This wiki has undergone a migration to Confluence found Here
Difference between revisions of "ClinicalGenomics FHIR IG Proposal"
Jump to navigation
Jump to search
Bob Milius (talk | contribs) |
|||
| (22 intermediate revisions by 4 users not shown) | |||
| Line 3: | Line 3: | ||
<div style="float: left;">[[Image:OpenHotTopic.GIF|35px| ]]</div> | <div style="float: left;">[[Image:OpenHotTopic.GIF|35px| ]]</div> | ||
<div style="background:#F0F0F0"> | <div style="background:#F0F0F0"> | ||
| − | This page documents a [[:category: | + | This page documents a [[:category:Approved FHIR IGProposal|Approved]] [[:category:FHIR IG Proposal|FHIR IG Proposal]] |
</div> | </div> | ||
</div> | </div> | ||
[[Category:FHIR IG Proposal]] | [[Category:FHIR IG Proposal]] | ||
| − | [[Category: | + | [[Category:Approved FHIR IG Proposal]] |
| Line 14: | Line 14: | ||
=PutProposedIGNameHere= | =PutProposedIGNameHere= | ||
| − | + | Genetic Reporting Implementation Guide | |
<!-- Resource names should meet the following characteristics: | <!-- Resource names should meet the following characteristics: | ||
* Title Case | * Title Case | ||
| Line 33: | Line 33: | ||
==Committee Approval Date:== | ==Committee Approval Date:== | ||
<i>Please enter the date that the committee approved this IGproposal</i> | <i>Please enter the date that the committee approved this IGproposal</i> | ||
| − | + | * Feb 13, 2014 | |
| + | |||
==Contributing or Reviewing Work Groups== | ==Contributing or Reviewing Work Groups== | ||
| Line 44: | Line 45: | ||
==Scope of coverage== | ==Scope of coverage== | ||
| − | The | + | The Genetic Reporting Implementation Guide will identify and define extensions, profiles, terminology standards necessary for the reporting of clinical genetic/genomic/biomolecular findings and interpretations related to the domain of clinical genetics/genomics sufficient for precision medicine. This includes items like extensions, profiles, domain specific examples. This work will be defined using the available FHIR tooling and in accordance with documented quality guidelines. This includes, but not limited to, profiles on Observation, DiagnosticReport, ServiceRequest, Specimen, and Sequence. |
| + | |||
| + | '''At present, this implementation guide focuses solely on data structures - what data should be/might be present and how it should be organized. It does <u>not</u> address workflows around how reports are requested, created, approved, routed, delivered, amended, etc. The implementation guide is also paradigm-independent - the data structures presented here could be used in RESTful, messaging, documents or other mechanisms. | ||
| + | ''' | ||
<!-- Define the full scope of coverage for the IG. The scope must be clearly delineated such that it does not overlap with any other existing or expected HL7 Int'l-maintained IG. 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 IG. The scope must be clearly delineated such that it does not overlap with any other existing or expected HL7 Int'l-maintained IG. 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%" | ||
| Line 58: | Line 62: | ||
<!-- Why is this IG necessary? --> | <!-- Why is this IG necessary? --> | ||
| − | Current Clinical Genomics FHIR work includes a number of profiles on Observation, DiagnosticReport, DiagnosticRequest, FamilyMemberHistory that relies on heavy use of extensions. and a Sequence Resource. Refactoring these profiles into a consistent approach emphasizing components in the case of Observation, and separating them from FHIR core spec | + | Current Clinical Genomics FHIR work includes a number of profiles on Observation, DiagnosticReport, DiagnosticRequest, FamilyMemberHistory that relies on heavy use of extensions. and a Sequence Resource. Refactoring these profiles into a consistent approach, emphasizing components in the case of Observation, and separating them from FHIR core spec will simplify their use and understanding as well as comform to FHIR design going forward (reducing the number of Profiles in the core spec). |
==Content location== | ==Content location== | ||
| Line 69: | Line 73: | ||
<!-- What is the realm code (2-character country code or 'uv') and IG code to use for the path when the IG is published under http://hl7.org/fhir? E.g. us/ccda --> | <!-- What is the realm code (2-character country code or 'uv') and IG code to use for the path when the IG is published under http://hl7.org/fhir? E.g. us/ccda --> | ||
| − | + | uv/genreport | |
==Short Description== | ==Short Description== | ||
<!-- 1-2 sentences describing the purpose/scope of the IG for inclusion in the registry --> | <!-- 1-2 sentences describing the purpose/scope of the IG for inclusion in the registry --> | ||
| − | + | This implementation guide tries to provide guidance that will enable improved interoperable and computable sharing of genetic testing results. | |
==Long Description== | ==Long Description== | ||
