->doco

< xmlns="http://hl7.org/fhir"

<extension xmlns="http://hl7.org/fhir"

     url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass" >
  <!-- from Element: extension -->
 <

 <valueCodeableConcept><!-- 1..1 CodeableConcept 
     Value of extension --></valueCodeableConcept>

</extension>

JSON Template 

{ // GenomicSource
  // from Element: extension
    "url" : "http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass", // R! 
    "

    "valueCodeableConcept" : { CodeableConcept } // R! Value of extension

  }

Structure Summary

Name Flags Card. Type Description & Constraints doco
. . extension 0..1 CodeableConcept Extension URL = http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass
GenomicSource: The genomic Genomic source class means category of source of tissue sample used to determine the variant: Germline for inherited genome, somatic sequence. Here is the loinc answer List for cancer genome (e.g. DNA from tumor cells), and prenatal Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6.
Use on element: Observation

doco Documentation for fetal genome. Associated with LOINC this format

Full Structure

identifies the meaning of the extension Fixed Value:
Name Flags Card. Type Description & Constraints doco
.. extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass
GenomicSource: Genomic source class means category of source of tissue sample used to determine the sequence. Here is the loinc answer list: 48002-0. List for Allelic state:1. Germline LA6683-2; 2. Somatic LA6684-0; 3. Prenatal LA6685-7; 4. Likely Germline LA18194-3; 5. Likely Somatic LA18195-0; 6. Likely Prenatal LA18196-8; 7. Unknown Genomic Origin LA18197-6.
Use on element: Observation
. . . extension 0..* Extension 0 .. 0 Additional Content defined by implementations
. . . url 1..1 uri http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass "http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass"
. . valueCode . valueCodeableConcept 0..1 1..1 code CodeableConcept Value of extension

doco Documentation for this format

XML Template 

<!-- GenomicSource -->doco

< xmlns="http://hl7.org/fhir"

<extension xmlns="http://hl7.org/fhir"

     url="http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass" >
  <!-- from Element: extension -->
 <

 <valueCodeableConcept><!-- 1..1 CodeableConcept 
     Value of extension --></valueCodeableConcept>

</extension>

JSON Template

to do 
{ // GenomicSource
  // from Element: extension
    "url" : "http://hl7.org/fhir/StructureDefinition/geneticsGenomicSourceClass", // R! 
    "valueCodeableConcept" : { CodeableConcept } // R! Value of extension
  }