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(Adding sync for genes stream under the CG track per the instruction of Bob Freimuth and the FMG)
m (Absorbing extra text from post-deadline edit into previously approved scenario 1 where it was intended to be scoped.)
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:'''Precondition''': The instances do not exist in server prior to action. <!-- What setup is required prior to executing this step? -->
 
:'''Precondition''': The instances do not exist in server prior to action. <!-- What setup is required prior to executing this step? -->
 
:'''Success Criteria''': Instances created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? -->
 
:'''Success Criteria''': Instances created correctly on server and in the desired format. <!-- How will the participants know if the test was successful? -->
:'''Bonus point''': New profiles from the IG can be built on top of the MolecularSequence resource for complex representation<!-- Any additional complexity to make the scenario more challenging -->
+
:'''Bonus point''': GenomicsReport resources tailored to individual use cases can be sent and received.<!-- Any additional complexity to make the scenario more challenging -->
 
<!-- Provide a description of each task -->
 
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[[File:PharmacogenomicsCDS2.png|600px]]
 
[[File:PharmacogenomicsCDS2.png|600px]]
 
===Scenario 10 Sync for Genes Phase 2 Pilot Sites===
 
To learn what types of local modifications the Sync for Genes phase 2 pilot sites require to enable exchange of FHIR resources and uncover gaps in the specification, which will help to advance the FHIR standard by providing actionable feedback to the HL7 clinical genomics workgroup. The pilot sites will demonstrate the successful exchange of a pilot site-specific FHIR Genomics Diagnostic Report (GDR) via a FHIR server preconfigured with the Genomics resource profiles and updated with any findings from work leading up to the Connectathon. Outputs from working with the pilot sites to prepare for the Connectathon, including learning what types of local modifications the pilot sites require to enable exchange of FHIR resources and uncovering gaps in the specification, will help to advance the FHIR standard by providing actionable feedback to the HL7 clinical genomics workgroup.
 
 
:'''Action''': Client (pilot site) exchanges a pilot-specific FHIR GDR with a receiver via a FHIR server preconfigured with the Genomics resource profiles and updated with any findings from pilot work.
 
 
:'''Precondition''': Pilot-specific FHIR GDR and preconfigured FHIR server
 
 
:'''Success Criteria''': Receiver and FHIR server accept the GDR
 
 
:'''Bonus point''': Successful mapping and exchange of an additional GDR that hasn’t been pre-mapped to FHIR
 
 
  
 
==TestScript(s)==
 
==TestScript(s)==

Revision as of 21:38, 12 November 2018


Clinical Genomics Track

Zulip Chat

The Zulip Chat will be used to coordinate among participants during the connectathon:

Zulip Chat


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, Lloyd Mckenzie, Bret Heale, Bob Millius, Joel Schneider, Bob Dolin, ...

Roles

FHIR Client

Support the sending of the MolecularSequence resource and genetics profiles operations: create, history, read, search and update.

FHIR Server

Support the receiving and processing of the MolecularSequence 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, July 2018 Informative Publication. See links below each scenario for relevant DAM excerpts. A couple new use cases may be considered as approved by the CG workgroup and time permits.

Scenario 1 Register a New MolecularSequence, DescribedVariant, and GenomicsReport

Action: (FHIR Client) (FHIR Client) Create 1 or all of: a MolecularSequence instance, a (DescribedVariant-profiled) Observation instance, and/or a (GenomicsReport-profiled) DiagnosticReport instance to represent genetics data and interpretations (DNA variant, RNA sequence, structural variant, etc).
Precondition: The instances do not exist in server prior to action.
Success Criteria: Instances created correctly on server and in the desired format.
Bonus point: GenomicsReport resources tailored to individual use cases can be sent and received.

Scenario 2 Clinical Sequencing - Germline Testing

More on Scenario 2

Action: (FHIR Client) Search target genetic-profile-based observation with given patient ID. This target observation has a component - Genomic Source Class (code={"coding":[{"system":"http://loinc.org","code":"48002-0"}]}, value="LA6683-2") corresponding to 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

Scenario 3 Family Member History

More on Scenario 3

Action: (FHIR Client) 1. Search the genomics reports of a given patient. Get the reference id of this patient’s familymemberhistory from the supportingInfo extension - Family History (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/dr-supportingInfo). 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

More on Scenario 4

Action: (FHIR Client) Search for all observations with a given described variant (e.g. rs587778247)
Precondition: Observation instances with this variant have been created
Success Criteria: A bundle of describedVariant observations, where the code value of component - dbSNP Id ({"coding":[{"system":"http://loinc.org","code":"81255-2"}]} is rs587778247.
Bonus point: More parameters can be added for searching

Scenario 5 HLA Typing

More on Scenario 5

Action: (FHIR Client) Create an HLA genotyping genomics report.
Precondition: This genomicsReport instance does not exist in service prior to action.
Success Criteria: The genomics report carrying HLA information is created correctly on server and in the desired format.
Bonus point: Extensions can be added

Scenario 6 Species Identification

More on Scenario 6

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 genomicsReport profile has the capability to support results with simple or complex genetics observations.
Precondition: This genomics report has never been created
Success Criteria: Report 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

Scenario 9 PGx CDS

This scenario demonstrates an implementation of CPIC Pharmacogenomic Guidelines [1] based on FHIR, CDS Hooks [2], and genomics results formatted per our latest HL7 FHIR Clinical Genomics Reporting guide [3]

Action: In this scenario, a medication order arises in the EHR (which is also a CDS Hooks client), triggering a notification to a PGx CDS Service (which is also a CDS Hooks server). The "medication-prescribe" hook also provides the PGX CDS Service with a FHIR Medication resource that includes an RxNorm code for the ordered drug. 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. The PGx CDS Service returns a CDS hooks “suggestion card” back to the EHR, with appropriate recommendations.
Precondition: Genomic observation(s) are available for some patients.
Success Criteria: Retrieve relevant observations (variants, haplotype, genotype, etc) on a pharmacogene where they exist.
Bonus point: Correctly identify that there are no observations for the gene in question.

A swim-lane overview of the scenario is here ('GACS' is a Genomic Archiving and Communication System, used to store genomic test results):

PharmacogenomicsCDS2.png

TestScript(s)

The supporting TestScripts and corresponding fixtures have been committed to the FHIR documents Github repository at: https://github.com/FHIR/documents/tree/master/connectathons/NewOrleansJan2018/Connectathon17/Genomics


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