201801 Genomics

FHIR Genomics

Submitting WG/Project/Implementer Group

Clinical Genomics

Justification

Genomic data are of increasing importance to clinical care and secondary analysis. 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.

We will also look to compare current FHIR extension model with a component based model. http://build.fhir.org/ig/HL7/genomics2/index.html

Proposed Track Lead

Kevin Power <kpower@cerner.com> (likely transitioning to Gil Alterovitz <gil.alterovitz@gmail.com>)

See Connectathon_Track_Lead_Responsibilities

Roles

Please include information here regarding how much advance preparation will be required if creating a client and/or server.

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). 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) 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.

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.
2. Retrieve this FamilyMemberHistory instance and get the reference id of Observation instances from extension - Genetic markers, ethnicity, etc.
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

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

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