p.avillach experience, issues and future work using tran-smart at the pompidou university hospital...
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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 :
www.recomdata.com
www.i2b2.org
www.transmartproject.org