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==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. --> | ||
| 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 | + | Gil Alterovitz, David Kreda, Heming Yao, Bob Milius, Joey Yang, David Hay, Jeremy Warner, Fei Wang, Larry Babb |
==Roles== | ==Roles== | ||
| Line 27: | Line 27: | ||
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. | ||
| − | == | + | == Scenarios == |
<!-- What will be the actions performed by participants? --> | <!-- What will be the actions performed by participants? --> | ||
| − | Scenarios are taken from use | + | 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=== | + | ===Scenario 1 Register a New Sequence and Observation=== |
| − | :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 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 | + | :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 created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? --> | + | :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 40: | 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 --> | ||
| Line 76: | Line 81: | ||
===Scenario 6 Specimen Identification=== | ===Scenario 6 Specimen Identification=== | ||
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.tyjcwt?usp=sharing/ More on Scenario 6] | [https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.tyjcwt?usp=sharing/ More on Scenario 6] | ||
| − | :Action: (FHIR Client) | + | :Action: (FHIR Client) Represent the specimen of origin, i.e. microorganism and/or tumor. Search for sequences from microorganism or tumor. |
| − | :Precondition: | + | :Precondition: Specimen has been created. |
| − | :Success Criteria: A bundle of sequences from microorganism are returned. | + | :Success Criteria: A bundle of sequences from microorganism or tumor are returned. |
| − | ===Scenario 7 Comprehensive | + | ===Scenario 7 Comprehensive Pathology Report=== |
| − | A comprehensive 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 | + | :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. | ||
| Line 90: | Line 95: | ||
===Scenario 8 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 233: | Line 239: | ||
|- | |- | ||
|} | |} | ||
| + | |||
==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 | + | The supporting TestScripts and corresponding fixtures have been committed to the FHIR SVN repository at: |
| − | http:// | + | http://gforge.hl7.org/svn/fhir/trunk/connectathons/OrlandoJan2016/Connectathon11/Track6-FHIR-Genomics |
Latest revision as of 21:35, 22 December 2015
Contents
- 1 FHIR Genomics
- 1.1 Submitting WG/Project/Implementer Group
- 1.2 Justification
- 1.3 Proposed Track Lead
- 1.4 Expected participants
- 1.5 Roles
- 1.6 Scenarios
- 1.6.1 Scenario 1 Register a New Sequence and Observation
- 1.6.2 Scenario 2 Clinical Sequencing - Germline Testing
- 1.6.3 Scenario 3 Family Member History
- 1.6.4 Scenario 4 Clinical and Research Data Warehouses
- 1.6.5 Scenario 5 HLA Typing
- 1.6.6 Scenario 6 Specimen Identification
- 1.6.7 Scenario 7 Comprehensive Pathology Report
- 1.6.8 Scenario 8 Sequence quality
- 1.7 Useful links
- 1.8 Sample data
- 1.9 TestScript(s)
FHIR Genomics
Submitting WG/Project/Implementer Group
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.
- Genetics Observation for BRCA1 c.181T>G
- Genetics Observation for BRCA1 c.181T>A
- Genetics Observation for BRCA1 n.342T>G
Scenario 2 Clinical Sequencing - Germline Testing
- 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 HLA Typing
- 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
- 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
