臺灣博碩士論文加值系統

乾癬；俗稱牛皮癬，為一慢性皮膚病，根據台灣衛生機關統計其發生率佔皮膚科病人的百分之一至百分之二，而男女兩性的發生率則無差別。其主要症狀為上皮細胞及微血管過度增生造成皮膚的發炎現象。在成因方面，目前說法不一，很多組織學、生化學、免疫學及遺傳學的研究顯示出此慢性疾病可能由多種因子協同造成，如外在環境壓力、病毒、細菌、自體免疫等可能都為引發乾癬的因子之一。而近代遺傳學的研究發現本症受到遺傳因素之影響似乎相當明顯，雖然其遺傳成分佔形成乾癬病因的比重仍為未知。
早在六十年代就有文獻記載著乾癬與遺傳因子間的關係，隨著遺傳分析法的進步，鎖定於造成乾癬的基因位範圍也逐漸縮小，而且鎖定的基因群大部分都與免疫系統有關。在人類第六號染色體的短臂有一區域存在與人類白血球抗原（HLA）有關的基因群，而此區域是目前已知的功能基因中最具多態性的基因群之一。根據最新之文獻，人類白血球抗原基因群中HCR基因的單一核苷酸多態性分佈似乎與乾癬的發病率有顯著的相關性。本文使用DNA定序法輔以解旋式高效能液相層析法（dHPLC）分析台灣族群的乾癬病患其HCR基因的單一核苷酸多態性分佈，並與未患任何自體免疫相關疾病的健康對照組做比較，藉此探討台灣族群中HCR基因的多態性是否與乾癬的形成有相關。實驗結果發現在乾癬病患的HCR基因與對照組中同樣的多態性位置作比較，對照組中鹼基改變的頻率相對偏低，表示這些多態性的確與乾癬的發生與否有顯著的相關性。而某些多態性更進一步造成氨基酸序列的改變。
本文的另一目的是以HCR基因的多態性作為資料來源以建立屬於台灣本土的單一核苷酸多態性資料庫，利用電腦高速運算、資料庫內容易於分析整理及程式模組化的特性，整合一般資料庫搜尋資料的功能再加上開發出的模組，建置出一系列利於研究人員及醫療從事人員使用的系統，期望此一加值型資料庫能成為單一核苷酸多態性的研究邁向個人化醫療等實用目的之輔助工具。
雖然HCR基因的功能及乾癬的致病機制仍然渾沌未明，但期望以此研究成果及資料庫系統作為未來針對乾癬甚至其他遺傳性疾病其基因多態性研究之參考。

Psoriasis is a chronic skin disorder occurring in 1%~2% of dermatosis cases. There is no difference between male and female for the frequency of psoriasis. Characteristic features include epidermal keratinocyte hyperproliferation, altered epidermal maturation, vascular proliferation, and inflammatory cell accumulation. Whereas the pathogenesis of psoriasis remains uncertain, some evidence suggest that multiple factors, including environmental stress, virus, microbe, autoimmune system can cause psoriasis synergistically. Although the genetic component of psoriasis is still unknown, modern genetic analysis suggest the transmission of psoriasis is affected by genetic factors.
Previous studies suggest that the psoriasis and genetic factors are highly correlated. The psoriasis candidate loci have been narrowed down by applying improve on genetic assay methods. One of the candidate locus contains immune gene cluster, called HLA-C cluster or PSOR1, which locates on the chromosome 6p. This locus is one of the highly polymorphic gene clusters ever known. Recent studies indicate that one of the PSOR1 genes, called HCR, correlates with the pathogenesis of psoriasis. The distribution of single nucleotide polymorphisms (SNP) in HCR will affect the frequency of psoriasis. Using the genomic DNA sequencing and dHPLC, screen of the SNPs in HCR gene of Taiwanese patients with psoriasis. By the case-control study we find some significant SNPs have higher allele frequency in patients than in healthy controls. Furthermore, some SNPs alter the amino acid sequence of the HCR protein. Wishing genetic epidemiology and functional studies, these SNPs will provide some clues to understanding the pathogeny of psoriasis.
The other purpose in our research is to establish a SNP database of pathogenic genes in Taiwanese patients. At the beginning, data of SNPs in HCR genes isused to generate the prototype of this database. We create a lot of functional modules to fit the requirement of personal medical care and other practical applications.
In the future, expansion and improvement of the database is necessary increase to a capacity for more and more SNPs discovery. Combination of the wet-bench experiences and bioinformatics techniques, we give an example for large-scale SNP data analysis and friendly query system for the research of pathogenic SNP screen.

中文摘要..............................................I
英文摘要..............................................II
圖表目次..............................................III
第一章 導論
1.1 乾癬之簡介...................................1
1.2 乾癬之遺傳性.................................6
1.3 乾癬致病基因的探索...........................6
1.4 HCR基因......................................9
1.5 PHP及MySQL簡介..............................9
1.6 資料庫系統建置的起因與動機...................11
第二章 實驗材料及方法
2.1 研究對象.....................................13
2.2 實驗方法.....................................13
2.2.1 去氧核醣核酸萃取.....................13
2.2.2 引子設計及合成.......................13
2.2.3 聚合脢連鎖反應.......................14
2.2.4 洋菜膠體電泳.........................14
2.2.5 引子及其他碎裂DNA 片段之去除........15
2.2.6 定序反應.............................15
2.2.7 酒精沉澱及定序.......................15
2.2.8 伺服主機之建置.......................16
2.2.9 基因序列分析.........................16
2.2.10 HCR 基因單倍體分析...................17
2.2.11 資料庫及網頁搜尋介面之建立...........17
第三章 實驗結果
3.1 HCR 基因
3.1.1 定序反應及序列分析...................18
3.1.2 單一核苷酸多態性分析.................18
3.1.3 HCR 蛋白質二級結構預測...............19
3.1.4 HCR 基因單倍體分析...................
3.2 單一核苷酸多態性資料庫之建立.................20
3.2.1 伺服主機建置及設定...................20
3.2.2 資料處理程式之建立...................21
3.2.3 資料庫之建立.........................21
3.2.4 網頁搜尋介面之建立...................22
3.2.4.1 資料搜尋引擎..................23
3.2.4.2 資料上傳引擎..................24
第四章 討論.........................................26
參考文獻................................................32
Appendix A..............................................36
Appendix B..............................................38

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