Advancing sharing of phenotypic data through - FHIR Year 1 Final Briefing December 17th, 2020 - HL7 ...
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Advancing sharing of phenotypic data through Year 1 Final Briefing FHIR December 17th, 2020
Our Team
Principal Investigators
Bob Fre imuth - Mayo Clinic
Moni Munoz-Torre s (PM) - OSU
Melissa Haendel - OHSU
Shahim Essaid - OHSU
Pe te r Robinson - Jackson Lab
Yiqing Zhao - Mayo Clinic
Matt Brush - OHSU
More GA4GH Contributors
Allison He ath - CHOP (KF)
Jules Jacobsen -
Ge nomics England/QMUL
Natasha Singh - CHOP (KF)
Harold Solbrig -
Johns Hopkins Unive rsity
Ale jandro Me tke Jime ne z
- CSIRO (AU)
Lindsay Smith - GA4GH
Outline
● Proje ct Obje ctive & Scope
● GA4GH Phe nopacke ts Sche ma Update
● Ye ar 1: Major De live rable s
○ Domain Analysis Docume nt
○ Core FHIR Imple me ntation Guide
○ Re port of Pilot Te st Findings
● Ye ar 2: Planne d Scope and De live rable s
Project Objective
Increase the availability of high-quality standardized phenotypic information for
genomic research and genomic medicine by advancing sharing of phenotypic
information using the Fast Healthcare Interoperability Resources® (FHIR®) standard
● Re pre se ntation of phe notypic information for clinical ge ne tics in FHIR
○ Base d on the Phe nopacke ts standard
○ Supporting e xchange into/out of EHRs and othe r clinical syste ms
● Use cases we re de ve lope d so that the y de scribe phe notypic information
ne e de d for clinical ge ne tics spe cifically and translational re se arch ge ne rally.
● This work is focuse d on cre ating a FHIR core Imple me ntation Guide and
provide s fe e dback to both the FHIR and GA4GH communitie s.
Scope
Approve d on 20 20 -0 7-0 8
1. Coordinate with the appropriate HL7 FHIR work group(s) and develop aFHIR Implementation
Guide (IG) base d on the data mode le d in the GA4GH Phe nopacke ts sche ma
2. Ide ntify se ts of translational re se arch partne rs to demonstrate data exchange using FHIR
application programing inte rface s (APIs) for se le cte d use case s
3. De ve lop Driver Use Cases to inform IG de ve lopme nt and for pilot-te sting
4. Support pilot -testing
5. Compile pilot test results into a re port
6. Provide feedback to HL7 to re vise re le vant FHIR re source s, profile s, and/or IGs
7. Provide feedback to GA4GH on Phe nopacke ts sche ma and application to use case s
8. Disseminate deliverables and obtain fe e dback for future de ve lopme nt.
Phenopackets Schema Update
Primary Entities Referenced Entities (e.g. in other Features for next release v2.0
● Individual standards/EHR locations) ●Te mporality standardization
● Biosample ● Ge nomics (variants, WES/WGS) ○ E.g., additional fie lds for
● Phe notype ● Pe digre e COVID-19 re se arch
○ Onse t ● Fe ature s for cance r (Phe nopacke ts
○ Se ve rity Cance r Task Force ; GA4GH)
● Cohort ○ Tre atme nt
● Family ○ Me dical actions
● Inte rpre tation ● Incorporation of VRS hash
phenopackets.org
ga4gh.org
Use Cases
Kids First Data Resource Center: Phe notype -Drive n Mole cular
Pe diatric Cance rs and Structural Ge ne tic Diagnostics
Birth De fe cts
An infant with cardiac defects (abnormal atrial septum and Communicate relevant clinical information (a Phenopacket)
pulmonary valve) was diagnosed with an atrial septal defect. from the provider’s office to a laboratory and medical
As part of the diagnostic process, genomic testing was geneticist when an exome analysis is ordered, to aid in the
performed. Compare VUS to other patients with similar interpretation of the results and identification of an underlying
phenotypes to identify potential causative genomic factors. genetic cause.