<!-- 1 paragraph describing the purpose/scope of the IG in more detail for inclusion in the version history --> | <!-- 1 paragraph describing the purpose/scope of the IG in more detail for inclusion in the version history --> | ||
| + | Genomics is a rapidly evolving area of healthcare that involves complex data structures. There is significant value in sharing this information in a way that is consistent, computable and that can accomodate onging evolution of medical science and practice. The value comes from the ability to easily sort, filter and perform decision support on such information and the resulting improvements in care and reduction in costs such as the elimination of redundant testing. This implementation guide tries to provide guidance that will enable improved interoperable and computable sharing of genetic testing results. | ||
| + | This guide covers all aspects of genetic reporting, including: | ||
| + | |||
| + | * Human and veterinary as well as bacterial and viral specimens | ||
| + | * Representation of simple discrete variants, structural variants including copy number variants, complex variants as well as gross variations such as extra or missing chromosomes | ||
| + | * Representation of both known/catalogued variants as well as fully describing non-catalogued variations | ||
| + | * Germline and somatic variations | ||
| + | * Relevance of identified variations from the perspective of disease pathology, pharmacogenoomics, transplant suitability (e.g. HLA typing), etc. | ||
| + | * Full and partial DNA sequencing, including whole genome and exome studies | ||
| + | * Mosaicism (differing genetic characteristics for different specimens from the same subject) | ||
| + | * Mitochondrial DNA variations | ||
==Involved parties== | ==Involved parties== | ||
<!-- 1 paragraph describing who is sponsoring or involved in creating the IG for inclusion in the version history --> | <!-- 1 paragraph describing who is sponsoring or involved in creating the IG for inclusion in the version history --> | ||
| − | + | * National Library of Medicine/NIH | |
| + | * Boston Children's Hospital | ||
==Expected implementations== | ==Expected implementations== | ||
<!--Key resources are justified by CCDA, for resources not deemed "key", what interest is there by implementers in using this particular resource. Provide named implementations if possible - ideally provide multiple independent implementations. --> | <!--Key resources are justified by CCDA, for resources not deemed "key", what interest is there by implementers in using this particular resource. Provide named implementations if possible - ideally provide multiple independent implementations. --> | ||
| − | National Marrow Donor Program | + | * National Marrow Donor Program |
| − | Center for International Blood and Marrow Transplant Research | + | * Center for International Blood and Marrow Transplant Research |
==Content sources== | ==Content sources== | ||
| Line 97: | Line 113: | ||
Are there any source specifications that you wish to consult but are concerned about access to or expertise to consider? --> | Are there any source specifications that you wish to consult but are concerned about access to or expertise to consider? --> | ||
| + | No other source specifications, but we have garthered input from | ||
| + | * Global Alliance for Global Health (GA4GH) | ||
| + | * FDA | ||
| + | * National Academies | ||
| + | * ClinGen/ClinVar | ||
| + | * Variant Modelling Collaboration (VMC) | ||
| + | * CDISC PGx | ||
| + | * ISO TC215 | ||
==Example Scenarios== | ==Example Scenarios== | ||
| Line 102: | Line 126: | ||
<!-- Provide a listing of the types of scenarios to be represented in the examples produced for this IG. They should demonstrate the full scope of the IG and allow exercising of the IG's capabilities (all profiles, different types of applications, etc.) --> | <!-- Provide a listing of the types of scenarios to be represented in the examples produced for this IG. They should demonstrate the full scope of the IG and allow exercising of the IG's capabilities (all profiles, different types of applications, etc.) --> | ||
| − | + | * General Genomic Reporting | |
| − | * | + | * Sequence Variants |
| − | * | + | * Cytogenetic Reporting |
| − | * | + | * Pharmacogenomic Reporting |
| − | * | + | * Somatic Genomic Reporting |
| − | * | + | * Genomic Profiling for Transplantation |
| − | * | ||
| − | |||
| − | |||
==IG Relationships== | ==IG Relationships== | ||
| Line 119: | Line 140: | ||
==Timelines== | ==Timelines== | ||
<!-- Indicate the target date for having the IGcomplete from a committee perspective and ready for vetting and voting --> | <!-- Indicate the target date for having the IGcomplete from a committee perspective and ready for vetting and voting --> | ||
| − | * May | + | * May 2018 Ballot for R4 |
* Sep 2018 Ballot for R4 after ballot reconciliation | * Sep 2018 Ballot for R4 after ballot reconciliation | ||
Latest revision as of 19:43, 7 March 2018
This page documents a Approved FHIR IG Proposal
