Dev days16 medical research

Medical Research with FHIR

Research Data Service Center, DFL Universitätsspital Zürich, Universität Zürich

Computational Health Informatics Program, Boston Children’s Hospital, Harvard Medical School

Pascal Pfiffner

FHIR DevDays Amsterdam • 2016-11-17

Computational

Health Informatics

© 2016 HL7 ® International. Licensed under Creative Commons. HL7, Health Level Seven & FHIR are registered trademarks of Health Level Seven International. Reg. U.S. TM Office.

• Types of medical research

• ResearchKit & ResearchStack

• FHIR in medical research

• Data return & evaluation


Typesof Medical Research


• Clinical Trials

• Registries & Cohorts

• Patient Networks

• Pragmatic Trials


Clinical Trials• Prospective trials on human participants

• Best known for studies about new drugs

• Phase 0 (first in human) to phase 3 (large group efficacy & effectiveness study)

• Phase 4: post-marketing surveillance

‣ Patients seen clinically, highly controlled environment, data usually collected in-clinic but experimenting with sensors, home data collection, …


Registries & Cohorts• “Network” of patients with the same disease

• Often run by a group of physicians or researchers securing a large grant (e.g. CARRA ➔ CARRAnet)

• Thousands of registries exist worldwide, collecting a wast array of data

• Many custom data backends

‣ Often available for nested research projects


Patient Networks• Similar to registries: network of patients suffering

from same disease

• Often started by patients or their family as patient community (e.g. PatientsLikeMe)

• Patients donate data (responding to surveys, uploading EHR data, access to social media, …)

‣ Increasingly important for research


Pragmatic Trials• Technically Phase 4 clinical trials

• Compares effectiveness between health care interventions (comparative effectiveness research)

• Pragmatic randomized controlled trial: randomize patients to receive “equivalent” standard of care

• Often mentioned when using retrospective data from EHR, insurance and other data sources


Research DB != EHR


Regulations & Guidelines• GCP: Good Clinical Practice

‣ tight guidelines on ethical aspects of a clinical study

• FDA 21 CFR Part 11: Code of Federal Regulations

• HIPAA: Health Insurance Portability and Accountability Act

‣ US data privacy and security provision legislation

• National legislation

Record-Number

Research DB

EHR

Random-ID

IDENTIFIED RESEARCH DATA

RID MRN

Identity Store

≍

Research DB

EHR

Random-ID


Commercial Solutions

• Tens to hundreds of solutions to manage clinical trial data http://www.capterra.com/clinical-trial-management-software/

• ResearchKit: SAGE Bionetworks, IBM Watson Health for ResearchKit and probably more to come

http://www.capterra.com/clinical-trial-management-software/

http://sagebase.org/platforms/

https://www.ibm.com/marketplace/cloud/simplify-crowd-sourced-research-studies/details/us/en-us#product-header-top

https://www.ibm.com/marketplace/cloud/simplify-crowd-sourced-research-studies/details/us/en-us#product-header-top


iOS & AndroidResearchKit and ResearchStack


Medical Data StoresHealthKit, Google Fit (2014), S Health (2015)


Medical ResearchResearchKit (2015), ResearchStack (2016)


• Open source frameworks for iOS and Android

• Guide through consent • Sign on screen, render to PDF

• Render surveys

• Multitude of “tasks” • Tapping speed • 6-min walk distance • Memory games • Phonation • …


Medical CareCareKit (2016)


More on the Topic

ResearchKit: tomorrow 09:00 Room 2

Sync4Science: tomorrow 10:00 Room 2


Consent


Informed Consent• Legal requirement

• “informed” means that the patient has to fully understand what will happen

‣ Children ➔ “Assent”, consent by their parents

‣ Intoxication, stress, … ➔ may be unable to consent

• The consent document must be approved by ethical review boards

• electronic consent is not (yet) legal in many countries


Where does FHIR come in?


Contract

Questionnaire

C3-PRO Mobile

Frameworks

QuestionnaireResponse

Patient

ObservationCarePlan


FHIR QuestionnarieFHIR Contract

C3-PRO Mobile

Frameworks Resources

C3-PRO Receiver Server

SQS Queue

Fire

wal

l

i2b2 FHIR Cell

i2b2

C3-PRO Consumer

In-HouseWeb Hosting (AWS)Research App


Site i2b2 query

i2b2 Patient Set(PDO xml)

RxConnect Transponder

Request for Rx for specific patient withtoken from CRH

TextRxConnect

RxConnect Request:patient ID + identifiers(signed JSON)

