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SMART-on-FHIR Genomics: Enabling Precision Medicine by Bridging Clinical and
Genomic Information
FHIR® and the FHIR Icon are trademarks of HL7, Inc. (http://hl7.org)
Presented by:
Gil AlterovitzAssistant Professor, Harvard Medical School
and Computational Health Informatics Program, Boston Children's Hospital
Today’s Presentation
The Problem: How to enable Precision Medicine at point of care.
Clinical Genomic Apps for EMRsPrecision Cancer Medicine
SMART on FHIR/FHIR/GA4GHPrecision Medicine
SMART on FHIR 2.1+
Use Cases
2Clinical Informatics webinar series. Nov. 05, 2015
Precision Cancer Medicine (PCM) AppWarner & Alterovitz
DB (Diabetes Bear) EMR App Alterovitz & Yang
Genomics Advisor AppAlterovitz & Zhang
5
GA4GH
Electronic Medical
Record (Clinical
and Genomic)
Genomic
Datasets
SMART on FHIR
Genomic
Sequence/Lab
Tests
SMART on FHIR
6
SMART
Server
SMART+FHIR+G
A4GH
Genomics Advisor App
7
Problem
EMR apps only include clinical information, but genomics can add complementary information about risk of disease, drug susceptibility, and related conditions
Solution
Create a module that can be integrated into disease-specific apps.
Features
Present relative risks of diseases based on patient's’ genotype.
Clinical Informatics webinar series. Nov. 05, 2015
Clinical Informatics webinar series. Nov. 05, 2015 8
SMART Clinical
server
SMART Genomic
server
SMART on FHIR
Genomics
(Ga4gh)
Genomics Advisor
Get /Patient
Get /Medication
Get /Observation
…
Clinical
data
Get /Sequence
Get /DiagnosticReport?
profile=genetics
Get /callSet
…
Genetic
data
Call variantSet,
readGroupSet
Reads,
Variant info
Genomics Advisor Integrated with Ga4gh and 1KGP
9Clinical Informatics webinar series. Nov. 05, 2015
Precision Cancer Medicine (PCM)
Problem
Many rare somatic mutations needs to be taken into account for cancer prognostics
Solution
iPad app for clinicians to compare patient variations with those of population on site.
Features
View variants of patient and population PlannedBayesian updates on statsIn-app comparison of patient-based prognostics for different drugs
10
Precision Cancer MedicinePCM App
Clinical Informatics webinar series. Nov. 05, 2015
11
GA4GH
SMART
FHIR
Clinical Informatics webinar series. Nov. 05, 2015
12
GA4GH
SMART
FHIR
Target: Developers,
Clinicians/patients as end-
users.
Use: Access and search
patient clinical, genomic
records, and genomics
datasets/repositories.
Clinical Informatics webinar series. Nov. 05, 2015
13
GA4GH
SMART
FHIR
Target: Clinicians, Hospital
IT Professionals
Use: Standard for access
and search of patient
clinical and genomic
records
Clinical Informatics webinar series. Nov. 05, 2015
14
GA4GH
SMART
FHIR
Target: Genomic
researchers, others.
Use: Standard to share
genomic data for
research/development.
Clinical Informatics webinar series. Nov. 05, 2015
Details
15
GA4GH
SMART
FHIR
- Genomics integrated
directly into clinical
model.
- Genomics as a profile
on top of Observation
resource
- Sequence and non-
sequence based
genomic tests
- Genomics adopted in
FHIR DSTU 2.0
- Uses current standards
Clinical Informatics webinar series. Nov. 05, 2015
16
GA4GH
SMART
FHIR
- FHIR Profiles
- Alignment (e.g. MU 2.0)
- Patient record scope/
authentication
- Single sign-on layer
- UI Integration Layer
(Launch within EHR)
- Integrates GA4GH and
FHIR Genomics
- Provides genomic data
shadowing/constraints/ma
ppings
Details
Clinical Informatics webinar series. Nov. 05, 2015
FHIR Genomics Development
17
Sequence+
ObservationResources
ObservationResource
DSTU1 DSTU2 DSTU2.1+ Normative
Jan 2014 Sep 2015 Dec 2015? 2016?