● Patie nt de mographics (age , se x)
Data types
● Phe notypic fe ature s (obse rve d clinically)
represented: ● Diagnosis
● Spe cime n
● Ge nomic re sults from WES
Domain Analysis Document (DAD)
Each domain entity is studied and discussed in partnership with
collaborators from the GA4GH and HL7 communities. While time
consuming, these discussions better enable us to represent the domain
modeled in the Phenopackets schema.
https://phenopackets -analysis.rtfd.io
Domain Analysis Document (DAD)
● De scription of e ntitie s and conce pts
inde pe nde ntly of any particular
imple me ntation.
● This de fine s the core se mantics of the
obje cts (but not the re lationships
be twe e n the m).
● Links to public discussion forum on
this topic.
While the domain e ntity Individualhas not yet
been profiled in FHIR, we have created profiles
for Phenotypeand Karyotypic Sex
. Their DAD pages
guided their profiling implementation in the IG.Domain Analysis Document (DAD)
● De scribe s how the se e ntitie s and
conce pts are use d and re pre se nte d
within the Phe nopacke ts spe cification,
the core FHIR spe cification, and the
initial Phe nopacke ts FHIR IG.
● Docume nts de sign choice s and
highlights diffe re nce s.Domain Analysis Document (DAD)
● Summarize s our analysis of the de fine d
e ntitie s and conce pts, re vie ws de sign
choice s and discussions, and pre se nts a
brie f narrative about our chose n
re pre se ntation for the ne w
Phe nopacke ts FHIR IG.
● The targe t audie nce are domain
e xpe rts; FHIR e xpe rts and te chnical
audie nce s should re fe r to the FHIR IG.Core FHIR Implementation Guide
github.com/phenopackets/core -ig
Phe nopacke ts FHIR Re source s,
Sche ma Profile s, & IGs
Driver Scope Domain Analysis
PP Core IG
Use Case s Document (DAD)
GA4GH initial mapping Phe nopacke ts FHIR IG
(Clinical Picture v0 .1.0 )Core FHIR Implementation Guide
FHIR
artifacts
phenopackets.org/core -igCore FHIR Implementation Guide
Phenotypic abnormality profile
● Phenotypic abnormality
is an Observation (O)
● Profiled to capture a phenotype’s presence or
absence with
○ O.code for an HPO code
○ O.value Boole an for pre se nt/abse nt
○ O.dataAbse ntRe ason for missing value
re ason
● Additional aspe cts of a phe notype as
compone nt “slice s”
○ O.compone nt:Se ve rity
○ O.compone nt:ClinicalModifie r
○ O.compone nt:Onse t
● Group phe notype Obse rvation instance s
○ O.cate goryCore FHIR Implementation Guide
Vocabulary content
● Prototyping a HPO Code Syste m
○ Issue for full HPO CodeSystem
● Phenopacket’s KaryotypicSex as a
CodeSystem
● Define and expand ValueSets
○ Phenotypic abnormalities
○ Clinical modifiersPilot Testing: Year 1
FHIR Resources: Kids First (Use Case 1):
● Patie nt ● Query: patie nt phe notypic profile
● Obse rvation ● Response: bundle of re cords re pre se nting
● DiagnosticRe port patie nts that match the que ry parame te rs,
● Se rvice Re que st and the ir full se t of phe notype s and
● Spe cime n conditions.
