Sub category of FHIR Connectathon Track Proposals for the current connectathon: May 2017 Connectathon 15

Proposals due by : March 21, 2017

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Use this page to submit proposals for tracks for inclusion in the May 6-7, 2017 connectathon. These proposals will be reviewed and prioritized by the FMG as per the FHIR_Connectathon_Track_Process.

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FHIR Genomics

Submitting WG/Project/Implementer Group

CG

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

Report

Report

Expected participants

Gil Alterovitz - HMS/BCH

Bob Milius - NMDP

Martin Maiers - NMDP

Cat Lasome - iON Informatics

Grant Wood - Intermountain Healthcare

Joel Schneider - NMDP

Shennon Lu - National Library of Medicine

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

More on Scenario 2

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

More on Scenario 3

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

More on Scenario 4

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

More on Scenario 5

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

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

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

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/BaltimoreSep2016/Connectathon13/FHIRGenomics