This wiki has undergone a migration to Confluence found Here

Difference between revisions of "201601 FHIR Genomics"

From HL7Wiki
Jump to navigation Jump to search
Line 15: Line 15:
 
==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 Milnus, Joey Yang, David Hay
  
 
==Roles==
 
==Roles==
Line 29: Line 29:
 
==Steps==
 
==Steps==
 
<!-- 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 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]
* Scenario 2: Page 5
+
 
* Scenario 3: Page 11
 
* Scenario 4: Page 13
 
 
===Scenario 1 Register a new sequence===
 
===Scenario 1 Register a new sequence===
 
+
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.gjdgxs?usp=sharing/ Refer to Here]
 
: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 -->
 
: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 -->
 
:Precondition: This sequence instance does not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
 
:Precondition: This sequence instance does not exist in service prior to action. <!-- What setup is required prior to executing this step? -->
Line 45: Line 43:
 
<!-- 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/ Refer to Here]
 
: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
Line 69: Line 67:
  
 
===Scenario 5 Comprehensive genetics report===
 
===Scenario 5 Comprehensive genetics report===
 +
 
:Action: (FHIR Client) Create a comprehensive genetics report for a patient.
 
:Action: (FHIR Client) Create a comprehensive genetics report for a patient.
 
:Precondition: This diagnostic report has never been created
 
:Precondition: This diagnostic report has never been created
Line 87: Line 86:
 
*[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]
  
==TestScript(s)==
 
<!-- 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:
 
http://genomics-advisor.smartplatforms.org:4000/resourcelist.html
 
  
 
==Sample data==
 
==Sample data==
Line 224: Line 219:
 
|-
 
|-
 
|}
 
|}
 +
 +
==TestScript(s)==
 +
<!-- 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:
 +
http://genomics-advisor.smartplatforms.org:4000/resourcelist.html

Revision as of 15:47, 18 November 2015

FHIR Genomics

Submitting WG/Project/Implementer Group

CG

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.

Proposed Track Lead

Gil Alterovitz

Expected participants

�Gil Alterovitz, David Kreda, Heming Yao, Bob Milnus, Joey Yang, David Hay

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.

Steps

Scenarios are taken from use case in the HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot

Scenario 1 Register a new sequence

Refer to Here

Action: (FHIR Client) Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc).
Precondition: This sequence instance does not exist in service prior to action.
Success Criteria: Sequence 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:

Scenario 2 Clinical Sequencing - Germline Testing

Refer to Here

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

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

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 Comprehensive genetics report

Action: (FHIR Client) Create a comprehensive genetics report 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 xml codes for comprehensive report

Scenario 6 Sequence quality

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 staging page can be found at: http://genomics-advisor.smartplatforms.org:4000/resourcelist.html