Contents
- 1 PutProposedIGNameHere
- 1.1 Owning work group name
- 1.2 Committee Approval Date:
- 1.3 Contributing or Reviewing Work Groups
- 1.4 FHIR Development Project Insight ID
- 1.5 Scope of coverage
- 1.6 IG Purpose
- 1.7 Content location
- 1.8 Proposed IG realm and code
- 1.9 Short Description
- 1.10 Long Description
- 1.11 Involved parties
- 1.12 Expected implementations
- 1.13 Content sources
- 1.14 Example Scenarios
- 1.15 IG Relationships
- 1.16 Timelines
- 1.17 When IG Proposal Is Complete
- 1.18 FMG Notes
PutProposedIGNameHere
Genetic Reporting Implementation Guide
Owning work group name
Clinical Genomics
Committee Approval Date:
Please enter the date that the committee approved this IGproposal
- Feb 13, 2014
Contributing or Reviewing Work Groups
- Orders and Observations
FHIR Development Project Insight ID
1217
Scope of coverage
The Genetic Reporting Implementation Guide will identify and define extensions, profiles, terminology standards necessary for the reporting of clinical genetic/genomic/biomolecular findings and interpretations related to the domain of clinical genetics/genomics sufficient for precision medicine. This includes items like extensions, profiles, domain specific examples. This work will be defined using the available FHIR tooling and in accordance with documented quality guidelines. This includes, but not limited to, profiles on Observation, DiagnosticReport, ServiceRequest, Specimen, and Sequence.
At present, this implementation guide focuses solely on data structures - what data should be/might be present and how it should be organized. It does not address workflows around how reports are requested, created, approved, routed, delivered, amended, etc. The implementation guide is also paradigm-independent - the data structures presented here could be used in RESTful, messaging, documents or other mechanisms.
IG Purpose
Current Clinical Genomics FHIR work includes a number of profiles on Observation, DiagnosticReport, DiagnosticRequest, FamilyMemberHistory that relies on heavy use of extensions. and a Sequence Resource. Refactoring these profiles into a consistent approach, emphasizing components in the case of Observation, and separating them from FHIR core spec will simplify their use and understanding as well as comform to FHIR design going forward (reducing the number of Profiles in the core spec).
Content location
http://build.fhir.org/ig/HL7/genomics-unified/index.html
Proposed IG realm and code
uv/genreport
Short Description
This implementation guide tries to provide guidance that will enable improved interoperable and computable sharing of genetic testing results.
Long Description
Genomics is a rapidly evolving area of healthcare that involves complex data structures. There is significant value in sharing this information in a way that is consistent, computable and that can accomodate onging evolution of medical science and practice. The value comes from the ability to easily sort, filter and perform decision support on such information and the resulting improvements in care and reduction in costs such as the elimination of redundant testing. This implementation guide tries to provide guidance that will enable improved interoperable and computable sharing of genetic testing results.
This guide covers all aspects of genetic reporting, including:
- Human and veterinary as well as bacterial and viral specimens
- Representation of simple discrete variants, structural variants including copy number variants, complex variants as well as gross variations such as extra or missing chromosomes
- Representation of both known/catalogued variants as well as fully describing non-catalogued variations
- Germline and somatic variations
- Relevance of identified variations from the perspective of disease pathology, pharmacogenoomics, transplant suitability (e.g. HLA typing), etc.
- Full and partial DNA sequencing, including whole genome and exome studies
- Mosaicism (differing genetic characteristics for different specimens from the same subject)
- Mitochondrial DNA variations
Involved parties
- National Library of Medicine/NIH
- Boston Children's Hospital
Expected implementations
- National Marrow Donor Program
- Center for International Blood and Marrow Transplant Research
Content sources
No other source specifications, but we have garthered input from
- Global Alliance for Global Health (GA4GH)
- FDA
- National Academies
- ClinGen/ClinVar
- Variant Modelling Collaboration (VMC)
- CDISC PGx
- ISO TC215
Example Scenarios
- General Genomic Reporting
- Sequence Variants
- Cytogenetic Reporting
- Pharmacogenomic Reporting
- Somatic Genomic Reporting
- Genomic Profiling for Transplantation
IG Relationships
No, there not any IGs this resource depends on or that depend on this IG
Timelines
- May 2018 Ballot for R4
- Sep 2018 Ballot for R4 after ballot reconciliation
When IG Proposal Is Complete
When you have completed your proposal, please send an email to FMGcontact@HL7.org
