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[http://wiki.hl7.org/index.php?title=Category:201605_FHIR_Connectathon_Track_Proposals Return to May 2016 Proposals]
 
[[Category:201605_FHIR_Connectathon_Track_Proposals|May 2016 Proposals]]
 
[[Category:201605_FHIR_Connectathon_Track_Proposals|May 2016 Proposals]]
 
__NOTOC__
 
__NOTOC__
=Track Name=
+
=FHIR Genomics=
  
 
==Submitting WG/Project/Implementer Group==
 
==Submitting WG/Project/Implementer Group==
 +
[[CG]]
 
<!-- Who is asking for this track? -->
 
<!-- Who is asking for this track? -->
  
 
==Justification==
 
==Justification==
 +
Genomic data are of increasing importance to clinical care and secondary analysis. Please see [http://www.ncbi.nlm.nih.gov/pubmed/26198304 this recent JAMIA article] for a primer on some of the work to date on bringing genomic data definitions into the FHIR specification. FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-genetics profile). The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data. FHIR Genomics focuses on clinical genetics data reporting.
 
<!--Why is this an important track to include in the connectathon - include implementer need, impact on ballot, FMM readiness of the resources, etc. -->
 
<!--Why is this an important track to include in the connectathon - include implementer need, impact on ballot, FMM readiness of the resources, etc. -->
  
 
==Proposed Track Lead==
 
==Proposed Track Lead==
<!-- Name, email and Skype id of individual who will coordinate the track at the connectathon -->
+
[mailto:gilusa@gmail.com Gil Alterovitz]
See [[Connectathon_Track_Lead_Responsibilities]]
 
  
 
==Expected participants==
 
==Expected participants==
Line 19: Line 20:
 
==Roles==
 
==Roles==
 
<!-- Roles are sets of functionality (generally defined by a Conformance resource) that a single system can take on -->
 
<!-- Roles are sets of functionality (generally defined by a Conformance resource) that a single system can take on -->
===Role 1 Name===
+
===FHIR Client===
 
<!-- Provide a description of the capabilities this role will have within the connectathon -->
 
<!-- Provide a description of the capabilities this role will have within the connectathon -->
 +
Support the sending of the Sequence resource/genetics profiles operations: create, history, read, search and update.
  
==Scenarios==
+
===FHIR Server===
 +
<!-- Provide a description of the capabilities this role will have within the connectathon -->
 +
Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.
 +
 
