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Data Integration and Clinical Decision Support for Personalized Medicine and Healthcare Shanghai Center for Bioinformation Technology and Shanghai Institute for Biological Sciences, CAS Shanghai Center for Bioinformation Technology and Shanghai Institute for Biological Sciences, CAS Lei Liu, Ph.D. 3/29/2010 Slide 2 Clinical Research Pathology Molecular Biology Imaging Translational Medicine Integration of Basic and Clinical Research From Bench to Bedside From Introduction of caBIG Slide 3 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 Slide 4 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, 2009,9:44 Slide 5 Shanghai Public R&D Shanghai Public R&D Service Platform Service Platform Clinical Data Repository Paper Record HL7 Non-HL7 Integrated Clinical Information Systems and Service Platform Tissue Bank Genotype Data Repository Comprehensive Data-Warehouse Key city hospitals Community hospitals Integrated Bioinformatics Platform(IBP) Slide 6 Domain Workspaces Cross Cutting & Strategic Workspaces Clinical Trials Management Systems (CTMS ) https://cabig.nci.nih.gov/workspaces/CTMS/ https://cabig.nci.nih.gov/workspaces/CTMS/ Integrative Cancer Research (ICR ) https://cabig.nci.nih.gov/workspaces/ICR https://cabig.nci.nih.gov/workspaces/ICR Tissue Banks & Pathology Tools (TBPT & ) https://cabig.nci.nih.gov/workspaces/TBPT In Vivo Imaging Vivo https://cabig.nci.nih.gov/workspaces/Imaging Vocabularies&Common Data Elements (VCDE & ) https://cabig.nci.nih.gov/workspaces/VCDE https://cabig.nci.nih.gov/workspaces/VCDE Architecture ( ) https://cabig.nci.nih.gov/workspaces/Architecture Data Sharing & Intellectual Capital (DSIC & ) https://cabig.nci.nih.gov/working_groups/DSIC_SLWG https://cabig.nci.nih.gov/working_groups/DSIC_SLWG Documentation & Training (D&T & ) https://cabig.nci.nih.gov/working_groups/Training_SLWG https://cabig.nci.nih.gov/working_groups/Training_SLWG caBIG Workspaces Slide 7 Ongoing Projects Clinical Decision Support Medical Natural Language Processing Synchronous Liver Metastasis Model Drug Knowledge Base Data Sharing Decision Support Data Sharing Decision Support Others Medical Channel Common Data Element Editor Research Data Entry System CDA Transfer Engine HL7 V3 Message Model Tissue Bank Annotation Medical Terminology Service Clinical Data Warehouse Clinical Guideline Computerization Slide 8 Clinical Data Warehouse Slide 9 R-MIM Model Database Structure Clinical Document XML Clinical Document XML Database Records SOA Service Bus Clinical Data Warehouse Slide 10 MetaManager: Common Element Editor Data Science Data Sharing Technology Standard SDS/T 2131-2004 ISO/IEC 11179 Slide 11 Metamanager: Clinical Research Data Entry System Automatic Tansfer MetaManager 1.40 Slide 12 Clinical Document CDA Transfer Engine Schema for Clinical Document HL7 CDA Schema Transfer Engine Discharge Summary CDA File Mapping Slide 13 Construction of HL7 V3 Message Model V3Generator Slide 14 Natural Language Processing Slide 15 Information Retrieval Slide 16 Common Medical Terminology Service Slide 17 SNP Drug Information Gene Functions dbSNP Integration of Drugs and Genetic Information Slide 18 Integration of Disease and Gene Mutation Information Literatures Support Experiment Samples Mutations Disease Information Disease Classification Gene Functions Main Table Slide 19 COSMIC Catalogue Of Somatic Mutations In Cancer GAD Slide 20 Disease Orientated Text Mining 5445 Full articles 109259 Abstracts on colon cancer Interaction networks among proteins,genes and drugs Slide 21 Text Mining MLH1and MSH2 5- Slide 22 Rate of Occurring of Colorectal Cancer in Shanghai Slide 23 98 suspected HNPCC patients hMSH2 and hMLH1 genes PCR Patient DNA Sequencing Mutation Analysis Study of HNPCC Related Gene Mutation in Chinese Population Slide 24 HNPCC Database Clinical Information Follow Ups Pathology Family History Mutation Slide 25 Hereditary Gene Mutation Screening Platform (HNPCC) Registry Self-Update Clinical Data Blood Follow Up Data Genetic Mutation CRC - Colorectal Cancer microsatellite instability Doctor Patients Screen Model Slide 26 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 Slide 27 trainingvalidation Liver metastasisNo liver metastasis Liver metastasis No liver metastasis Number of subject8165726335 age58.9112.0057.5313.585512.0058.3312.76 Gender(male)60.5%(49)56.9%(374)61.5%(16)54.3%(182) Colon Cancer Patients at Shanghai Tumor Hospital from 2000 to 2005 Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis Slide 28 Ranked scoreattributes 0.11024461CEA_before 0.05664258CA50 0.04814296CA19-9 0.01944378max_diamete 0.01589365rectum 0.00876265abdominal_mass 0.00795528hepatic_flexure 0.0071461bellyache 0.00697108hemafecia 0.0041877straining_feeling_in_anus 0.00298395sigmoid_colon 0.00297911tenesmus_stool 0.00161622hypodynamia 0.00136573excrement_frequency_more_than_10 0.00104763appendix Feature Extraction Slide 29 Prediction results for 152 patients in 2006 Sensitivity 62.5% Specificity 91.7% Accuracy 90.1% ROC 0.85 Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis Slide 30 TissBank Information System Slide 31 Combined Tissue Bank Annotation from Operation Summary and Pathology Report Medical Natural Language Processing Slide 32 Rule-based Clinical Decision Support Input Expert Knowledge Medical Logic Module MLM Slide 33 Computerization of Clinical Guidelines Arden Syntax Slide 34 Clinical Decision Support Slide 35 Medical ChannelOrthopedic http://expert.91guke.com/ Slide 36 Medical ChannelOrthopedic http://expert.91guke.com/ Slide 37 Summary Slide 38 Shanghai Public Center for Healthcare Shanghai Public Center for Healthcare Acknowledgement Slide 39 Thank you!