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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 陳沛隆(Pei-Lung Chen) | |
| dc.contributor.author | Ju-Mei Shao | en |
| dc.contributor.author | 邵如梅 | zh_TW |
| dc.date.accessioned | 2021-06-15T11:51:50Z | - |
| dc.date.available | 2019-08-26 | |
| dc.date.copyright | 2016-08-26 | |
| dc.date.issued | 2016 | |
| dc.date.submitted | 2016-08-11 | |
| dc.identifier.citation | 1 Northrup, H., Krueger, D. A. & International Tuberous Sclerosis Complex Consensus, G. Tuberous sclerosis complex diagnostic criteria update: recommendations of the 2012 Iinternational Tuberous Sclerosis Complex Consensus Conference. Pediatr Neurol 49, 243-254, doi:10.1016/j.pediatrneurol.2013.08.001 (2013).
2 Sampson, J. R., Scahill, S. J., Stephenson, J. B., Mann, L. & Connor, J. M. Genetic aspects of tuberous sclerosis in the west of Scotland. J Med Genet 26, 28-31 (1989). 3 van Slegtenhorst, M. et al. Interaction between hamartin and tuberin, the TSC1 and TSC2 gene products. Hum Mol Genet 7, 1053-1057 (1998). 4 Budde, K. & Gaedeke, J. Tuberous sclerosis complex-associated angiomyolipomas: focus on mTOR inhibition. Am J Kidney Dis 59, 276-283, doi:10.1053/j.ajkd.2011.10.013 (2012). 5 Green, A. J., Smith, M. & Yates, J. R. Loss of heterozygosity on chromosome 16p13.3 in hamartomas from tuberous sclerosis patients. Nat Genet 6, 193-196, doi:10.1038/ng0294-193 (1994). 6 Gomez, M. R. Phenotypes of the tuberous sclerosis complex with a revision of diagnostic criteria. Ann N Y Acad Sci 615, 1-7 (1991). 7 Rayer, P. F. O. Traits' theoriqué et pratique des maladies de la peau. Second edn, (J.B. Baillère, 1835). 8 File:TuberousSclerosis-Rayer-ColourSmall.jpg, <https://commons.wikimedia.org/wiki/File:TuberousSclerosis-Rayer-ColourSmall.jpg> (1835). 9 vonRecklinghausen, F. Ein Herz von einem Neugeborene welches mehrere theils nach aussen. theils nach den Hohlen prominirende Tumoren (Myomen) trug. Monatsschr Geburtsheilk 20, 1-2 (1862). 10 Bourneville, D. Sclerose tubereuse des circonvolutions cerebrales: idiotie et epilepaie hemiplegique. Arch. Neural. (Paris) 1, 81-91 (1880). 11 Lendvay, T. S. & Marshall, F. F. The tuberous sclerosis complex and its highly variable manifestations. J Urol 169, 1635-1642, doi:10.1097/01.ju.0000058253.40352.60 (2003). 12 Vogt, H. Zur Pathologie und pathologishcen Anatomie der verschiedenen Idiotieform. Monatsschrift für Psychiatrie und Neurologie 24, 106-150 (1908). 13 vanderHoeve, J. Eye symptoms in tuberous sclerosis of the brain. Trams Ophthalmol Sot UK 20, 329-334 (1920). 14 Crithchley, M. & Earl, C. Tuberose Sclerosis and Allied conditions. Brain 55, 311-346 (1932). 15 Moolten, S. Hamartial nature of the tuberous sclerosis complex and its bearing on the tumor problem. Archives of Internal Medicine 69, 589 (1942). 16 Lagos, J. C. & Gomez, M. R. Tuberous sclerosis: reappraisal of a clinical entity. Mayo Clin Proc 42, 26-49 (1967). 17 Gomez, M. Tuberous sclerosis., (Raven Press, 1979). 18 Connor, J. M., Pirrit, L. A., Yates, J. R., Fryer, A. E. & Ferguson-Smith, M. A. Linkage of the tuberous sclerosis locus to a DNA polymorphism detected by v-abl. J Med Genet 24, 544-546 (1987). 19 Kandt, R. S. et al. Linkage of an important gene locus for tuberous sclerosis to a chromosome 16 marker for polycystic kidney disease. Nat Genet 2, 37-41, doi:10.1038/ng0992-37 (1992). 20 Roach, E. S. et al. Diagnostic criteria: tuberous sclerosis complex. Report of the Diagnostic Criteria Committee of the National Tuberous Sclerosis Association. J Child Neurol 7, 221-224 (1992). 