 +
== Scenarios ==
 
<!-- What will be the actions performed by participants? -->
 
<!-- What will be the actions performed by participants? -->
 +
Scenarios 2-6 are taken from use cases in the [HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot].  See links below each scenario for relevant DAM excerpts.
 +
A couple new use cases may be considered as approved by CG workgroup and time permits.
 +
 +
===Scenario 1 Register a New Sequence and Observation===
 +
:Action: (FHIR Client) (FHIR Client) Create a sequence instance and a genetic-profile-based observation instance to represent genetics data and interpretations (DNA variant, RNA sequence, structural variant, etc). <!--Who does what?  (Use the role names listed above when referring to the participants -->
 +
:Precondition: The sequence instance and observation instance do not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
 +
:Success Criteria: Sequence and observation instances created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? -->
 +
:Bonus point: New profiles can be built on top of the Sequence resource for complex representation<!-- Any additional complexity to make the scenario more challenging -->
 +
<!-- Provide a description of each task -->
 +
 +
===Scenario 2 Clinical Sequencing - Germline Testing===
 +
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.gjdgxs?usp=sharing/ More on Scenario 2]
 +
:Action: (FHIR Client) Search target genetic-profile-based observation with given patient ID. This target observation has an extension - Genomic Source Class (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass
 +
) and the value is germline (code: LA6683-2).
 +
:Precondition: Relevant patient and observations have been created
 +
:Success Criteria: A bundle of genetics observations from germline analysis of that patient are returned.<!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
 +
===Scenario 3 Family Member History===
 +
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.3dy6vkm?usp=sharing/ More on Scenario 3]
 +
:Action: (FHIR Client) 1. Search the genetics diagnostic reports of a given patient.  Get the reference id of this patient’s familymemberhistory from extension - Family History (url: http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsFamilyMemberHistory
 +
). 2. Retrieve this FamilyMemberHistory instance and get the reference id of Observation instances from extension - Genetic markers, ethnicity, etc.
 +
(url: http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation). 3. Retrieve the target Observation instance.
 +
:Precondition: Relevant diagnostic report, observation, family member history have been created.
 +
:Success Criteria: The target Observation instances of the given patient's family member are returned.<!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
 +
===Scenario 4 Clinical and Research Data Warehouses===
 +
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.4d34og8?usp=sharing/ More on Scenario 4]
 +
:Action: (FHIR Client) Search for all genetic-profile-based observations with a given variant (e.g. rs587778247)
 +
:Precondition: Observation instances with this variant have been created
 +
:Success Criteria: A bundle of genetics observations, where the code value of extension - Variant Id (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariationId
 +
) is rs587778247. <!-- How will the participants know if the test was successful? -->
 +
:Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging -->
 +
 +
===Scenario 5 HLA Typing===
 +
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.17dp8vu?usp=sharing/ More on Scenario 5]
 +
:Action: (FHIR Client) Create an HLA genotyping genetics report.
 +
:Precondition: This DiagnosticReport-hlaresults instance does not exist in service prior to action.
 +
:Success Criteria: The HLA genetics report is created correctly on server and in the desired format.
 +
:Bonus point: Extensions can be added<!-- Any additional complexity to make the scenario more challenging -->
 +
 +
===Scenario 6 Species Identification===
 +
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.tyjcwt?usp=sharing/ More on Scenario 6]
 +
:Action: (FHIR Client) Search for sequences from human (Homo sapiens).
 +
:Precondition: Sequence(s) have been created where the species is defined as human (Homo sapiens).
 +
:Success Criteria: A bundle of Sequence instances where the value of the species element is Homo sapiens.
 +
 +
===Scenario 7 Comprehensive Pathology Report===
 +
A comprehensive pathology report integrates pertinent information gathered from various methods (e.g. morphology, immunohistochemistry, flow cytometry, cytogenetics, fluorescence ''in situ'' hybridization [FISH], and molecular testing [e.g., NGS]). The DiagnosticReport-genetics profile has the capability to support results with simple or complex genetics observations.
 +
:Action: (FHIR Client) Create a comprehensive pathology report which includes genetic information for a patient.
 +
:Precondition: This diagnostic report has never been created
 +
:Success Criteria: Sequence created correctly on server and in the desired format.
 +
:Bonus point: Extensions can be added.
 +
 +
===Scenario 8 Sequence quality===
 +
In the sequencing reads, each base is assigned with a quality score generated by the sequencer, which represents the confidence of a base call. Base quality is a critical factor for accurate variant detection in the downstream analysis.
 +
:Action: (FHIR Client) Get the quality of the sequence under consideration.
 +
:Precondition: This sequence instance has been created
 +
:Success Criteria: Target sequence instance is returned.
 +
:Bonus point: More parameters can be added for searching
 +
 +
==Useful links==
 +
*[http://genomics-advisor.smartplatforms.org:2048/ FHIR Genomics sandbox]
 +
*[http://genomics-advisor.smartplatforms.org:4000/fhir-genomics/fhir-genomics-toc.html FHIR Genomics staging site]
 +
 +
 +
==Sample data==
 +
===Sequence===
 +
 +
{|border="1" cellpadding="2" cellspacing="0"
 +
| width="30%" colspan="1" align="left" style="background:#f0f0f0;"|'''Element'''
 +
| width="35%" colspan="1" align="left" style="background:#f0f0f0;"|'''Sequence #1'''
 +
| width="35%" colspan="1" align="left" style="background:#f0f0f0;"|'''Sequence #2'''
 +
|-
 +
||variationID
 +
||rs58238559
 +
||rs58238560
 +
|-
 +
||coordinate.chromosome
 +
||7
 +
||7
 +
|-
 +
||coordinate.start
 +
||87452957
 +
||87082273
 +
|-
 +
||coordinate.end
 +
||87452958
 +
||87082274
 +
|-
 +
||coordinate.genomeBuild
 +
||GRCh38.p2
 +
||GRCh38.p2
 +
|-
 +
||gene
 +
||ABCB4
 +
||ABCB4
 +
|-
 +
||region
 +
||Exon 23
 +
||Exon 6
 +
|-
 +
||species
 +
||human
 +
||human
 +
|-
 +
||observedAllele
 +
||T
 +
||T
 +
|-
 +
||referenceAllele
 +
||C
 +
||A
 +
|-
 +
|}
 +
===Observation-genetics===
  