Clinical Informatics webinar series. Nov. 05, 2015
18
FHIR Genomics+
SMART on FHIRSep 2015
Recommendation Actions to Advance
FHIR could be included as an emerging standard4, especially for transport of data. Argonaut may provide opportunities to advance. Sample uses of FHIR: authorization; genetics, family health history, build on current work on SMART on FHIR Genomics1
Apply accelerators (e.g., S&I Initiative, pilot project, policy guidance) to existing standards by ONC
Recommendation Actions to Advance
2016 PMI S&I: Additional ONC investment in pilots of FHIR for PMIresearch/individual data donation use case
Apply accelerators (e.g., S&I Initiative, pilot project, policy guidance) to existing standards by ONC
Clinical Informatics webinar series. Nov. 05, 2015
Preparing For Precision Medicine
19
High-dimensionalDifferent format
Different ways to interpretNew data in the future Representation
StorageAnalysis
?
Omics Data
Clinical Informatics webinar series. Nov. 05, 2015
20
Observation-genetics:Subject, performer, device,
specimen,..
Genetics and sequence
pointer
Clinical data
Genetics
data
Diagnostic
Report
Subject, …
Order
result
result
result
Standard Genetics Profile:
AssessedCondition,familyMemberHistory
DiagnosticOrder-
genetics:Subject, orderer
ItemsClinical data
Genetics
data
SMART on FHIR Genomics and GA4GH
21
Sequence
Observation: clinic info, knowledge-based analysis, variant
Atomic result
Diagnostic Reportresultresultresult
Variant info in ga4gh
(coordinate, name, id)
Other info not in ga4gh
(species, source, etc)
Read info
Ga4gh read group
Genetic Profile: Assessed Condition
Family Member History
SMART on FHIR Genomics and GA4GH
Ga4gh variant info
SMART on FHIR
Genomics
Ga4ghClinical Informatics webinar series. Nov. 05, 2015
22
Observation 1
Clinic info 1
Sequence 1
Observation 2 Observation 3
Clinic info 2
Sequence 2
Clinic info 3
Sequence 3
Clinical context 1: condition, patient,…
DiagnosticReport 1
Clinical Informatics webinar series. Nov. 05, 2015
Integrated into Clinical
Data Model and Workflow
Single variant and key elements or a sequence
Cross references to GA4GH
Extensible to future omics
Sequence Resource
23Clinical Informatics webinar series. Nov. 05, 2015
Sequence Resource
24
GA4GH API:https://www.googleapis.com/genomics/v1beta2
http://grch37.rest.ensembl.org/ga4gh , etc.
