tranSMART Community Meeting 5-7 Nov 13 - Session 2: Creating a Comprehensive Clinical and...

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  

Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease Report from National academy of science, USA, 2011

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HEGP background

Hôpital Laennec (1634)

Hôpital Boucicaut Hôpital Broussais

Opening : July 2000-

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

Pr Patrice Degoulet CIO

PI: Isaac Kohane – Harvard - CBMI

HEGP i2b2

HEGP CDW use i2b2 CDW queries

+’omics

CDW  

Health care Health Information System

Clinical Research

Pathology

HEGP

DRG

Biology

EHR forms

Imaging

Browser tools available

for MD & Pharm

EHR reports i2b2

‘omics

ETL

onc

e a

wee

k

‘omics data

ETL

Structured data from research

studies

ETL

Rx

BDW

Analysis tools  

•  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  

HEGP BDW

Objectives : 1.  Integration of clinical, biological and ‘omics

data in one place – hypothesis free – 2.  Generation of hypothesis by Clinicians /

Researchers

!h0p://www.transmartproject.org  

“Omics” data integration

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

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

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

HEGP:  Joubert  F,  Avillach  P  

06/05/2013

Badoual Cancer Res. 2013

p  =  0,04  

HEGP:  Joubert  F,  Avillach  P  

p  =  0,07  p  =  0,03  

AVG  :  10  months  of  addiIonal  follow  up  with  i2b2  data  

HEGP:  Joubert  F,  Avillach  P  

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

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Workflow

Phenotype  

Thiopurine    dose  

Low  acHvity  

Intermediate  acHvity  

Normal  AcHvity  

10  %  dose  

30  –  70  %  dose  

100  %  dose  

FDA & EMA recommendations

?  

Methodes: Selection of trait: enzymatic Activity TPMT

TPMT

HEGP:  Neuraz  A,…,    Avillach  P  

ICD9-­‐CM  Mapping  

Very  High  TPMT  acIvity  VS  others  

HEGP:  Neuraz  A,…,    Avillach  P  

HEGP:  Neuraz  A,…,    Avillach  P  

Acknowledgments HEGP

Informatics & Public Health Dept : •  Eric Zapletal, •  Vincent Canuel, •  Antoine Neuraz, •  Fabien Joubert

Contact : paul.avillach@egp.aphp.fr Anita.burgun@egp.aphp.fr

www.i2b2.org  

www.transmartproject.org  

Prof  Patrice  Degoulet,  past  CIO  Prof  Anita  Burgun,  CIO    

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

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

EMIF project: European Medical Information Framework

Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease Report from National academy of science, USA, 2011

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ASDs SSC Cohort to BCH

Type   NaHonal  SSC   Lou  Kunkel  SSC   Link  to  BCH  i2b2  AuIsm   1  899   356   186  Pdd   549   314   163  Nonspectrum   0   34   20  Aspergers   275   43   17  ReEs   0   1   0  Typical-­‐no-­‐dx   0   153   93  NA   2   19   18  

Total   2  725   920   497  

Probands  +  sibblings  

#  paHents   #  observaHons  Vital:Weight   367   4  727  Vital:Height   359   7  220  SER   421   17  915  Radiology  Procedures   174   1  142  Procedures  (CPT)   209   1  470  MedicaIons  (PrescripIon)   212   3  171  Pathology  Repports   220   2  255  Clinical  Notes   419   33  978  MedicaIons   189   19  321  Lab  tests   360   72  433  Insurance  Payors   375   8  869  MedicaIons  (History)   217   835  Diagnosis  (ICD9)   421   26  323  Clinic   421   14  169  AMED   164   7  142  Allergy   246   583  

AVG  =  298    TOTAL  =  221  553  

ASDs SSC Cohort to i2b2 BCH

Autism information commons From SSC National cohort to BCH i2b2

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