===Scenario Step 1 Name===
+
{|border="1" cellpadding="2" cellspacing="0"
:Action: <!--Who does what? (Use the role names listed above when referring to the participants -->
+
| width="16%" colspan="1" align="left" style="background:#f0f0f0;"|'''Element'''
:Precondition: <!-- What setup is required prior to executing this step? -->
+
| width="28%" colspan="1" align="left" style="background:#f0f0f0;"|'''Observation #1'''
:Success Criteria: <!-- How will the participants know if the test was successful? -->
+
| width="28%" colspan="1" align="left" style="background:#f0f0f0;"|'''Observation #2'''
:Bonus point: <!-- Any additional complexity to make the scenario more challenging -->
+
| width="28%" colspan="1" align="left" style="background:#f0f0f0;"|'''Observation #3'''
 +
|-
 +
||category
 +
||complex
 +
||complex
 +
||simple
 +
|-
 +
||code
 +
||49874-1: ABCB4 gene mutation analysis in Blood or Tissue by Molecular genetics method Narrative
 +
||49874-1: ABCB4 gene mutation analysis in Blood or Tissue by Molecular genetics method Narrative
 +
||54447-8: LT3 gene mutation analysis in Bone marrow by Molecular genetics method Narrative
 +
|-
 +
||subject
 +
||Marry Chalmers
 +
||Marry Chalmers
 +
||Marry Chalmers
 +
|-
 +
||effectiveTime
 +
||2015-3-11 10:28:00
 +
||2015-3-11 10:28:00
 +
||2015-3-10 11:05:00
 +
|-
 +
||issued
 +
||2015-3-12 15:40:00
 +
||2015-3-12 15:40:00
 +
||2015-3-12 15:40:00
 +
|-
 +
||performer
 +
||Molecular Diagnostic Laboratory  
 +
||Molecular Diagnostic Laboratory
 +
||Molecular Diagnostic Laboratory
 +
|-
 +
||value
 +
||Positive
 +
||Positive
 +
||Positive
 +
|-
 +
||GeneticsSequence
 +
||(refer to) Sequence #1
 +
||(refer to) Sequence #2
 +
||None
 +
|}
 +
 
 +
===DiagnosticReport-genetics===
 +
 
 +
{|border="1" cellpadding="2" cellspacing="0"
 +
| width="30%" colspan="1" align="left" style="background:#f0f0f0;"|'''Element'''
 +
| width="70%" colspan="1" align="left" style="background:#f0f0f0;"|'''DiagnosticReport #1''
 +
|-
 +
||status
 +
||final
 +
|-
 +
||code
 +
||Comprehensive genetics report
 +
|-
 +
||subject
 +
||Marry Chalmers
 +
|-
 +
||effectiveTime
 +
||2015-3-11 10:28:00
 +
|-
 +
||issued
 +
||2015-3-12 15:40:00
 +
|-
 +
||specimen
 +
||Venous blood specimen
 +
|-
 +
||result
 +
||Observation #1
 +
|-
 +
||result
 +
||Observation #2
 +
|-
 +
||result
 +
||Observation #3
 +
|-
 +
|}
  
<!-- Provide a description of each task -->
 
  
 
==TestScript(s)==
 
==TestScript(s)==
<!-- Optional (for initial proposal): Provide links to the TestScript instance(s) that define the behavior to be tested
+
<!-- Optional (for initial proposal): Provide links to the TestScript instance(s) that define the behavior to be tested-->
These should be committed to SVN under trunk/connectathons/[connectathon]
+
The supporting TestScripts and corresponding fixtures will be committed to the FHIR SVN repository at:
-->
+
http://gforge.hl7.org/svn/fhir/trunk/connectathons/MontrealMay2016/Connectathon12/Track-08-FHIRGenomics
 +
 
 +
===TestScript Definitions===
 +
TBD

Latest revision as of 14:29, 5 May 2016

Return to May 2016 Proposals

FHIR Genomics

Submitting WG/Project/Implementer Group

CG

Justification

Genomic data are of increasing importance to clinical care and secondary analysis. Please see this recent JAMIA article for a primer on some of the work to date on bringing genomic data definitions into the FHIR specification. FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-genetics profile). The Sequence resource is a core resource in FHIR Genomics. It is used to represent complex genetics data. FHIR Genomics focuses on clinical genetics data reporting.

Proposed Track Lead

Gil Alterovitz

Expected participants

Roles

FHIR Client

Support the sending of the Sequence resource/genetics profiles operations: create, history, read, search and update.

FHIR Server

Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.

Scenarios

Scenarios 2-6 are taken from use cases in the [HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot]. See links below each scenario for relevant DAM excerpts. A couple new use cases may be considered as approved by CG workgroup and time permits.

Scenario 1 Register a New Sequence and Observation

Action: (FHIR Client) (FHIR Client) Create a sequence instance and a genetic-profile-based observation instance to represent genetics data and interpretations (DNA variant, RNA sequence, structural variant, etc).
Precondition: The sequence instance and observation instance do not exist in service prior to action.
Success Criteria: Sequence and observation instances created correctly on server and in the desired format.
Bonus point: New profiles can be built on top of the Sequence resource for complex representation

Scenario 2 Clinical Sequencing - Germline Testing

More on Scenario 2

Action: (FHIR Client) Search target genetic-profile-based observation with given patient ID. This target observation has an extension - Genomic Source Class (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass

) and the value is germline (code: LA6683-2).