GA4GH full sequence links
callSet1 sample
Variant info
Variant callgenotype determination for 1 variant
Read groupcollections of reads produced by a sequencer
Search Reads:Read group set ID,start,end
Clinical Informatics webinar series. Nov. 05, 2015
25
Observation Resource
Examples for component.code
Clinical Informatics webinar series. Nov. 05, 2015
26
Example for Observation resource - Somatic mutation
Clinical Informatics webinar series. Nov. 05, 2015
Example for Sequence resource - EGFR mutation
27Clinical Informatics webinar series. Nov. 05, 2015
28
Domain Analysis Model (DAM) Use Cases, Release 2
1. Specimen Identification2. Clinical Sequencing (Germline)3. Cancer Profiling (Somatic)4. CDS (Family History and Drug Dosage Calculator)5. Public Health Reporting6. Clinical and Research Data Warehouses
Clinical Informatics webinar series. Nov. 05, 2015
Specimen Identification
29
Explore antibacterial drug resistance over time (non-patient DNA)
Get references to all DNA sequences of tuberculosis bacteria(SNOMED code: 56717001) from given patient:
GET /Observation?value-reference.species=http://snomed.info/sct|56717001&subject=123
DAM Case 1
Clinical Informatics webinar series. Nov. 05, 2015
30
DAM Case 1
Search results:<Bundle>
<entry><resource>
<Observation><id value=“o1”/><subject>
<reference value=“123”/></subject><valueReference>
<reference value=“s1”/></valueReference>…
</Observation></resource>
</entry>…
</Bundle>
<Sequence><id value="s1"/>...<species>
<coding><system value="http://snomed.info/sct"/><code value="56717007"/><display value="tuberculosis bacteria"/>
</coding></species>
</Sequence>
Clinical Informatics webinar series. Nov. 05, 2015
31
Family History – Genetics – Search Results
Clinical Informatics webinar series. Nov. 05, 2015
32
<Observation><status value="final"/><code><coding><system value="http://loinc.org"/><code value="55233-1"/><display value="Genetic analysis master panel"/>
</coding></code><subject><reference value="Patient/example"/><display value="Peter James Chalmers(MRN: 12345)"/>
</subject><issued value="2015-05-26T15:30:10+01:00"/><method>
<coding><system value="http://www.ncbi.nlm.nih.gov/gtr/"/><code value="GTR000521311.1"/><display value="BRACAnalysis CDx Offered by Myriad Genetic Laboratories, Inc"/>
</coding></method>
</Observation>
Family History – Genetics – Search Results
Clinical Informatics webinar series. Nov. 05, 2015
33
<DiagnosticReport><id value=“dl”><subject value=“mrn12345”><extension
url=http://hl7.org/fhir/StructureDefinition/geneticsFamilyMemberHistory/>
<valueReference><reference value=“f1”/>
</valueReference></extension>…
</DiagnosticReport>
<FamilyMemberHistory><id value=“fl”><relationship value=“mother”><extension url=“http://hl7.org/fhir/StructureDefinition/family-
member-history-genetics”/><valueReference>
<reference value=“d2”/></valueReference>
</extension>…
</FamilyMemberHistory>
<DiagnosticReport><id value=“d2”><subject value=“mrn23456”><result value=“111”>…
</DiagnosticReport>
Genetic test Report forPeter James Chalmers (MRN: 12345)
Genetic test Report for the mother ofPeter James Chalmers (MRN: 12345)
Family History – Genetics – Search Results
Clinical Informatics webinar series. Nov. 05, 2015
Desiderata For Improved Clinical-Genomics Apps
FHIR for clinical ‘omics
Concise & consistency over diverse data resources
Focus on relevance to clinical-genomic apps
Leverages GA4GH research models for translation
34Clinical Informatics webinar series. Nov. 05, 2015
FHIR Genomics Connectathon
• January Orlando
• FHIR Genomics use cases
• Experts meet with teams beforehand or available in-person/video conferencing/skype at event.
• Develop apps and put completed ones in gallery
35Clinical Informatics webinar series. Nov. 05, 2015
Ver. 2.1 Staging URLs
Sequence Resourcehttp://genomics-advisor.smartplatforms.org:4000/sequence.html
Standard Profile for Geneticshttp://genomics-advisor.smartplatforms.org:4000/observation-genetics-cg-
prf.html
Standard Profile for Family Member History Geneticshttp://genomics-advisor.smartplatforms.org:4000/family-member-history-
genetics.html
36Clinical Informatics webinar series. Nov. 05, 2015
Other Links
FHIR Clinical Genomics (DSTU 2)http://hl7.org/fhir/observation-genetics-cg-prf-1a.html
GA4GH Clinical Working Grouphttps://genomicsandhealth.org/working-groups/clinical-working-group
JAMIA Paper on SMART Genomics/FHIR DSTU 2.0http://jamia.oxfordjournals.org/content/early/2015/07/21/jamia.ocv045.lon
g
SMART Genomics (direct link)http://projects.iq.harvard.edu/smartgenomics/home
SMART Platformhttp://smarthealthit.org/
37Clinical Informatics webinar series. Nov. 05, 2015
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