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Difference between revisions of "GenomicVariantObservation FHIR Profile Proposal"

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<div style="float: left;">[[Image:OpenHotTopic.GIF|35px| ]]</div>
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Current version: https://confluence.hl7.org/display/FHIR/GenomicVariantObservation+FHIR+Profile+Proposal<div style="float: left;">[[Image:OpenHotTopic.GIF|35px| ]]</div>
 
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This page documents a [[:category:Pending FHIR Resource Proposal|Pending]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]]
 
This page documents a [[:category:Pending FHIR Resource Proposal|Pending]] [[:category:FHIR Resource Proposal|FHIR Resource Proposal]]
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<!--Put a link to the resource/datatype (or group of resources) that will be profiled here.-->
 
<!--Put a link to the resource/datatype (or group of resources) that will be profiled here.-->
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* [[http://wiki.hl7.org/index.php?title=Observation_FHIR_Resource_Proposal| Observation FHIR Resource]]
+
*[[http://wiki.hl7.org/index.php?title=Observation_FHIR_Resource_Proposal| Observation FHIR Resource]]
  
 
====Constraints to be Applied====
 
====Constraints to be Applied====
  
 
<!--Describe how the current resource will be constrained.-->
 
<!--Describe how the current resource will be constrained.-->
−
* Constraints to integrate clinical genomic standards into FHIR, as outlined in the following 2 guides:
+
*Constraints to integrate clinical genomic standards into FHIR, as outlined in the following 2 guides:
 +
 
 
:HL7 Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 2
 
:HL7 Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 2
−
:[http://www.hl7.org/implement/standards/product_brief.cfm?product_id=23|HL7 Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 1 (US Realm)]  
+
:[http://www.hl7.org/implement/standards/product_brief.cfm?product_id=23|HL7 Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 1 (US Realm)]
 
:HL7 IG for CDA R2: Genetic Testing Reports, Release 1 - GTR
 
:HL7 IG for CDA R2: Genetic Testing Reports, Release 1 - GTR
 
:[http://www.hl7.org/implement/standards/product_brief.cfm?product_id=292\:HL7 Implementation Guide for CDA® Release 2: Genetic Testing Reports, Release 1]
 
:[http://www.hl7.org/implement/standards/product_brief.cfm?product_id=292\:HL7 Implementation Guide for CDA® Release 2: Genetic Testing Reports, Release 1]
−
* Extensions to support genomic coordinates, chromosome, and genome build and HLA typing will be coded in LOINC and added to these terms
+
 
−
* Additional extensions maybe added as necessary.
+
*Extensions to support genomic coordinates, chromosome, and genome build and HLA typing will be coded in LOINC and added to these terms
−
** Note the use of LOINC codes to qualify genetic/genomic results will be strongly recommended but not required.
+
*Additional extensions maybe added as necessary.
−
** Additionally, using these same LOINC codes/panels to qualify genetic/genomic data has also been demonstrated in HL7 IG for CDA R2: Genetic Testing Reports, Release 1 - GTR
+
**Note the use of LOINC codes to qualify genetic/genomic results will be strongly recommended but not required.
 +
**Additionally, using these same LOINC codes/panels to qualify genetic/genomic data has also been demonstrated in HL7 IG for CDA R2: Genetic Testing Reports, Release 1 - GTR
 +
 
 
:[http://www.hl7.org/implement/standards/product_brief.cfm?product_id=292\:HL7 Implementation Guide for CDA® Release 2: Genetic Testing Reports, Release 1]
 
:[http://www.hl7.org/implement/standards/product_brief.cfm?product_id=292\:HL7 Implementation Guide for CDA® Release 2: Genetic Testing Reports, Release 1]
−
* Finally, the genetic/genomic information will be aligned with the Clinical Genomic DAM and DIM to be balloted in Sept 2014
+
 
−
** The DAM & DIM will also be backwards compatible to the v.2.5.1 and CDA Genetic Test Report (mentioned above)
+
*Finally, the genetic/genomic information will be aligned with the Clinical Genomic DAM and DIM to be balloted in Sept 2014
 +
**The DAM & DIM will also be backwards compatible to the v.2.5.1 and CDA Genetic Test Report (mentioned above)
  
 
====Extensions to be Applied====
 
====Extensions to be Applied====
  
 
<!--Describe how the current resource will be extended.-->
 
<!--Describe how the current resource will be extended.-->
−
* For extensions to the current genetic/genomic LOINC panels see above
+
*For extensions to the current genetic/genomic LOINC panels see above
  
 
===Example Scenarios===
 
===Example Scenarios===
  
 
<!-- Provide a listing of the types of scenarios to be represented in the examples produced for this Profile.  They should demonstrate the full scope of the Profile and allow exercising of the Profiles capabilities (full element coverage, inclusion & omission of optional elements, repeating and singleton repeating elements, etc.) -->
 
<!-- Provide a listing of the types of scenarios to be represented in the examples produced for this Profile.  They should demonstrate the full scope of the Profile and allow exercising of the Profiles capabilities (full element coverage, inclusion & omission of optional elements, repeating and singleton repeating elements, etc.) -->
−
* Full scenarios are outlined within the v 2.5.1 IG for genetic test reporting and the DAM.  These include:
+
*Full scenarios are outlined within the v 2.5.1 IG for genetic test reporting and the DAM.  These include:
−
** Genetic test reporting of gene variants found without interpretation, with interpretation associated with drug efficacy and/or resistance, drug metabolism, disease diagnosis, and disease risk
+
**Genetic test reporting of gene variants found without interpretation, with interpretation associated with drug efficacy and/or resistance, drug metabolism, disease diagnosis, and disease risk
−
** Transmission of a genetic/genomic data file containing 'raw' data from the test
+
**Transmission of a genetic/genomic data file containing 'raw' data from the test
−
** HLA typing for stem cell matching
+
**HLA typing for stem cell matching
  
