Experience, issues and future work usingtranSMART at the Pompidou University Hospital           in Paris (APHP - HEGP)   P...
HEGP BackgroundLocation• Paris 15th districtWithin AP-HP• HEGP is the most recent acutecare hospital within the 38 AP-HPho...
HEGP background  Shared Biobank (2008-)
HEGP BDW                                  EHR/BDW integrationProduction environment                Evaluation/Research env...
HEGP         Health care                                      Clinical Research Health Information System                 ...
HEGP i2b2
HEGP tranSMART
HEGP tranSMART
HEGP tranSMART
HEGP tranSMART • tranSMART HEGPPublished figure in JCO
tranSMART + i2b2 = Phenotypic augmentation                                         Head and Neck                          ...
CARPEM: CAncer Research and PErsonalized Medicine• 7.5 Million euros• PI: Prof Pierre Laurent Puig : Onco pharmacologist• ...
CARPEM: Retrospective cohort studies  CARPEM: Prospective cohort• REDCAP -> tranSMART
CARPEM: CAncer Research and PErsonalized MedicinetranSMART• Servers for tranSMART: 40k euros• 1 full time developper + 1 p...
EMIF project: European Medical Information Framework•   58 partners•   48 Million euros•   Started 1st jan 2013•   PI: Bar...
EMIF project: European Medical Information Framework3 projects, 3 datasources:• EHR derived patient data: 48 millions pati...
Postdoc fellowshipHarvard Medical school• June 2013 to june 2014• Director: Prof Isaak Kohane  Project:• Semantic integrat...
Acknowledgments                              www.i2b2.orgInformatics &Public Health Dept.           www.transmartproject.o...
 P.Avillach   Experience, issues and future work using tran-smart at the pompidou university hospital in paris
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P.Avillach Experience, issues and future work using tran-smart at the pompidou university hospital in paris

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

  1. 1. Experience, issues and future work usingtranSMART at the Pompidou University Hospital in Paris (APHP - HEGP) 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 24th Feb 2013
  2. 2. HEGP BackgroundLocation• Paris 15th districtWithin AP-HP• HEGP is the most recent acutecare hospital within the 38 AP-HPhospitals• HEGP meets the needs of the600, 000 inhabitants of the Parissouth-west
  3. 3. HEGP background Shared Biobank (2008-)
  4. 4. HEGP BDW EHR/BDW integrationProduction environment Evaluation/Research environment ETL suite (Talend Open Studio) EHR : External EHR : Biomedical Data Operational Databases Mirrored Warehouse Database Database (BDW) (ODS) R Real time requests i2b2/tranSMART tools Business Object Data Analysis IBM Ilog Rules Data Mining
  5. 5. HEGP Health care Clinical Research Health Information System Browser and Analysis DRG tools available for MD & PharmEHR forms BDW ETL once a weekEHR reports i2b2 Structured data ETL from research Biology CDW studies Imaging ‘omics ETL +’omics ‘omics data Pathology Rx
  6. 6. HEGP i2b2
  7. 7. HEGP tranSMART
  8. 8. HEGP tranSMART
  9. 9. HEGP tranSMART
  10. 10. HEGP tranSMART • tranSMART HEGPPublished figure in JCO
  11. 11. tranSMART + i2b2 = Phenotypic augmentation Head and Neck Cancer StudyType of Data Vital Status DeathCinical Data Head and Neck Cancer Cancer recurrence Biology Patology Study sprecific samples Re-intervention Treatment Electronic Health Record Head and Neck Study
  12. 12. CARPEM: CAncer Research and PErsonalized Medicine• 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
  13. 13. CARPEM: Retrospective cohort studies CARPEM: Prospective cohort• REDCAP -> tranSMART
  14. 14. CARPEM: CAncer Research and PErsonalized MedicinetranSMART• Servers for tranSMART: 40k euros• 1 full time developper + 1 postdoc
  15. 15. EMIF project: European Medical Information Framework• 58 partners• 48 Million euros• Started 1st jan 2013• PI: Bart Vannieuwenhuyse (Janssen)• 5 year project• Detect new biomakers: – prediposition Alzheimers disease – Metabolic complication diabetes
  16. 16. EMIF project: European Medical Information Framework3 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
  17. 17. Postdoc fellowshipHarvard Medical school• June 2013 to june 2014• Director: Prof Isaak Kohane Project:• Semantic integration within the tranSMART platform to enable: 1) meta-analysis from multiple cohorts 2) phenotypic augmentation in genomic driven research
  18. 18. Acknowledgments www.i2b2.orgInformatics &Public Health Dept. www.transmartproject.org www.recomdata.com Contacts : patrice.degoulet@egp.aphp.fr anita.burgun@egp.aphp.fr paul.avillach@egp.aphp.fr

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