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 -->
�Gil Alterovitz, David Kreda, Heming Yao, Bob Milnus, Joey Yang, David Hay  
+
Gil Alterovitz, David Kreda, Heming Yao, Bob Milnus, Joey Yang, David Hay  
  
 
==Roles==
 
==Roles==
Line 31: Line 31:
 
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]
 
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 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 44: Line 43:
  
 
===Scenario 2 Clinical Sequencing - Germline Testing===
 
===Scenario 2 Clinical Sequencing - Germline Testing===
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.gjdgxs?usp=sharing/ Refer to Here]
+
[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
Line 51: Line 50:
 
[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
Line 58: Line 58:
 
[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
Line 66: Line 66:
 
[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===
 +
[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) Searching for sequences from microorganism
 +
:Precondition: Sequences have been created
 +
:Success Criteria: A bundle of sequences from microorganism are returned.
  
 +
===Scenario 7 Comprehensive Genetics Report===
 +
A comprehensive report contains all information gathered from various method (e.g. morphology, IHC, flow cytometry, cytogenetics, FISH, and NGS). The DiagnosticReport-genetics profile have the capability to support a plenty of results with simple or complex genetics observations.
 
: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 73: Line 87:
 
: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===
 
: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

Revision as of 16:39, 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

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

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) Searching for sequences from microorganism
Precondition: Sequences have been created
Success Criteria: A bundle of sequences from microorganism are returned.

Scenario 7 Comprehensive Genetics Report

A comprehensive report contains all information gathered from various method (e.g. morphology, IHC, flow cytometry, cytogenetics, FISH, and NGS). The DiagnosticReport-genetics profile have the capability to support a plenty of results with simple or complex genetics observations.

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 Example codes for comprehensive report

Scenario 8 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