 
===Scope of coverage===
 
===Scope of coverage===
−
* Human
+
 
−
* Clinical testing scenarios, clinical trails, and translational medicine
+
*Human
−
* Universal with match to guidance to US Realm
+
*Clinical testing scenarios, clinical trails, and translational medicine
 +
*Universal with match to guidance to US Realm
  
 
<!-- Define the full scope of coverage for the Profile.  The scope must be clearly delineated such that it does not overlap with any other existing or expected Profile.  The scope will be used to govern "what is the set of potential applications to consider when evaluating what elements are 'core' – i.e. in the 80%"
 
<!-- Define the full scope of coverage for the Profile.  The scope must be clearly delineated such that it does not overlap with any other existing or expected Profile.  The scope will be used to govern "what is the set of potential applications to consider when evaluating what elements are 'core' – i.e. in the 80%"
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<!-- Additional work groups that may have an interest in contributing to, or reviewing  the content of the Profile (optional) -->
 
<!-- Additional work groups that may have an interest in contributing to, or reviewing  the content of the Profile (optional) -->
−
* Anatomic Pathology
+
*Anatomic Pathology
−
* Orders and Observations
+
*Orders and Observations
−
* Image Integration
+
*Image Integration
  
 
===Expected implementations===
 
===Expected implementations===
  
 
<!--Key Profiles are justified by CCDA, for Profiles not deemed "key", what interest is there by implementers in using this particular Profile. Provide named implementations if possible - ideally provide multiple independent implementations. -->
 
<!--Key Profiles are justified by CCDA, for Profiles not deemed "key", what interest is there by implementers in using this particular Profile. Provide named implementations if possible - ideally provide multiple independent implementations. -->
−
* Harvard - Partners
+
*Harvard - Partners
−
* Haifa University
+
*Haifa University
−
* Intermountain Healthcare
+
*Intermountain Healthcare
−
* NMDP - National Marrow Donor Program
+
*NMDP - National Marrow Donor Program
  
 
===gForge Users===
 
===gForge Users===
  
 
<!-- Identify the userids who will require commit access to gForge to maintain the Profile.  (Ensure all users have registered for gForge.) -->
 
<!-- Identify the userids who will require commit access to gForge to maintain the Profile.  (Ensure all users have registered for gForge.) -->
−
 
  
 
===FHIR Profile Development Project Insight ID===
 
===FHIR Profile Development Project Insight ID===
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Choose one:
 
Choose one:
 +
 
*Ballot with next FHIR DSTU or Normative Edition
 
*Ballot with next FHIR DSTU or Normative Edition
  
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<!-- Indicate the desired ballot date.-->
 
<!-- Indicate the desired ballot date.-->
 
Desired Ballot Date
 
Desired Ballot Date
 +
 
*Aug/Sept 2014 DSTU
 
*Aug/Sept 2014 DSTU

Latest revision as of 16:17, 31 October 2019

Current version: https://confluence.hl7.org/display/FHIR/GenomicVariantObservation+FHIR+Profile+Proposal
OpenHotTopic.GIF

This page documents a Pending FHIR Resource Proposal



GeneticVariantObservation

Resource Details

Parent Resource

Constraints to be Applied

  • Constraints to integrate clinical genomic standards into FHIR, as outlined in the following 2 guides:
HL7 Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 2
Version 2 Implementation Guide: Clinical Genomics; Fully LOINC-Qualified Genetic Variation Model, Release 1 (US Realm)
HL7 IG for CDA R2: Genetic Testing Reports, Release 1 - GTR
Implementation Guide for CDA® Release 2: Genetic Testing Reports, Release 1
  • Extensions to support genomic coordinates, chromosome, and genome build and HLA typing will be coded in LOINC and added to these terms
  • Additional extensions maybe added as necessary.
    • Note the use of LOINC codes to qualify genetic/genomic results will be strongly recommended but not required.
    • Additionally, using these same LOINC codes/panels to qualify genetic/genomic data has also been demonstrated in HL7 IG for CDA R2: Genetic Testing Reports, Release 1 - GTR
Implementation Guide for CDA® Release 2: Genetic Testing Reports, Release 1
  • Finally, the genetic/genomic information will be aligned with the Clinical Genomic DAM and DIM to be balloted in Sept 2014
    • The DAM & DIM will also be backwards compatible to the v.2.5.1 and CDA Genetic Test Report (mentioned above)

Extensions to be Applied

  • For extensions to the current genetic/genomic LOINC panels see above

Example Scenarios

  • Full scenarios are outlined within the v 2.5.1 IG for genetic test reporting and the DAM. These include:
    • Genetic test reporting of gene variants found without interpretation, with interpretation associated with drug efficacy and/or resistance, drug metabolism, disease diagnosis, and disease risk
    • Transmission of a genetic/genomic data file containing 'raw' data from the test
    • HLA typing for stem cell matching

Scope of coverage

  • Human
  • Clinical testing scenarios, clinical trails, and translational medicine
  • Universal with match to guidance to US Realm


Ownership

Owning committee name

Clinical Genomics Workgroup

Contributing or Reviewing Work Groups

  • Anatomic Pathology
  • Orders and Observations
  • Image Integration

Expected implementations

  • Harvard - Partners
  • Haifa University
  • Intermountain Healthcare
  • NMDP - National Marrow Donor Program

gForge Users

FHIR Profile Development Project Insight ID

Plans

Timelines

  • TargetDateForInternalReview

Balloting Requirements

Choose one:

  • Ballot with next FHIR DSTU or Normative Edition


Desired Ballot Date

  • Aug/Sept 2014 DSTU
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