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==Justification==
 
==Justification==
FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-geneitcs 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.
+
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. -->
  
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==Expected participants==
 
==Expected participants==
 
<!-- List of the individuals and/or organizations that have indicated a desire to attend the connectathon and implement this track -->
 
<!-- List of the individuals and/or organizations that have indicated a desire to attend the connectathon and implement this track -->
The number of the participants may be 20-50.
+
Gil Alterovitz, David Kreda, Heming Yao, Bob Milius, Joey Yang, David Hay, Jeremy Warner, Fei Wang, Larry Babb
  
 
==Roles==
 
==Roles==
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Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.
 
Support the receiving and processing of the Sequence resource/genetics profiles operations: create, history, read, search and update.
  
==Steps==
+
== Scenarios ==
 
<!-- What will be the actions performed by participants? -->
 
<!-- What will be the actions performed by participants? -->
Scenario 2/3/4 are taken from use case in the [https://www.hl7.org/documentcenter/public_temp_E815EAB1-1C23-BA17-0C77D5BDAF63744A/wg/clingenomics/docs/V3DAM_CG_CLINSEQ_R1_O1_2013JAN.pdf HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot]
+
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 2: Page 5
 
* Scenario 3: Page 11
 
* Scenario 4: Page 13
 
===Scenario 1 Register a new sequence===
 
  
:Action: (FHIR Client) Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc). <!--Who does what?  (Use the role names listed above when referring to the participants -->
+
===Scenario 1 Register a New Sequence and Observation===
:Precondition: This sequence instance does not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
+
: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 -->
:Success Criteria: Sequence created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? -->
+
: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 -->
 
: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 -->
 
Example for genetics data representation:
 
Example for genetics data representation:
Line 43: Line 40:
 
* [http://genomics-advisor.smartplatforms.org:4000/sequence-genetics-example3.html RNA variant]
 
* [http://genomics-advisor.smartplatforms.org:4000/sequence-genetics-example3.html RNA variant]
 
* [http://genomics-advisor.smartplatforms.org:4000/sequence-genetics-example4.html structural variant]
 
* [http://genomics-advisor.smartplatforms.org:4000/sequence-genetics-example4.html structural variant]
 +
 +
It should be noted that the variantID is not unique per allele observed. Here are three examples for c.181T>G, c.181T>A and n.342T>G on BRCA1 where c.181T>G is equivalent with n.342T>G and  different with c.181T>A.
 +
* [http://genomics-advisor.smartplatforms.org:4000/observation-example-genetics-6-1.xml.html Genetics Observation for BRCA1 c.181T>G]
 +
* [http://genomics-advisor.smartplatforms.org:4000/observation-example-genetics-6-2.xml.html Genetics Observation for BRCA1 c.181T>A]
 +
* [http://genomics-advisor.smartplatforms.org:4000/observation-example-genetics-6-3.xml.html Genetics Observation for BRCA1 n.342T>G]
 
<!-- Provide a description of each task -->
 
<!-- Provide a description of each task -->
  
===Scenario 2 Search genetics observations from germline analysis===
+
===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")
 
:Action: (FHIR Client) Search target observation with patient ID and value for source ("germline")
 
:Precondition: Relevant patient and observations have been created
 
:Precondition: Relevant patient and observations have been created
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[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tuuqdmgk56k3 Example for corresponding API call and search results]
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tuuqdmgk56k3 Example for corresponding API call and search results]
  
===Scenario 3 Family member history===
+
===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.
 
:Action: (FHIR Client) Get the genetics diagnostic reports of patient's family members.
 
:Precondition: Relevant diagnostic reports have been created
 
:Precondition: Relevant diagnostic reports have been created
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[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.djh8kninnwp4 Example for corresponding API call and search results]
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.djh8kninnwp4 Example for corresponding API call and search results]
  
===Scenario 4 Clinical and research data warehouses===
+
===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
 
:Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
 
:Precondition: Relevant observations have been created
 
:Precondition: Relevant observations have been created
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[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tsazjrove5a1 Example for corresponding API call and search results]
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.tsazjrove5a1 Example for corresponding API call and search results]
  
===Scenario 5 Comprehensive genetics report===
+
===Scenario 5 HLA Typing===
:Action: (FHIR Client) Create a comprehensive genetics report for a patient.
+
[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 -->
 +
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-hla-genetics-results-example.xml.html Example codes for HLA report]
 +
 
 +
===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
 
:Precondition: This diagnostic report has never been created
 
:Success Criteria: Sequence created correctly on server and in the desired format.  
 
:Success Criteria: Sequence created correctly on server and in the desired format.  
 
:Bonus point: Extensions can be added.
 
:Bonus point: Extensions can be added.
 
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-genetics-comprehensive-bone-marrow-report.html Example for comprehensive report] and  
 
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-genetics-comprehensive-bone-marrow-report.html Example for comprehensive report] and  
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-genetics-comprehensive-bone-marrow-report.xml.html xml codes for comprehensive report]
+
[http://genomics-advisor.smartplatforms.org:4000/diagnosticreport-genetics-comprehensive-bone-marrow-report.xml.html Example codes for comprehensive report]
  
===Scenario 6 Sequence quality===
+
===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.
 
:Action: (FHIR Client) Get the quality of the sequence under consideration.
 
:Precondition: This sequence instance has been created
 
:Precondition: This sequence instance has been created
Line 83: Line 102:
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.9njcsh48uy26 Example for corresponding API call and search results]
 
[https://docs.google.com/document/d/10qofQPivQTwF7KpD4kSVudr-1LT2sDQCdJLUCbKmP-k/edit#heading=h.9njcsh48uy26 Example for corresponding API call and search results]
  
==Sample data==
 
[http://www.example.com link title]
 
 
==Useful links==
 
==Useful links==
 
*[http://genomics-advisor.smartplatforms.org:8005/ FHIR Genomics sandbox]
 
*[http://genomics-advisor.smartplatforms.org:8005/ FHIR Genomics sandbox]
 
*[http://genomics-advisor.smartplatforms.org:4000/fhir-genomics/fhir-genomics-toc.html FHIR Genomics staging site]
 
*[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
 +
|-
 +
|}
 +
  
 
==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-->
The staging page can be found at:
+
The supporting TestScripts and corresponding fixtures have been committed to the FHIR SVN repository at:
http://genomics-advisor.smartplatforms.org:4000/resourcelist.html
+
http://gforge.hl7.org/svn/fhir/trunk/connectathons/OrlandoJan2016/Connectathon11/Track6-FHIR-Genomics

Latest revision as of 21:35, 22 December 2015

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

Gil Alterovitz, David Kreda, Heming Yao, Bob Milius, Joey Yang, David Hay, Jeremy Warner, Fei Wang, Larry Babb

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

Example for genetics data representation:

It should be noted that the variantID is not unique per allele observed. Here are three examples for c.181T>G, c.181T>A and n.342T>G on BRCA1 where c.181T>G is equivalent with n.342T>G and different with c.181T>A.

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

Example for corresponding API call and search results

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

Example for corresponding API call and search results

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

Example for corresponding API call and search results

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

Example codes for HLA report

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.

Example for comprehensive report and Example codes for comprehensive report

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

Example for corresponding API call and search results

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 have been committed to the FHIR SVN repository at: http://gforge.hl7.org/svn/fhir/trunk/connectathons/OrlandoJan2016/Connectathon11/Track6-FHIR-Genomics