Presentation is loading. Please wait.

Presentation is loading. Please wait.

Lei Liu, Ph.D. Shanghai Center for Bioinformation Technology and

Similar presentations


Presentation on theme: "Lei Liu, Ph.D. Shanghai Center for Bioinformation Technology and"— Presentation transcript:

1 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

2 Translational Medicine
Integration of Basic and Clinical Research From Bench to Bedside Clinical Research Imaging Presenter: “NCIA is one in a set of complementary tools called the “Life Science Bundle.” Like all of the caBIG™ tools, NCIA plays a specific role in the cancer research continuum – which can be loosely grouped into four categories - Clinical Research, Imaging, Pathology, and Molecular Biology.” (the last 4 correspond with animations in the figure, so click while speaking). NCIA supports the Imaging aspects of this research continuum.” Presenter: “NCIA is ……. (read the text from the slide).” From Introduction of caBIG Molecular Biology Pathology 2

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 The materialization of an emerging idea for personalized medicine – purported to apply the right drug in the right dose for the right person at the right time – relies critically on our ability to identify all relevant genetic variants in each patient and interpret this information in a clinically meaningful manner

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 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

5 Integrated Clinical Information Systems and Service Platform
Key city hospitals Community hospitals HL7 Non-HL7 Paper Record Shanghai Public R&D Service Platform Clinical Data Repository Tissue Bank Genotype Data Repository Integrated Bioinformatics Platform(IBP) Comprehensive Data-Warehouse

6 caBIG® Workspaces Domain Workspaces Clinical Trials Management Systems
(CTMS,临床实验管理系统) https://cabig.nci.nih.gov/workspaces/CTMS/ Integrative Cancer Research (ICR,综合肿瘤研究) https://cabig.nci.nih.gov/workspaces/ICR Domain Workspaces Tissue Banks & Pathology Tools (TBPT,组织库&病理学工) https://cabig.nci.nih.gov/workspaces/TBPT In Vivo Imaging (Vivo成像) https://cabig.nci.nih.gov/workspaces/Imaging Vocabularies&Common Data Elements (VCDE,词汇&公共数据元素) https://cabig.nci.nih.gov/workspaces/VCDE Architecture (体系构架) https://cabig.nci.nih.gov/workspaces/Architecture Cross Cutting & Strategic Workspaces Data Sharing & Intellectual Capital (DSIC,数据共享&智能财产) https://cabig.nci.nih.gov/working_groups/DSIC_SLWG Documentation & Training (D&T,文件&培训) https://cabig.nci.nih.gov/working_groups/Training_SLWG

7 Ongoing Projects Data Sharing + Decision Support Medical Channel
Clinical Data Warehouse Medical Channel Common Data Element Editor Clinical Decision Support Medical Natural Language Processing Research Data Entry System Data Sharing Decision Support CDA Transfer Engine Synchronous Liver Metastasis Model Drug Knowledge Base HL7 V3 Message Model Clinical Guideline Computerization Tissue Bank Annotation Medical Terminology Service Others 7

8 Clinical Data Warehouse
Registry Information Model (RIM) 8

9 Clinical Data Warehouse
R-MIM Model Database Structure SOA Service Bus Clinical Document (XML) Database Records

10 MetaManager: Common Element Editor Data
Science Data Sharing Technology Standard(SDS/T ) ISO/IEC 11179

11 Metamanager: Clinical Research Data Entry System
Automatic Tansfer MetaManager 1.40

12 Clinical Document CDA Transfer Engine
HL7 CDA Schema Schema for Clinical Document Discharge Summary Transfer Engine Mapping CDA File

13 Construction of HL7 V3 Message Model
V3Generator

14 Natural Language Processing
这张图是整个自然语言处理的流程 首先,看蓝色虚线部分,这是人工标注阶段。张韡德医生和我用protégé对一部分手术记录进行手工标注,标注的内容主要是医生感兴趣的内容,标注的方式是按照医生的思维,先找到表明该信息点整句话,然后找到查找词和答案,比如,我们以肿瘤大小为例。整句话为“大小约4.5*5*8cm”,查找词为“大小”,答案为4.5*5*8cm (动画还没做,打算采用复制的办法)

