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||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 | ||
||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 | ||subject | ||
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||Positive | ||Positive | ||
||Positive | ||Positive | ||
| − | || | + | ||Positive |
|- | |- | ||
||GeneticsSequence | ||GeneticsSequence | ||
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||(refer to) Sequence #2 | ||(refer to) Sequence #2 | ||
||None | ||None | ||
| + | |} | ||
| + | |||
| + | ===DiagnosticReport-genetics=== | ||
| + | |||
| + | {|border="1" cellpadding="2" cellspacing="0" | ||
| + | | width="30%" colspan="1" align="left" style="background:#f0f0f0;"|'''Element''' | ||
| + | | width="70%" colspan="1" align="left" style="background:#f0f0f0;"|'''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 | ||
| + | |- | ||
|} | |} | ||
Revision as of 23:07, 17 November 2015
Contents
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
The number of the participants may be 20-50.
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
Scenario 2/3/4 are taken from use case in the HL7 Domain Analysis Model (DAM): Clinical Genomics, Release 1, September 2014 Informative Ballot
- Scenario 2: Page 5
- Scenario 3: Page 11
- Scenario 4: Page 13
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 Search genetics observations from germline analysis
- 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 Comprehensive genetics report
- 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 xml codes for comprehensive report
Scenario 6 Sequence quality
- 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
TestScript(s)
The staging page can be found at: http://genomics-advisor.smartplatforms.org:4000/resourcelist.html
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 | A. Langeveld |
| 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 |
