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:Bonus point: More parameters can be added for searching | :Bonus point: More parameters can be added for searching | ||
| + | :'''Action''': [1] (EHR) Manually enter an order for "Imuran 50mg 1 tablet twice a day by mouth" into order entry system. This triggers a “medication-prescribe” CDS hook with a hook context of MedicationOrder which includes RxNorm code 197388 for azathioprine 50mg oral tablet; [2] (PGx CDS Service) Having been triggered by the “medication-prescribe” CDS hook, the PGx CDS Service now executes a decision support rule that [1] determines if the ordered drug has a known gene interaction; [2] determines, where there is a known drug-gene interaction, whether or not the patient has genetic test results on file; [3] determines, where there are genetic test results on file, if the patient has an interacting genotype; [4] determines, where there are not genetic test results on file, if the patient needs pre-testing. PGx CDS Service returns a CDS hooks “information card” back to the EHR, with appropriate recommendations. | ||
| − | + | :'''Precondition''': Genomic observation(s) are available for some patients. | |
| − | |||
| − | + | :'''Success Criteria''': Retrieve relevant observations (on TPMT gene, on allelic state) where they exist. | |
| − | + | :'''Bonus point''': Search OMIC data store for different potential representations.==TestScript(s)== | |
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| − | ==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. | ||
These should be committed to SVN under trunk/connectathons/[connectathon] | These should be committed to SVN under trunk/connectathons/[connectathon] | ||
Revision as of 20:01, 2 November 2018
Clinical Genomics Track
Zulip Chat
The Zulip Chat will be used to coordinate among participants during the connectathon:
Submitting WG/Project/Implementer Group
Justification
Genomic data are of increasing importance to clinical care and secondary analysis. After initial Feedback from the first ballot of the Clinical Genomics Implementation Guide, considerable updates have been made, and the recently balloted IG and profiles should be tested in the Connectathon for more feedback and trial use.
Proposed Track Lead
Gil Alterovitz, Patrick Werner
Expected participants
Gil Alterovitz, James Jones, Kevin Power ...
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) 1. 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 Species Identification
- Action: (FHIR Client) Search for sequences from human (Homo sapiens).
- Precondition: Sequence(s) have been created where the species is defined as human (Homo sapiens).
- Success Criteria: A bundle of Sequence instances where the value of the species element is Homo sapiens.
Scenario 7 Comprehensive Pathology Report
- Action: (FHIR Client) Create a comprehensive pathology report which includes genetic information for a patient. 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.
- 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
- Action: (FHIR Client) Get the quality of the sequence under consideration. 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.
- Precondition: This sequence instance has been created
- Success Criteria: Target sequence instance is returned.
- Bonus point: More parameters can be added for searching
- Action: [1] (EHR) Manually enter an order for "Imuran 50mg 1 tablet twice a day by mouth" into order entry system. This triggers a “medication-prescribe” CDS hook with a hook context of MedicationOrder which includes RxNorm code 197388 for azathioprine 50mg oral tablet; [2] (PGx CDS Service) Having been triggered by the “medication-prescribe” CDS hook, the PGx CDS Service now executes a decision support rule that [1] determines if the ordered drug has a known gene interaction; [2] determines, where there is a known drug-gene interaction, whether or not the patient has genetic test results on file; [3] determines, where there are genetic test results on file, if the patient has an interacting genotype; [4] determines, where there are not genetic test results on file, if the patient needs pre-testing. PGx CDS Service returns a CDS hooks “information card” back to the EHR, with appropriate recommendations.
- Precondition: Genomic observation(s) are available for some patients.
- Success Criteria: Retrieve relevant observations (on TPMT gene, on allelic state) where they exist.
- Bonus point: Search OMIC data store for different potential representations.==TestScript(s)==