21 Roach, E. S., Gomez, M. R. & Northrup, H. Tuberous sclerosis complex consensus conference: revised clinical diagnostic criteria. J Child Neurol 13, 624-628 (1998). 22 Tello, R., Blickman, J. G., Buonomo, C. & Herrin, J. Meta analysis of the relationship between tuberous sclerosis complex and renal cell carcinoma. Eur J Radiol 27, 131-138 (1998). 23 Webb, D. W., Clarke, A., Fryer, A. & Osborne, J. P. The cutaneous features of tuberous sclerosis: a population study. Br J Dermatol 135, 1-5 (1996). 24 Jozwiak, S., Schwartz, R. A., Janniger, C. K. & Bielicka-Cymerman, J. Usefulness of diagnostic criteria of tuberous sclerosis complex in pediatric patients. J Child Neurol 15, 652-659 (2000). 25 Zimmer-Galler, I. E. & Robertson, D. M. Long-term observation of retinal lesions in tuberous sclerosis. Am J Ophthalmol 119, 318-324 (1995). 26 Gumbinger, C. et al. Focal cortical dysplasia: a genotype-phenotype analysis of polymorphisms and mutations in the TSC genes. Epilepsia 50, 1396-1408, doi:10.1111/j.1528-1167.2008.01979.x (2009). 27 Geipel, A., Krapp, M., Germer, U., Becker, R. & Gembruch, U. Perinatal diagnosis of cardiac tumors. Ultrasound Obstet Gynecol 17, 17-21, doi:10.1046/j.1469-0705.2001.00314.x (2001). 28 Casper, K. A., Donnelly, L. F., Chen, B. & Bissler, J. J. Tuberous sclerosis complex: renal imaging findings. Radiology 225, 451-456, doi:10.1148/radiol.2252011584 (2002). 29 Brook-Carter, P. T. et al. Deletion of the TSC2 and PKD1 genes associated with severe infantile polycystic kidney disease--a contiguous gene syndrome. Nat Genet 8, 328-332, doi:10.1038/ng1294-328 (1994). 30 Bissler, J. J. & Kingswood, J. C. Renal angiomyolipomata. Kidney Int 66, 924-934, doi:10.1111/j.1523-1755.2004.00838.x (2004). 31 Zarogiannis, S., Hatzoglou, C., Molyvdas, P. A. & Gourgoulianis, K. Lymphangioleiomyomatosis. Eur Respir J 28, 1284, doi:10.1183/09031936.00099606 (2006). 32 Carsillo, T., Astrinidis, A. & Henske, E. P. Mutations in the tuberous sclerosis complex gene TSC2 are a cause of sporadic pulmonary lymphangioleiomyomatosis. Proc Natl Acad Sci U S A 97, 6085-6090 (2000). 33 Steffen, C. Diagnosis of tuberous sclerosis. JAMA 250, 1977-1978 (1983). 34 Sparling, J. D., Hong, C. H., Brahim, J. S., Moss, J. & Darling, T. N. Oral findings in 58 adults with tuberous sclerosis complex. J Am Acad Dermatol 56, 786-790, doi:10.1016/j.jaad.2006.11.019 (2007). 35 Miyamoto, Y., Satomura, K., Rikimaru, K. & Hayashi, Y. Desmoplastic fibroma of the mandible associated with tuberous sclerosis. J Oral Pathol Med 24, 93-96 (1995). 36 Gould, S. R. Hamartomatous rectal polyps are common in tuberous sclerosis. Ann N Y Acad Sci 615, 71-80 (1991). 37 Kwiatkowski, D. J., Whittemore, V. H. & Thiele, E. A. Tuberous sclerosis complex : genes, clinical features, and therapeutics. (Wiley-Blackwell, 2010). 38 Krueger, D. A., Northrup, H. & International Tuberous Sclerosis Complex Consensus, G. Tuberous sclerosis complex surveillance and management: recommendations of the 2012 International Tuberous Sclerosis Complex Consensus Conference. Pediatr Neurol 49, 255-265, doi:10.1016/j.pediatrneurol.2013.08.002 (2013). 39 Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17, 405-424, doi:10.1038/gim.2015.30 (2015). 40 Dabora, S. L. et al. Mutational analysis in a cohort of 224 tuberous sclerosis patients indicates increased severity of TSC2, compared with TSC1, disease in multiple organs. Am J Hum Genet 68, 64-80, doi:10.1086/316951 (2001). 