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===Scenario 1 Register a New Sequence and Observation=== | ===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 --> | + | :Action: (FHIR Client) (FHIR Client) Create a sequence instance and a genetic-profile-based 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: | + | :Precondition: The 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? --> | :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 --> | ||
| Line 42: | Line 42: | ||
===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/ More on Scenario 2] | [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 | + | :Action: (FHIR Client) Search target genetic-profile-based observation with given patient ID. This target observation has an extension - Genomic Source Class (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass |
| + | ) and the value is germline (code: LA6683-2). | ||
:Precondition: Relevant patient and observations have been created | :Precondition: Relevant patient and observations have been created | ||
| − | :Success Criteria: A bundle of genetics observations from germline analysis of that patient are returned. | + | :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 --> | :Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging --> | ||
===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] | [https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.3dy6vkm?usp=sharing/ More on Scenario 3] | ||
| − | :Action: (FHIR Client) | + | :Action: (FHIR Client) Search the genetics diagnostic reports of a given patient. Get the reference id of this patient’s familymemberhistory from extension - Family History (url: http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsFamilyMemberHistory |
| − | :Precondition: Relevant diagnostic | + | ). 2. Retrieve this FamilyMemberHistory instance and get the reference id of Observation instances from extension - Genetic markers, ethnicity, etc. |
| − | :Success Criteria: The | + | (url: http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation). 3. Retrieve the target Observation instance. |
| + | :Precondition: Relevant diagnostic report, observation, family member history have been created. | ||
| + | :Success Criteria: The target Observation instances of the given patient's family member 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 --> | :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=== | ===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] | [https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.4d34og8?usp=sharing/ More on Scenario 4] | ||
| − | :Action: (FHIR Client) | + | :Action: (FHIR Client) Search for all genetic-profile-based observations with a given variant (e.g. rs587778247) |
| − | :Precondition: | + | :Precondition: Observation instances with this variant have been created |
| − | :Success Criteria: A bundle of genetics observations, | + | :Success Criteria: A bundle of genetics observations, where the code value of extension - Variant Id (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariationId |
| + | ) is rs587778247. <!-- 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 --> | :Bonus point: More parameters can be added for searching<!-- Any additional complexity to make the scenario more challenging --> | ||
===Scenario 5 HLA Typing=== | ===Scenario 5 HLA Typing=== | ||
[https://docs.google.com/document/d/1-PULyIwtpCZmsANpafzYA2CKJ1ZMiIysdNnFoGf2-KY/edit#heading=h.17dp8vu?usp=sharing/ More on Scenario 5] | [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 | + | :Action: (FHIR Client) Create an HLA genotyping genetics report. |
:Precondition: This DiagnosticReport-hlaresults instance does not exist in service prior to action. | :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. | :Success Criteria: The HLA genetics report is created correctly on server and in the desired format. | ||
| Line 70: | Line 74: | ||
===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) Search for sequences from human. |
:Precondition: Specimen has been created. | :Precondition: Specimen has been created. | ||
| − | :Success Criteria: A bundle of | + | :Success Criteria: A bundle of sequence instances where the value of species element is Homo sapiens. |
===Scenario 7 Comprehensive Pathology Report=== | ===Scenario 7 Comprehensive Pathology Report=== | ||
Revision as of 16:29, 28 April 2016
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
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. A couple new use cases may be considered as approved by CG workgroup and time permits.
Scenario 1 Register a New Sequence and Observation
- Action: (FHIR Client) (FHIR Client) Create a sequence instance and a genetic-profile-based observation instance to represent genetics data and interpretations (DNA variant, RNA sequence, structural variant, etc).
- Precondition: The 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
- Action: (FHIR Client) Search target genetic-profile-based observation with given patient ID. This target observation has an extension - Genomic Source Class (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass
) and the value is germline (code: LA6683-2).
- 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
- Action: (FHIR Client) Search the genetics diagnostic reports of a given patient. Get the reference id of this patient’s familymemberhistory from extension - Family History (url: http://hl7.org/fhir/StructureDefinition/DiagnosticReport-geneticsFamilyMemberHistory
). 2. Retrieve this FamilyMemberHistory instance and get the reference id of Observation instances from extension - Genetic markers, ethnicity, etc. (url: http://hl7.org/fhir/StructureDefinition/family-member-history-genetics-observation). 3. Retrieve the target Observation instance.
- Precondition: Relevant diagnostic report, observation, family member history have been created.
- Success Criteria: The target Observation instances of the given patient's family member are returned.
- Bonus point: More parameters can be added for searching
Scenario 4 Clinical and Research Data Warehouses
- Action: (FHIR Client) Search for all genetic-profile-based observations with a given variant (e.g. rs587778247)
- Precondition: Observation instances with this variant have been created
- Success Criteria: A bundle of genetics observations, where the code value of extension - Variant Id (url: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariationId
) is rs587778247.
- Bonus point: More parameters can be added for searching
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) Search for sequences from human.
- Precondition: Specimen has been created.
- Success Criteria: A bundle of sequence instances where the value of species element is Homo sapiens.
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)
The supporting TestScripts and corresponding fixtures will be committed to the FHIR SVN repository at: http://gforge.hl7.org/svn/fhir/trunk/connectathons/MontrealMay2016/Connectathon12/Track-08-FHIRGenomics
TestScript Definitions
TBD
