Creating a comprehensive
clinical and 'omics information
commons on autism
Paul	
  Avillach,	
  MD,	
  PhD	
  
Harvard	
  ...
Toward Precision Medicine: Building a Knowledge Network for
Biomedical Research and a New Taxonomy of Disease
Report from ...
Opening : July 2000-

HEGP background

Hôpital Laennec
(1634)

Hôpital Boucicaut

Hôpital Broussais
EHR/BDW integration

HEGP BDW
Pr Patrice Degoulet CIO
Production environment

EHR :
Operational
Database
(ODS)

Evaluation...
PI: Isaac Kohane – Harvard - CBMI
HEGP i2b2
HEGP CDW use

i2b2 CDW queries
HEGP
Health care

Clinical Research

Health Information System
DRG

Pathology
Rx

i2b2

CDW	
  

Structured data
from rese...
HEGP BDW

• 
• 
• 
• 

Integrated platform to support translational research
Initiated by Johnson & Johnson et Recombinant...
Objectives :
1.  Integration of clinical, biological and ‘omics
data in one place – hypothesis free –
2.  Generation of hy...
“Omics” data integration

h0p://www.transmartproject.org	
  
!
-­‐	
  Szalma	
  S,	
  Koka	
  V,	
  Khasanova	
  T,	
  Perakslis	
  ED.	
  EffecIve	
  knowledge	
  management	
  
in	
  t...
Pilot Study
HEGP - Paris
HEGP:	
  Canuel	
  V,	
  Avillach	
  P	
  
HEGP:	
  Canuel	
  V,	
  Avillach	
  P	
  
HEGP:	
  Canuel	
  V,	
  Avillach	
  P	
  
•  R module in
tranSMART

•  Published figure in
JCO
HEGP:	
  Canuel	
  V,	
  Avillach	
  P	
  
Phenotypic augmentation
Phenotypic augmentation
tranSMART + i2b2 = Phenotypic augmentation

Head and Neck
Cancer Study
Type of Data
Death

Vital Status
Cinical Data

Head...
p	
  =	
  0,04	
  

Badoual Cancer Res. 2013

06/05/2013
HEGP:	
  Joubert	
  F,	
  Avillach	
  P	
  
p	
  =	
  0,07	
  
p	
  =	
  0,03	
  
AVG	
  :	
  10	
  months	
  of	
  
addiIonal	
  follow	
  up	
  
with	
  i2b2	
  dat...
PheWAS study
on i2b2/tranSMART
Neuraz A, Chouchana L, Malamut G, Le Beller C, Roche D, Beaune P,
Degoulet P, Burgun A, Lor...
Workflow
Methodes: Selection of trait:
enzymatic Activity TPMT

Phenotype	
  

FDA & EMA
recommendations

Thiopurine	
  	
  
dose	
...
TPMT

HEGP:	
  Neuraz	
  A,…,	
  	
  Avillach	
  P	
  
Very	
  High	
  TPMT	
  acIvity	
  VS	
  others	
  
ICD9-­‐CM	
  
Mapping	
  

HEGP:	
  Neuraz	
  A,…,	
  	
  Avillach	
  ...
HEGP:	
  Neuraz	
  A,…,	
  	
  Avillach	
  P	
  
Acknowledgments
HEGP

Informatics &
Public Health Dept :
•  Eric Zapletal,
•  Vincent Canuel,
•  Antoine Neuraz,
•  Fabien...
European Medical
Information Framework
EMIF project: European Medical Information Framework
• 
• 
• 
• 
• 

58 partners
58 Million euros
Started 1st jan 2013
5 y...
EMIF project: European Medical Information Framework
3 projects, 3 datasources:
•  EHR derived patient data: 48 millions p...
Toward Precision Medicine: Building a Knowledge Network for
Biomedical Research and a New Taxonomy of Disease
Report from ...
ASDs SSC Cohort to BCH
Type	
  
AuIsm	
  
Pdd	
  
Nonspectrum	
  
Aspergers	
  
ReEs	
  
Typical-­‐no-­‐dx	
  
NA	
  
Tota...
ASDs SSC Cohort to i2b2 BCH
Vital:Weight	
  
Vital:Height	
  
SER	
  
Radiology	
  Procedures	
  
Procedures	
  (CPT)	
  
...
Autism information commons
From SSC National cohort to BCH i2b2
41
42
Dra]	
  
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Au...
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tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Autism

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tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Autism
Paul Avillach, Harvard University

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tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and 'Omics Information Commons on Autism

