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. 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
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
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
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
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
37.
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