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

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. 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. Opening : July 2000-
HEGP background
Hôpital Laennec
(1634)
Hôpital Boucicaut
Hôpital Broussais

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. PI: Isaac Kohane – Harvard - CBMI

6. HEGP i2b2

7. HEGP CDW use
i2b2 CDW queries

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. 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. Objectives :
1. Integration of clinical, biological and ‘omics
data in one place – hypothesis free –
2. Generation of hypothesis by Clinicians /
Researchers

11. “Omics” data integration
h0p://www.transmartproject.org
!

12. -­‐
Szalma
S,
Koka
V,
Khasanova
T,
Perakslis
ED.
EffecIve
knowledge
management
in
translaIonal
medicine.
J
Transl
Med.
2010;
8:68.
12

13. Pilot Study
HEGP - Paris

15. HEGP:
Canuel
V,
Avillach
P

16. HEGP:
Canuel
V,
Avillach
P

17. HEGP:
Canuel
V,
Avillach
P

18. • R module in
tranSMART
• Published figure in
JCO
HEGP:
Canuel
V,
Avillach
P

19. Phenotypic augmentation

20. Phenotypic augmentation

21. 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

22. p
=
0,04
Badoual Cancer Res. 2013
06/05/2013
HEGP:
Joubert
F,
Avillach
P

23. p
=
0,07
p
=
0,03
AVG
:
10
months
of
addiIonal
follow
up
with
i2b2
data
HEGP:
Joubert
F,
Avillach
P

24. 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

27. Workflow

28. 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
?

29. TPMT
HEGP:
Neuraz
A,…,
Avillach
P

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

31. HEGP:
Neuraz
A,…,
Avillach
P

32. 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

33. European Medical
Information Framework

34. 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

35. 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

36. 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

38. 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

39. 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

40. Autism information commons
From SSC National cohort to BCH i2b2

41. 41

42. 42

46. Dra]