  1. 1. Creating a comprehensive clinical and 'omics information commons on autism Paul  Avillach,  MD,  PhD   Harvard  Medical  School   HEGP  Hospital,  Paris  –  Paris  Descartes  University   INSERM  UMRS  872  eq  22   Erasmus  MC  University  
  2. 2. Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease Report from National academy of science, USA, 2011 2
  3. 3. Opening : July 2000- HEGP background Hôpital Laennec (1634) Hôpital Boucicaut Hôpital Broussais
  4. 4. EHR/BDW integration HEGP BDW Pr Patrice Degoulet CIO Production environment EHR : Operational Database (ODS) Evaluation/Research environment ETL suite (Talend Open Studio) EHR : Mirrored Database Biomedical Data Warehouse (BDW) Real time requests Data Analysis Data Mining External Databases R i2b2/tranSMART tools Business Object IBM Ilog Rules
  5. 5. PI: Isaac Kohane – Harvard - CBMI
  6. 6. HEGP i2b2
  7. 7. HEGP CDW use i2b2 CDW queries
  8. 8. HEGP Health care Clinical Research Health Information System DRG Pathology Rx i2b2 CDW   Structured data from research studies ETL Imaging BDW ETL Biology ETL once a week EHR forms EHR reports Analysis tools   Browser tools available for MD & Pharm ‘omics data ‘omics +’omics
  9. 9. HEGP BDW •  •  •  •  Integrated platform to support translational research Initiated by Johnson & Johnson et Recombinant 5 years ago Open-source since January, 2012 Installed at HEGP since May, 2012 •  Today, driven and maintained by the tranSMART Foundation & communitie hEp://transmarHoundaIon.org  
  10. 10. Objectives : 1.  Integration of clinical, biological and ‘omics data in one place – hypothesis free – 2.  Generation of hypothesis by Clinicians / Researchers
  11. 11. “Omics” data integration h0p://www.transmartproject.org   !
  12. 12. -­‐  Szalma  S,  Koka  V,  Khasanova  T,  Perakslis  ED.  EffecIve  knowledge  management   in  translaIonal  medicine.  J  Transl  Med.  2010;  8:68.   12
  13. 13. Pilot Study HEGP - Paris
  14. 14. HEGP:  Canuel  V,  Avillach  P  
  15. 15. HEGP:  Canuel  V,  Avillach  P  
  16. 16. HEGP:  Canuel  V,  Avillach  P  
  17. 17. •  R module in tranSMART •  Published figure in JCO HEGP:  Canuel  V,  Avillach  P  
  18. 18. Phenotypic augmentation
  19. 19. Phenotypic augmentation
  20. 20. tranSMART + i2b2 = Phenotypic augmentation Head and Neck Cancer Study Type of Data Death Vital Status Cinical Data Head and Neck Cancer Cancer recurrence Biology Patology Study sprecific samples Re-intervention Treatment Electronic Health Record Head and Neck Study HEGP:  Joubert  F,  Avillach  P  
  21. 21. p  =  0,04   Badoual Cancer Res. 2013 06/05/2013 HEGP:  Joubert  F,  Avillach  P  
  22. 22. p  =  0,07   p  =  0,03   AVG  :  10  months  of   addiIonal  follow  up   with  i2b2  data   HEGP:  Joubert  F,  Avillach  P  
  23. 23. PheWAS study on i2b2/tranSMART Neuraz A, Chouchana L, Malamut G, Le Beller C, Roche D, Beaune P, Degoulet P, Burgun A, Loriot MA, Avillach P. Phenome-wide association studies on a quantitative trait: Application to TPMT enzyme activity and thiopurine therapy in pharmacogenomics. PLoS Comput Biol. 2013 in press 24
  24. 24. Workflow
  25. 25. Methodes: Selection of trait: enzymatic Activity TPMT Phenotype   FDA & EMA recommendations Thiopurine     dose   Low   acHvity   Intermediate   acHvity   Normal   AcHvity   10  %   dose   30  –  70  %   dose   100  %   dose   ?  
  26. 26. TPMT HEGP:  Neuraz  A,…,    Avillach  P  
  27. 27. Very  High  TPMT  acIvity  VS  others   ICD9-­‐CM   Mapping   HEGP:  Neuraz  A,…,    Avillach  P  
  28. 28. HEGP:  Neuraz  A,…,    Avillach  P  
  29. 29. Acknowledgments HEGP Informatics & Public Health Dept : •  Eric Zapletal, •  Vincent Canuel, •  Antoine Neuraz, •  Fabien Joubert Prof  Patrice  Degoulet,  past  CIO   Prof  Anita  Burgun,  CIO     www.i2b2.org   www.transmartproject.org   Contact : paul.avillach@egp.aphp.fr Anita.burgun@egp.aphp.fr
  30. 30. European Medical Information Framework
  31. 31. EMIF project: European Medical Information Framework •  •  •  •  •  58 partners 58 Million euros Started 1st jan 2013 5 year project PI: Bart Vannieuwenhuyse (Janssen) & Prof. Simon Lovestone (KCL) •  PI Platform: Prof. Johan van der Lei •  Detect new biomakers: –  prediposition Alzheimer's disease –  Metabolic complication diabetes
  32. 32. 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 : ~10 000 patients •  WP11 : Semantic harmonization •  Same concepts across all database : ETL process Jerboa & tranSMART
  33. 33. Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease Report from National academy of science, USA, 2011 36
  34. 34. ASDs SSC Cohort to BCH Type   AuIsm   Pdd   Nonspectrum   Aspergers   ReEs   Typical-­‐no-­‐dx   NA   Total   NaHonal  SSC   Lou  Kunkel  SSC   Link  to  BCH  i2b2   1  899   356   186   549   314   163   0   34   20   275   43   17   0   1   0   0   153   93   2   19   18   2  725   920   497   Probands  +  sibblings  
  35. 35. ASDs SSC Cohort to i2b2 BCH Vital:Weight   Vital:Height   SER   Radiology  Procedures   Procedures  (CPT)   MedicaIons  (PrescripIon)   Pathology  Repports   Clinical  Notes   MedicaIons   Lab  tests   Insurance  Payors   MedicaIons  (History)   Diagnosis  (ICD9)   Clinic   AMED   Allergy   #  paHents   #  observaHons   367   4  727   359   7  220   421   17  915   174   1  142   209   1  470   212   3  171   220   2  255   419   33  978   189   19  321   360   72  433   375   8  869   217   835   421   26  323   421   14  169   164   7  142   246   583   AVG  =  298    TOTAL  =  221  553  
  36. 36. Autism information commons From SSC National cohort to BCH i2b2
  37. 37. 41
  38. 38. 42
  39. 39. Dra]  

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