P.Avillach Experience, issues and future work using tran-smart at the pompidou university hospital in paris

Experience, issues and future work using

tranSMART at the Pompidou University Hospital

in Paris (APHP - HEGP)

24th Feb 2013

Paul Avillach, Vincent Canuel, Fabien Joubert,

Eric Zapletal, Anita Burgun, Patrice Degoulet

Faculté de Médecine René Descartes, Université Paris 5

Hôpital Européen Georges Pompidou (HEGP)

INSERM UMR_S 872 eq22

Location

• Paris 15th district

Within AP-HP

• HEGP is the most recent acute

care hospital within the 38 AP-HP

hospitals

• HEGP meets the needs of the

600, 000 inhabitants of the Paris

south-west

HEGP Background

HEGP background

Shared Biobank (2008-)

HEGP BDW EHR/BDW integration

EHR :

Operational

Database

(ODS)

EHR :

Mirrored

Database

Production environment Evaluation/Research environment

ETL suite (Talend Open Studio)

Biomedical Data

Warehouse

(BDW)

External

Databases

Data Analysis

Data Mining

R

i2b2/tranSMART tools

Business Object

IBM Ilog Rules

Real time requests

+’omics

CDW

Health careHealth Information System

Clinical Research

Pathology

HEGP

DRG

Biology

EHR forms

Imaging

Browser and Analysis

tools available

for MD & Pharm

EHR reports i2b2

‘omics

ET

L

once a

week

‘omics data

ET

L

Structured data

from research

studies

ET

L

Rx

BDW

HEGP i2b2

HEGP tranSMART

HEGP tranSMART

HEGP tranSMART

• tranSMART HEGP

Published figure in JCO

HEGP tranSMART

Type of Data

Electronic Health Record

Head and Neck Study

Head and Neck

Cancer Study

Treatment

Vital Status

Cinical Data

Biology

Patology

Death

Re-intervention

Cancer recurrenceHead and Neck Cancer

Study sprecific samples

tranSMART + i2b2 = Phenotypic augmentation

• 7.5 Million euros

• PI: Prof Pierre Laurent Puig : Onco pharmacologist

• Started 1st Jan 2013 5 year project

• Integrated Center main Cancer teams East Paris

– Fundamental research

– Clinical trials

• Better understanding of the mechanisms of carcinogenesis

• The relationship between tumor and host microenvironment

• Translate this knowledge into an improved cancer patient

management

• tranSMART platform

CARPEM: CAncer Research and PErsonalized Medicine

CARPEM: Retrospective cohort studies

• REDCAP -> tranSMART

CARPEM: Prospective cohort

tranSMART

• Servers for tranSMART: 40k euros

• 1 full time developper + 1 postdoc

CARPEM: CAncer Research and PErsonalized Medicine

• 58 partners

• 48 Million euros

• Started 1st jan 2013

• PI: Bart Vannieuwenhuyse (Janssen)

• 5 year project

• Detect new biomakers:

– prediposition Alzheimer's disease

– Metabolic complication diabetes

EMIF project: European Medical Information Framework

3 projects, 3 datasources:

• EHR derived patient data: 48 millions patient records :

observational studies Jerboa tool

• Cohort clinical + ‘omics data from : tranSMART option

– AD

– Metabolic :

100 000 patients

• WP11 : Semantic harmonization

• Same concepts across all database : ETL process Jerboa &

tranSMART

EMIF project: European Medical Information Framework

Project:

• Semantic integration within the tranSMART platform to enable:

1) meta-analysis from multiple cohorts

2) phenotypic augmentation in genomic driven research

Harvard Medical school

• June 2013 to june 2014

• Director: Prof Isaak Kohane

Postdoc fellowship

Acknowledgments

Informatics &

Public Health Dept.

Contacts :

[email protected]

[email protected]

[email protected]

www.recomdata.com

www.i2b2.org

www.transmartproject.org