Data Integration and Clinical Decision Support for Personalized Medicine and Healthcare

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Data Integration and Clinical Decision Support
for Personalized Medicine and Healthcare
Lei Liu, Ph.D.

• Shanghai Center for Bioinformation Technology
• and
• Shanghai Institute for Biological Sciences, CAS

3/29/2010
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Translational Medicine

• Integration of Basic and Clinical Research
• From Bench to Bedside

Imaging
Clinical Research
Pathology
Molecular Biology
From Introduction of caBIG
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How to deliver the right healthcare and medicine
to the right people and at the right time?

• Collection of personalized genetic and
  physiological information
• Genome wide association studies, SNP, CNV
• Biosample Banking
• Phenotypic data collection CRF
• Biosensor technology
• Translated the information to clinical practice
• Data integration and mining
• Electronic Medical Record
• Clinical Decision Support

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Clinical Decision Support in Personalized Medicine
Gregory J Downing, et al. Information management
to enable personalized medicine stakeholder
roles in building clinical decision support. BMC
Medical Informatics and Decision Making, 2009,944
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Integrated Clinical Information Systems and
Service Platform
Key city hospitals
Community hospitals
HL7
Non-HL7
Paper Record


Shanghai Public RD

Service Platform
Clinical Data Repository
Tissue Bank
Genotype Data Repository
Integrated Bioinformatics Platform(IBP)
Comprehensive Data-Warehouse
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caBIG Workspaces
Clinical Trials Management Systems
(CTMS,????????)https//cabig.nci.nih.gov/workspa
ces/CTMS/
Integrative Cancer Research (ICR,??????)https//
cabig.nci.nih.gov/workspaces/ICR
Domain Workspaces
Tissue Banks Pathology Tools (TBPT,???????)htt
ps//cabig.nci.nih.gov/workspaces/TBPT
In Vivo Imaging(Vivo??) https//cabig.nci.nih.go
v/workspaces/Imaging
VocabulariesCommon Data Elements
(VCDE,????????)https//cabig.nci.nih.gov/workspa
ces/VCDE
Architecture(????) https//cabig.nci.nih.gov/work
spaces/Architecture
Cross Cutting Strategic Workspaces
Data Sharing Intellectual Capital
(DSIC,????????)https//cabig.nci.nih.gov/working
_groups/DSIC_SLWG
Documentation Training (DT,????)https//cabi
g.nci.nih.gov/working_groups/Training_SLWG
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Ongoing Projects
Medical Channel
Clinical Data Warehouse
Clinical Decision Support
Common Data Element Editor
Medical Natural Language Processing
Research Data Entry System
Data Sharing Decision Support
Synchronous Liver Metastasis Model
CDA Transfer Engine
Drug Knowledge Base
HL7 V3 Message Model
Clinical Guideline Computerization
Tissue Bank Annotation
Others
Medical Terminology Service
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Clinical Data Warehouse
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Clinical Data Warehouse
R-MIM Model
Database Structure
SOA Service Bus
Clinical Document (XML)
Database Records
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MetaManagerCommon Element Editor Data
Science Data Sharing Technology Standard(SDS/T
2131-2004) ISO/IEC 11179
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MetamanagerClinical Research Data Entry System
Automatic Tansfer
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Clinical Document CDA Transfer Engine
HL7 CDA Schema
Schema for Clinical Document
Discharge Summary
Transfer Engine
Mapping
CDA File
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Construction of HL7 V3 Message Model
V3Generator
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Natural Language Processing
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Information Retrieval
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Common Medical Terminology Service
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Integration of Drugs and Genetic Information
dbSNP
Gene Functions
SNP
Drug Information
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Integration of Disease and Gene Mutation
Information
Disease Information
Literatures Support
Disease Classification
Main Table
Experiment Samples
Gene Functions
Mutations
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GAD
COSMIC Catalogue Of Somatic Mutations In Cancer
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Disease Orientated Text Mining

• 5445 Full articles, 109259 Abstracts on colon
  cancer
• Interaction networks among proteins,genes and
  drugs

????????????????????,??????????,????????????
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Text Mining
MLH1and MSH2
?5-?????????????
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Rate of Occurring of Colorectal Cancer in Shanghai
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Study of HNPCC Related Gene Mutation in Chinese
Population

• 98 suspected HNPCC patients
• hMSH2 and hMLH1 genes

Patient DNA
PCR
Sequencing
Mutation Analysis
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HNPCC Database
Clinical Information
Pathology
Family History
Mutation
Follow Ups
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Hereditary Gene Mutation Screening
Platform (HNPCC)
Genetic Mutation
Registry
Doctor
Blood
Clinical Data
Self-Update
microsatellite instability
Patients
Screen Model
Screen Model
Follow Up Data
CRC - Colorectal Cancer
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Prognostic Effect of Biomarkers in Colorectal
Cancer Patients with Synchronous Liver Metastasis
Prediction Model with Multiple biomarkers New
Medical Knowledge Provide a Web-based tool for
clinical decision support
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Prognostic Effect of Biomarkers in Colorectal
Cancer Patients with Synchronous Liver Metastasis

• Colon Cancer Patients at Shanghai Tumor Hospital
  from 2000 to 2005

training training validation validation
Liver metastasis No liver metastasis Liver metastasis No liver metastasis
Number of subject 81 657 26 335
age 58.9112.00 57.5313.58 5512.00 58.3312.76
Gender(male) 60.5(49) 56.9(374) 61.5(16) 54.3(182)
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Feature Extraction
Ranked score attributes
0.11024461 CEA_before
0.05664258 CA50
0.04814296 CA19-9
0.01944378 max_diamete
0.01589365 rectum
0.00876265 abdominal_mass
0.00795528 hepatic_flexure
0.0071461 bellyache
0.00697108 hemafecia
0.0041877 straining_feeling_in_anus
0.00298395 sigmoid_colon
0.00297911 tenesmus_stool
0.00161622 hypodynamia
0.00136573 excrement_frequency_more_than_10
0.00104763 appendix
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Prognostic Effect of Biomarkers in Colorectal
Cancer Patients with Synchronous Liver Metastasis

• Prediction results for 152 patients in 2006
• Sensitivity62.5
• Specificity91.7
• Accuracy90.1

ROC0.85
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TissBank Information System
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Combined Tissue Bank Annotation from Operation
Summary and Pathology Report
Medical Natural Language Processing
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Rule-based Clinical Decision Support
Expert Knowledge Medical Logic Module MLM
Input
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Computerization of Clinical Guidelines
Arden Syntax
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Clinical Decision Support
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Medical ChannelOrthopedic
http//expert.91guke.com/
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Medical ChannelOrthopedic
http//expert.91guke.com/
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Summary
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Acknowledgement
???????? Shanghai Public Center for Healthcare
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Thank you!