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1、Bioinformatics in Dermatology 生物資訊學在皮膚科學研究中的應用,Xue-Jun Zhang from Anhui Medical University 安徽醫科大學 張學軍,Headlines,生物資訊學的研究內容 醫學研究中常用的生物資訊資源及資料庫 生物資訊學在皮膚科學研究中的應用舉例,The major tasks of bioinformatics. Sources of biological information and databases concerning medical academic researches Examples of combi
2、ning dermatology and bioinformatics,1. The major tasks of generalized bioinformatics 廣義生物資訊學,Biological genetic information Control of the life activities Bioelectromagnetics Visual system and Processing of photo-information Cerebrum, neural system and information Biological structure and electromec
3、hanical system Microchip focus on genes and proteins ,生物的遺傳信息 生命活動的調控 生物電磁學與電磁生物學 視覺系統與光資訊處理 腦和神經系統與資訊 生物體結構與微光機電系統 基因晶片、蛋白質晶片等,1. The major tasks of narrow bioinformatics 狹義生物資訊學的研究內容,生物資訊收集、存儲、管理與提供 基因組序列資訊的提取和分析 功能基因組相關資訊的分析,Collection, conservation, management and supplying of biological informa
4、tion Extracting and analysis of genomic information Analysis of functional genomic information,Collection, conservation, management and supplying of biological information,These are the main tasks of big website of bioinformatics,Analysis of functional genomic information,These are the most frontier
5、 of scientific research.,Most investigations of bioinformatics are focus on genomic sequence,Extracting and analysis of genomic information,2. Sources of bio-information and databases 醫學研究中常用的生物資訊資源及資料庫,Important bio-information websites and databases on the internet Full-text literature databases C
6、ross-search engine,Internet上的生物資訊資源重要網站及資料庫 文獻全文資料庫 多種資料庫交叉搜索引擎,(1)Important bio-information websites and databases on the internet Internet上的生物資訊資源重要網站及資料庫,GenBank (http:/www.ncbi.nlm.nih.gov/Genbank/index.html) SWISS-PROT (http:/www.ebi.ac.uk/swissprot/access.html) Protein Data Bank，PDB，(http:/www
7、.rcsb.org/pdb),2. Sources of bio-information and databases,核酸序列資料庫 SWISS-PROT蛋白質序列資料庫 生物大分子結構資料庫,2. Sources of bio-information and databases,ADAR,Annotation,Sequence of amino acid,Sequence of nucleotides,2. Sources of bio-information and databases,Collagen VII,collagen,(2)Full-text literature databa
8、ses 文獻全文資料庫,PubMed http:/www.ncbi.nlm.nih.gov OVID http:/ EBSCO http:/ ScienceDirect http:/ Blackwell http:/ OCLC http:/oclc.org Kluwer http:/ Springer http:/link.springer.de WILEY InterScience http:/ HighWire Press http:/highwire.stanford.edu FreeMedicalJournals http:/,2. Sources of bio-information
9、 and databases,Search area,Chinese *,Other literature databases,Ingenta: http:/ Karger: http:/ Dekker: http:/ Websites of single journal http:/www.jci.org for the Journal of Clinical Investigation and http:/www.dermatol.or.jp for the Journal of Dermatology,2. Sources of bio-information and databases
10、,(3)Cross-search engine 多種資料庫交叉搜索引擎,2. Sources of bio-information and databases,Psoriasis AND gene,Websites of dermatology,Localization of Dyschromatosis Symmetric Hereditaria (DSH) Gene and Novel Mutations of the ADAR Gene in Chinese Families with DSH 遺傳性對稱性色素異常症精細定位和相關基因的突變檢測,3. Examples of combin
11、ing dermatology and bioinformatics 生物資訊學在皮膚科學研究中的應用舉例,遺傳性對稱性色素異常症(DSH)，系常染色體顯性遺傳病。嬰兒期或兒童期發病，在亞洲人中較常見。典型表現爲肢端有色素沈著和色素減退形成的網狀斑，病損呈對稱性分佈，無自覺症狀。由於皮損部位爲色素沈著或脫失，俗稱“花手”、“花腿”、“花臉”，嚴重影響美觀，給患者造成沈重的思想負擔。,Background,A dyschromatosis symmetrica hereditaria (DSH) patient,Two families with DSH from Anhui,J Invest
12、Dermatol ，2003; 120(6): 776-780,Refined localization: Patients,在安徽省和遼寧省收集2個DSH大家系。所有患者均經過皮膚科醫師的確診，符合DSH的診斷標準。家系1累積四代人，包括9名患者和11名正常人. 家系2涉及四代人，包括8名患者和8名正常人,Two families with DSH from Anhui and Liaoning,To refine DSH locus, we genotyped all available family members with 14 polymorphic microsatellite m
13、arkers at 1p11-21. Primer sequences of these markers were obtained from the Genome Database (http: / gdbwww.gdb.org).,Selection of Microsatellite,Microsatellite and the primer information,Results of Genotyping,The data were processed by Pedcheck software in order to analyze linkage,Parameter linkage
14、 analysis,Z1: suggestive linkage,LOD (Z),Z3: significant linkage,Z-2: no linkage,2Z1: more evidence are required,Software: Linkage,Two-Point combined LOD scores for DSH and 14 markers on Chromosome 1p11-21,Br J Dermatol, 2004, 150:633-39,Haplotype analysis refined DSH locus to a 9.4-cM interval flan
15、ked by D1S2343 and D1S2635.,The result of Refined localization,通過兩個DSH大家系的分析，精細定位DSH位點在1號染色體長臂約9.4cM的範圍內。,What is DSRAD (ADAR)?,ADAR gene aligning,mRNA,Find out encoding area by BLAT in UCSC,encoding sequences,Design primers,Now, we have 6 families with DSH,PCR,PCR was performed in 15-l reaction volume： 20ng of genomic DNA 0.3mM dNTPs 0.3M of each primer 3.0 mM MgCl2 0.1 units of HotstarTaq DNA polymerase,Electrophoresis on agarose,Sequencing by 3730 DNA Analyzer,Splicing and connecting reads by