Precondition: Relevant patient and observations have been created
Success Criteria: A bundle of genetics observations from germline analysis of that patient are returned.
Bonus point: More parameters can be added for searching

Scenario 3 Family Member History

More on Scenario 3

Action: (FHIR Client) 1. Search the genetics diagnostic reports of a given patient. Get the reference id of this patient’s familymemberhistory from extension - Family History (url: http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsFamilyMemberHistory

). 2. Retrieve this FamilyMemberHistory instance and get the reference id of Observation instances from extension - Genetic markers, ethnicity, etc. (url: http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation). 3. Retrieve the target Observation instance.

Precondition: Relevant diagnostic report, observation, family member history have been created.
Success Criteria: The target Observation instances of the given patient's family member are returned.
Bonus point: More parameters can be added for searching

Scenario 4 Clinical and Research Data Warehouses

More on Scenario 4

Action: (FHIR Client) Search for all genetic-profile-based observations with a given variant (e.g. rs587778247)
Precondition: Observation instances with this variant have been created
Success Criteria: A bundle of genetics observations, where the code value of extension - Variant Id (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariationId

) is rs587778247.

Bonus point: More parameters can be added for searching

Scenario 5 HLA Typing

More on Scenario 5

Action: (FHIR Client) Create an HLA genotyping genetics report.
Precondition: This DiagnosticReport-hlaresults instance does not exist in service prior to action.
Success Criteria: The HLA genetics report is created correctly on server and in the desired format.
Bonus point: Extensions can be added

Scenario 6 Species Identification

More on Scenario 6

Action: (FHIR Client) Search for sequences from human (Homo sapiens).
Precondition: Sequence(s) have been created where the species is defined as human (Homo sapiens).
Success Criteria: A bundle of Sequence instances where the value of the species element is Homo sapiens.

Scenario 7 Comprehensive Pathology Report

A comprehensive pathology report integrates pertinent information gathered from various methods (e.g. morphology, immunohistochemistry, flow cytometry, cytogenetics, fluorescence in situ hybridization [FISH], and molecular testing [e.g., NGS]). The DiagnosticReport-genetics profile has the capability to support results with simple or complex genetics observations.

Action: (FHIR Client) Create a comprehensive pathology report which includes genetic information for a patient.
Precondition: This diagnostic report has never been created
Success Criteria: Sequence created correctly on server and in the desired format.
Bonus point: Extensions can be added.

Scenario 8 Sequence quality

In the sequencing reads, each base is assigned with a quality score generated by the sequencer, which represents the confidence of a base call. Base quality is a critical factor for accurate variant detection in the downstream analysis.

Action: (FHIR Client) Get the quality of the sequence under consideration.
Precondition: This sequence instance has been created
Success Criteria: Target sequence instance is returned.
Bonus point: More parameters can be added for searching

Useful links


Sample data

Sequence

Element Sequence #1 Sequence #2
variationID rs58238559 rs58238560
coordinate.chromosome 7 7
coordinate.start 87452957 87082273
coordinate.end 87452958 87082274
coordinate.genomeBuild GRCh38.p2 GRCh38.p2
gene ABCB4 ABCB4
region Exon 23 Exon 6
species human human
observedAllele T T
referenceAllele C A

Observation-genetics

Element Observation #1 Observation #2 Observation #3
category complex complex simple
code 49874-1: ABCB4 gene mutation analysis in Blood or Tissue by Molecular genetics method Narrative 49874-1: ABCB4 gene mutation analysis in Blood or Tissue by Molecular genetics method Narrative 54447-8: LT3 gene mutation analysis in Bone marrow by Molecular genetics method Narrative
subject Marry Chalmers Marry Chalmers Marry Chalmers
effectiveTime 2015-3-11 10:28:00 2015-3-11 10:28:00 2015-3-10 11:05:00
issued 2015-3-12 15:40:00 2015-3-12 15:40:00 2015-3-12 15:40:00
performer Molecular Diagnostic Laboratory Molecular Diagnostic Laboratory Molecular Diagnostic Laboratory
value Positive Positive Positive
GeneticsSequence (refer to) Sequence #1 (refer to) Sequence #2 None

DiagnosticReport-genetics

Element 'DiagnosticReport #1
status final
code Comprehensive genetics report
subject Marry Chalmers
effectiveTime 2015-3-11 10:28:00
issued 2015-3-12 15:40:00
specimen Venous blood specimen
result Observation #1
result Observation #2
result Observation #3


TestScript(s)

The supporting TestScripts and corresponding fixtures will be committed to the FHIR SVN repository at: http://gforge.hl7.org/svn/fhir/trunk/connectathons/MontrealMay2016/Connectathon12/Track-08-FHIRGenomics

TestScript Definitions

TBD