Surescripts HL7

ContactReply

PI SHRINE query

Contact Information Database

ContactRequest

Site i2b2 EHR or

i2b2 registry

Site i2b2 Admin

Workbench

RxConnect Response:patient ID + medications(signed JSON)

i2b2 Site Admin

MedRec App

Legend

Demographics

to be defined datastorage

database

i2me2 Patient Portal Cell

cCDA

Authentication token withsubject GUID and study ID

Research user locates research subject

via CRH plugin

SETL

cCDA

cell

enhancements

CRH plugin

RxC

onne

ct p

lugi

n

Rx PDO

JSON reconciled meds data

JSONmeds data plus demographics(at least name)[org. from Rx PDO]

indivo

cCDA JSONMDMI

i2b2

format trans.

CRC

QR code

1

2

patient checkQ/A Rx PDO -

meds data

34

5

6

7

8

Rx PDO with:- Rx data- Patient ID- Event ID

pat. info. (name etc.)

Pharmacy


Site i2b2 query

i2b2 Patient Set(PDO xml)

RxConnect Transponder

Request for Rx for specific patient withtoken from CRH

TextRxConnect

RxConnect Request:patient ID + identifiers(signed JSON)

Surescripts HL7

ContactReply

PI SHRINE query

Contact Information Database

ContactRequest

Site i2b2 EHR or

i2b2 registry

Site i2b2 Admin

Workbench

RxConnect Response:patient ID + medications(signed JSON)

i2b2 Site Admin

MedRec App

Legend

Demographics

to be defined datastorage

database

i2me2 Patient Portal Cell

cCDA

Authentication token withsubject GUID and study ID

Research user locates research subject

via CRH plugin

SETL

cCDA

cell

enhancements

CRH plugin

RxC

onne

ct p

lugi

n

Rx PDO

JSON reconciled meds data

JSONmeds data plus demographics(at least name)[org. from Rx PDO]

indivo

cCDA JSONMDMI

i2b2

format trans.

CRC

QR code

1

2

patient checkQ/A Rx PDO -

meds data

34

5

6

7

8

Rx PDO with:- Rx data- Patient ID- Event ID

pat. info. (name etc.)


Sync 4 Science

PHR

Research DB

EHR

0: Dump

1: PHR login & authorize 2: Data shared


• FHIR as API between systems deployed in a research setting

• FHIR as data format for questionnaires, consent (and more) on data collection endpoints


Consent vs. Contract• With STU-3, there is a Consent resource

• Aimed towards policy choices such as “do not resuscitate”

• Not suited as data format for research consent

• Contract is also only mildly suited but up for the task


Returning DataPhone ➔ Cloud ➔ Research DB


App Contact Point• On the open web

• Serve content and accept research data

• Deploy to publicly available services such as AWS, DigitalOcean, Exoscale, …

• Therefore may only ever receive encrypted data

• Should handle app registration and verification (OAuth2)


OAuth2• Only accept data sent from your app

‣ Do not embed secret into binary

‣ Use Apple’s App Store receipt during dynamic client registration ➔ verify with iTunes

• Request an access token using client credentials obtained before

• Sign all requests using this token, receiver rejects all other requests

Dynamic Client Registration & Access Token

FHIR QuestionnarieFHIR Contract

C3-PRO Mobile

Frameworks Resources

C3-PRO Receiver Server

SQS Queue

Fire

wal

l

i2b2 FHIR Cell

i2b2

C3-PRO Consumer

In-HouseWeb Hosting (AWS)iOS Research App


Data Grabber

• Deployed behind firewall

• Consume data from the App's contact point

‣ No need to puncture institution firewall

• Able to decrypt incoming data

• Emit FHIR resources to FHIR data store


Data Store

• Native FHIR stores or write adapters for existing research backends to accept FHIR resources

‣ e.g. FHIR Cell to extend i2b2’s functionality

• Likely needs ontology curation

‣ e.g. map FHIR data to i2b2 model


Data EvaluationWhat’s in your data?


Difficult Topic Because• Established research backend (e.g. i2b2)

‣ tons of modules to get data into R, CSV, …

• FHIR-native data store

‣ Use or build a FHIR tool

• Some DB (e.g. MongoDB)

‣ tweak generic tools such as Elastic & Kibana


Example: Kibana• Kibana: generic visualization tool pulling data from

Elastic

• FHIR: JSON serialization

‣ Store FHIR data into Elastic (even if just temporarily)

‣ Configure Kibana to draw data from raw FHIR questionnaire responses by way of configuration

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Questions & Answers

mailto:[email protected]

Healthcare

Dev days16 medical research