● Bundle
Molecular Diagnostics (Use Case 2):
Pilot Testing: ● Submit lab request : Se rvice Re que st
● KF-like data in a simulate d e nvironme nt (orde r for a ge nomic te st), including
● FHIR Profile s de fine d by the Core IG instance s of Obse rvation that spe cify
● GitHub re po: profile s, config, data, que rie s patie nt phe notype s
● Retrieve lab results : e nhance d FHIR
bundle that include s ge ne tic findingsUse Case 1 (KF): Demonstration and Testing The initial input consisted of two FHIR Bundle instances, as a representation of what could be returned from a Kids First FHIR server. Code found at the link below performs the following functions: https://github.com/phenopackets/core- ig/blob/master/projects/ig - tools/src/main/java/org/phenopackets/coreig/tools/command/kf/KFUseCase.java 1. Finds Observationinstances that match the search criteria. 2. Returns one Patientreference in the returned observation. 3. Patientinstance is retrieved from the server. 4. Searches for all Observationand Conditioninstances for that patient. 5. Another similarity search is done to find patients by a Conditionparameter. 6. One Patientreference is found with the Condition. 7. Step 3-4 is repeated for this second patient. Use case: https://phenopackets-analysis.readthedocs.io/en/latest/usecases-driver.html#use-case Input data 1:https://github.com/phenopackets/core-ig/blob/master/data/kf-data/Bundle-kf-bundle-1.xml Code: https://github.com/phenopackets/core-ig/blob/master/projects/ig -tools/src/main/java/org/phenopackets/coreig/tools/command/kf/KFUseCase.java Screen output: https://github.com/phenopackets/core-ig/blob/master/projects/ig -tools/savedMessages/kidsfirst-usecase/_screen-output.txt Messages: https://github.com/phenopackets/core-ig/tree/master/projects/ig-tools/savedMessages/kidsfirst-usecase
Use Case 2 (Clinical): Demonstration and Testing
Test Client FHIR Server Test Client FHIR Server
Query for request and
Lab searches for attached phenopacket
ServiceRequest and bundle
Create Patient related phenopacket data Server searches
Patient instance stored data
Patient Data
Search parameters
Link Bundle - Bundle type
to Patient - Status
Submit Phenopacket Data - Patient ID Update request to complete,
create Observation and
Diagnostic report
Phenopacket data Lab performs test Server updated
(FHIR Bundle) Lab updates data with results
FHIR Bundle instance
containing the phenopacket
3. Lab querying FHIR Server for ServiceRequest and Phenotype Observations
1. Clinician submits patient and Phenopacket data to the FHIR server
Test Client FHIR Server
Specimen instance, Test Client FHIR Server
Create Specimen linked to Patient Search for Observation and
Create blood Search for DiagnosticReport that are
specimen results with “basedOn” the indicated
Request ID ServiceRequest
from previous Server searches
Create Service Request
request stored data
(FHIR) Create ServiceRequest
- Patient ID ServiceRequest Server returns prototype
instance linked to Observation and Diagnostic
- Test Code (lab order)
Patient, Specimen, report instances
- Specimen ID
Request ID returned and Bundle
- Bundle ID
(phenopacket)
4. Clinician retrieves test results
2. Clinician submits exome order to the FHIR serverRoadmap
Resources
Phenopackets
○ Home: http://phenopackets.org
○ Reference implementation: https://github.com/phenopackets/phenopacket-schema
○ Documentation: https://phenopackets-schema.readthedocs.io/en/latest
○ Mailing lists
■ phe nopacke ts-de v@ga4gh.org
■ phe nopacke ts-use r@ga4gh.org
○ Slack
■ https://ga4gh.slack.com | #phe nopacke ts
Zulip - FHIR community chat: http://chat.fhir.org
Phenopackets FHIR Implementation Guide: http://phe nopacke ts.org/core -ig/maste r
● De ve lopme nt file s on GitHub https://github.com/phe nopacke ts/core -ig
○ IG source file s https://github.com/phe nopacke ts/core -ig/tre e /maste r/ig-root
○ Re late d tooling https://github.com/phe nopacke ts/core -ig/tre e /maste r/proje cts
○ Issue tracke r https://github.com/phe nopacke ts/core -ig/issue s
○ Publishe d ve rsion(s) https://github.com/phe nopacke ts/core -ig/tre e /gh-page s
■ Late st http://phe nopacke ts.org/core -ig/maste r/
● IG artifacts http://phe nopacke ts.org/core -ig/maste r/artifacts.htmlThank you
CONTRACT PROJECT TEAM GA4GH
Me lissa Hae nde l Lindsay Smith
Pe te r Robinson
Robe rt Fre imuth Kids First
Matthe w Brush Allison He ath
● GitHub Re pository:
Monica Munoz-Torre s Natasha Singh ○ https://github.com/phe nopacke ts
Shahim Essaid De anne Taylor ● Mailing lists
Yiqing Zhao Adam Re snick ○ phe nopacke ts-de v@ga4gh.org
○ phe nopacke ts-use r@ga4gh.org
CD2H ● Slack
Harold Solbrig ○ https://ga4gh.slack.com
Chris Chute #phe nopacke ts
Dazhi Jiao
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