201601 FHIR Genomics
Contents
- 1 FHIR Genomics
- 1.1 Submitting WG/Project/Implementer Group
- 1.2 Justification
- 1.3 Proposed Track Lead
- 1.4 Expected participants
- 1.5 Roles
- 1.6 Steps
- 1.6.1 Scenario 1 Register a New Sequence
- 1.6.2 Scenario 2 Clinical Sequencing - Germline Testing
- 1.6.3 Scenario 3 Family Member History
- 1.6.4 Scenario 4 Clinical and Research Data Warehouses
- 1.6.5 Scenario 5 HLA Typing
- 1.6.6 Scenario 6 Specimen Identification
- 1.6.7 Scenario 7 Comprehensive Genetics Report
- 1.6.8 Scenario 8 Sequence quality
- 1.7 Useful links
- 1.8 Sample data
- 1.9 TestScript(s)
FHIR Genomics
Submitting WG/Project/Implementer Group
Justification
FHIR Genomics consists of the Sequence resource and several profiles built on top of existing FHIR resources (DiagnosticReport-genetics profile, DiagnosticOrder-genetics profile, Observation-geneitcs 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
Gil Alterovitz, David Kreda, Heming Yao, Bob Milnus, Joey Yang, David Hay, Jeremy Warner
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.
Steps
Scenarios are taken from use case in the HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot
Scenario 1 Register a New Sequence
- Action: (FHIR Client) Create a sequence instance to represent genetics data (DNA variant, RNA sequence, structural variant, etc).
- Precondition: This sequence instance does not exist in service prior to action.
- Success Criteria: Sequence 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
Example for genetics data representation:
Scenario 2 Clinical Sequencing - Germline Testing
- Action: (FHIR Client) Search target observation with patient ID and value for source ("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
Example for corresponding API call and search results
Scenario 3 Family Member History
- Action: (FHIR Client) Get the genetics diagnostic reports of patient's family members.
- Precondition: Relevant diagnostic reports have been created
- Success Criteria: The genetics diagnostic reports of patient's family members are returned
- Bonus point: More parameters can be added for searching
Example for corresponding API call and search results
Scenario 4 Clinical and Research Data Warehouses
- Action: (FHIR Client) Get all genetic-profile-based observations of patients with the variant c.181T>G
- Precondition: Relevant observations have been created
- Success Criteria: A bundle of genetics observations, whose extesion 'sequence' referring to sequence instance of variant c.181T>G, are returned.
- Bonus point: More parameters can be added for searching
Example for corresponding API call and search results
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) Searching for sequences from microorganism
- Precondition: Sequences have been created
- Success Criteria: A bundle of sequences from microorganism are returned.
Scenario 7 Comprehensive Genetics Report
A comprehensive report contains all information gathered from various method (e.g. morphology, IHC, flow cytometry, cytogenetics, FISH, and NGS). The DiagnosticReport-genetics profile has the capability to support a plenty of results with simple or complex genetics observations.
- Action: (FHIR Client) Create a comprehensive genetics report 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.
Example for comprehensive report and Example codes for comprehensive report
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
Example for corresponding API call and search results
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 |