15 Information Retrieval
自然语言处理模块已经整合到临床数据收集系统Clindata Express中 15

16 Common Medical Terminology Service
16

17 Integration of Drugs and Genetic Information
dbSNP Gene Functions 整合后的数据库关系图 Drug Information SNP

18 Integration of Disease and Gene Mutation Information
Disease Information Literatures Support Disease Classification Main Table 整合后的数据库包括: 主表。基因信息表。实验(文章)信息表。疾病信息表。疾病分类表 主表: HGNC ID 基因相关 Association ID 疾病相关 Submitter 基因信息表: HGNC ID Approved Symbol Approved Name Status Previous Symbols Previous Names Aliases Name Aliases Chromosome Accession Numbers Pubmed IDs Gene Family Name Locus Specific Databases GDB ID (mapped data) Entrez Gene ID OMIM ID RefSeq UniProt ID Ensembl ID UCSC ID 实验(文章)信息表:Association ID Reference Pubmed ID Disease ID Sample ID Allele Author Discription Allele Functional Effects Population Method 疾病信息表: Disease ID Disease name Disease Aliases Disease Class ID Disease Phenotype 疾病分类表: Disease Class ID Disease Class Disease Class Code 样品信息:Sample ID HGNC ID Association ID Mutation ID Narrow Phenotype Sample gender Sample age Sample geographical location Sample parent tested Sample environment variables 突变信息: Mutation ID Mutation type Mutation intron Mutation exon Mutation DNA location Mutation DNA change Mutation RNA location Mutation RNA change Mutation protein location Mutation protein change Experiment Samples Gene Functions Mutations

19 GAD COSMIC Catalogue Of Somatic Mutations In Cancer

20 Disease Orientated Text Mining
5445 Full articles, Abstracts on colon cancer Interaction networks among proteins,genes and drugs 所有摘要中基因、蛋白质与药物相互作用网络,其中红色的点代表药物,蓝色的点代表基因或蛋白质

21 Text Mining MLH1and MSH2 与5-氟尿嘧啶相关的基因或蛋白质

22 Rate of Occurring of Colorectal Cancer in Shanghai

23 Study of HNPCC Related Gene Mutation in Chinese Population
98 suspected HNPCC patients hMSH2 and hMLH1 genes Patient DNA PCR Sequencing Mutation Analysis

24 HNPCC Database Clinical Information Pathology Family History Mutation
Follow Ups

25 Hereditary Gene Mutation Screening Platform
(HNPCC) Genetic Mutation Doctor Registry Blood Self-Update Clinical Data microsatellite instability Patients Screen Model Screen Model Follow Up Data CRC - Colorectal Cancer

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

27 Colon Cancer Patients at Shanghai Tumor Hospital from 2000 to 2005
Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis Colon Cancer Patients at Shanghai Tumor Hospital from 2000 to 2005 training validation Liver metastasis No liver metastasis Liver Number of subject 81 657 26 335 age 58.91±12.00 57.53±13.58 55±12.00 58.33±12.76 Gender(male) 60.5%(49) 56.9%(374) 61.5%(16) 54.3%(182)

28 Feature Extraction Ranked score attributes 0.11024461 CEA_before
CA50 CA19-9 max_diamete rectum abdominal_mass hepatic_flexure bellyache hemafecia straining_feeling_in_anus sigmoid_colon tenesmus_stool hypodynamia excrement_frequency_more_than_10 appendix

29 Prediction results for 152 patients in 2006:
Prognostic Effect of Biomarkers in Colorectal Cancer Patients with Synchronous Liver Metastasis Prediction results for 152 patients in 2006: Sensitivity:62.5% Specificity:91.7% Accuracy:90.1% ROC:0.85

30 TissBank Information System

31 Combined Tissue Bank Annotation from Operation Summary and Pathology Report
Medical Natural Language Processing 31

32 Rule-based Clinical Decision Support
Expert Knowledge Medical Logic Module ——MLM Input

33 Computerization of Clinical Guidelines
Arden Syntax

34 Clinical Decision Support

35 Medical Channel——Orthopedic
电子病历设计 35

36 Medical Channel——Orthopedic

37 Summary

38 Shanghai Public Center for Healthcare
Acknowledgement 上海公共卫生中心 Shanghai Public Center for Healthcare

39 Thank you!


Download ppt "Lei Liu, Ph.D. Shanghai Center for Bioinformation Technology and"

Similar presentations


Ads by Google