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Difference between revisions of "201605 FHIR Genomics on FHIR Connectathon Track Proposal"

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(Created page with "{{subst::Template for FHIR Connectathon Track Proposals}}")
 
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[[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.
 +
 +
===Scenario 1 Register a New Sequence and Observation===
 +
:Action: (FHIR Client) Create a sequence instance and a 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: This 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 observation with patient ID and value for source ("germline")
 +
: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) Get the genetics diagnostic reports of patient's family members.
 +
:Precondition: Relevant diagnostic reports have been created
 +
:Success Criteria: The genetics diagnostic reports of patient's family members 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) Get all genetic-profile-based observations of patients with the variant c.181T>G
 +
:Precondition: Relevant observations have been created
 +
:Success Criteria: A bundle of genetics observations, whose extesion 'sequence' referring to sequence instance of variant c.181T>G, 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 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 Specimen Identification===
 +
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.tyjcwt?usp=sharing/ More on Scenario 6]
 +
:Action: (FHIR Client) Represent the specimen of origin, i.e. microorganism and/or tumor.  Search for sequences from microorganism or tumor. 
 +
:Precondition: Specimen has been created.
 +
:Success Criteria: A bundle of sequences from microorganism or tumor are returned.
 +
 +
===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 Step 1 Name===
+
===Scenario 8 Sequence quality===
−
:Action: <!--Who does what?  (Use the role names listed above when referring to the participants -->
+
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.
−
:Precondition: <!-- What setup is required prior to executing this step? -->
+
:Action: (FHIR Client) Get the quality of the sequence under consideration.
−
:Success Criteria: <!-- How will the participants know if the test was successful? -->
+
:Precondition: This sequence instance has been created
−
:Bonus point: <!-- Any additional complexity to make the scenario more challenging -->
+
: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===
 +
 
 +
{|border="1" cellpadding="2" cellspacing="0"
 +
| width="16%" colspan="1" align="left" style="background:#f0f0f0;"|'''Element'''
 +
| width="28%" colspan="1" align="left" style="background:#f0f0f0;"|'''Observation #1'''
 +
| width="28%" colspan="1" align="left" style="background:#f0f0f0;"|'''Observation #2'''
 +
| 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]
 
−
-->
 

Revision as of 13:42, 3 February 2016


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.

Scenario 1 Register a New Sequence and Observation

Action: (FHIR Client) Create a sequence instance and a observation instance to represent genetics data and interpretations (DNA variant, RNA sequence, structural variant, etc).
Precondition: This 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 observation with patient ID and value for source ("germline")
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) Get the genetics diagnostic reports of patient's family members.
Precondition: Relevant diagnostic reports have been created
Success Criteria: The genetics diagnostic reports of patient's family members 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) Get all genetic-profile-based observations of patients with the variant c.181T>G
Precondition: Relevant observations have been created
Success Criteria: A bundle of genetics observations, whose extesion 'sequence' referring to sequence instance of variant c.181T>G, are returned.
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 Specimen Identification

More on Scenario 6

Action: (FHIR Client) Represent the specimen of origin, i.e. microorganism and/or tumor. Search for sequences from microorganism or tumor.
Precondition: Specimen has been created.
Success Criteria: A bundle of sequences from microorganism or tumor are returned.

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)

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