41 CFR - Code of Federal Regulations Title 21., <http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=11.10> (2016). 42 Electronic data capture, <https://en.wikipedia.org/wiki/Electronic_data_capture> (2016). 43 National Society of Genetic Counselors' Definition Task, F. et al. A new definition of Genetic Counseling: National Society of Genetic Counselors' Task Force report. J Genet Couns 15, 77-83, doi:10.1007/s10897-005-9014-3 (2006). 44 吳采姿. 建立以次世代定序為方法之結節硬化症基因檢測 碩士 thesis, 台灣大學, (2014). 45 Tyburczy, M. E. et al. Sun exposure causes somatic second-hit mutations and angiofibroma development in tuberous sclerosis complex. Hum Mol Genet 23, 2023-2029, doi:10.1093/hmg/ddt597 (2014). 46 Henske, E. P. et al. Allelic loss is frequent in tuberous sclerosis kidney lesions but rare in brain lesions. Am J Hum Genet 59, 400-406 (1996). 47 Tyburczy, M. E. et al. Mosaic and Intronic Mutations in TSC1/TSC2 Explain the Majority of TSC Patients with No Mutation Identified by Conventional Testing. PLoS Genet 11, e1005637, doi:10.1371/journal.pgen.1005637 (2015). 48 Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760, doi:10.1093/bioinformatics/btp324 (2009). 49 McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297-1303, doi:10.1101/gr.107524.110 (2010). 50 Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38, e164, doi:10.1093/nar/gkq603 (2010). 51 Kumar, P., Henikoff, S. & Ng, P. C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4, 1073-1081, doi:10.1038/nprot.2009.86 (2009). 52 Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nat Methods 7, 248-249, doi:10.1038/nmeth0410-248 (2010). 53 Genomes Project, C. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65, doi:10.1038/nature11632 (2012). 54 臨床研究資訊系統 (Clinical Study Information System, CSIS), <https://www.cims.tw/ch/csis-introduction> (2011). 55 Verhoef, S. et al. Somatic mosaicism and clinical variation in tuberous sclerosis complex. Lancet 345, 202 (1995). 56 Qin, W. et al. Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex. Hum Genet 127, 573-582, doi:10.1007/s00439-010-0801-z (2010). | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/49840 | - |
| dc.description.abstract | 結節硬化症（Tuberous sclerosis complex）是一種自體顯性遺傳，因TSC1或TSC2基因發生致病變異點而造成。能夠引起疾病的基因變異型態多樣，且有10-20%無法從以傳統分子檢驗診斷方法找到致病變異點。台大醫院結節硬化症基因研究案，以次世代定序方法檢驗110個結節硬化症之首位確診病患（proband）及其家族位於TSC1或TSC2基因變異點。共有96（87%）個家族於TSC1或TSC2基因找到致病變異點（pathogenic variant）或高度懷疑之致病變異點（likely pathogenic variant），14（13%）個家族並沒有找到致病變異點（no mutation identified）。在有找到致病變異點的 96 個家族中，57（59%）個家族屬於點突變（point mutation），28（29%）個家族為小片段插入、重複、或缺失（small indel），以及11（11%）個家族是大片斷缺失或重複（Large deletion/duplication）。十四（15%）個家族是TSC1基因變異造成的，而82（85%）個家族是TSC2基因變異造成。有5個家族首位確診患者（Proband）帶有鑲嵌型的致病變異點，另有2個帶有異型合子致病變異點之患病個案之其中一親代帶有鑲嵌型致病變異點，皆位於TSC2基因。另外，本研究亦於一家族發現一剪接位點變異位於TSC2, c.138+5G>T，其中2個患病之家族成員皆帶有此變異點，無患病者則無。
針對未能於正規次世代定序基因檢測直接找到致病變異點之患者，後續亦使用局部病灶來檢測可能之變異點，共有10個病灶檢體，從3個沒有找到變異點的個案及2個已發現致病點的個案（陽性對照）取得。經由此方式在一個原本沒有找到變異點個案的局部病灶檢體中檢測出一個位於TSC2基因的非常低對偶基因比率（Allele percentage）（0.6%）的變異點，推測此變異點可能為一個Second Hit變異點，並暗示可能此名個案的Germline變異也同樣位於TSC2基因。 根據以上的結果，針對少數基因檢測無法找出致病變異點之臨床確診結節硬化症患者，推測有以下幾個原因，提供未來研究之用：（1）落在TSC1或TSC2基因但非常低對偶基因比率的鑲嵌型變異點；（2）變異點發生在TSC1或TSC2基因非靠近外顯子的剪接位點、啟動子（Promoter）或強化子（enhancer）區域；（3）技術問題而導致沒有成功找到變異點；（4）發生在另外第三個結節硬化症目前未知的致病基因。 另外，為管理結節硬化基因研究所收集的臨床資料及基因檢測結果，設立了線上臨床研究資料庫 – 臨床研究資訊系統（Clinical Study Information System, CSIS），根據結節硬化症基因研究設計了客製化之資料建置表單，且此系統是以授權研究人員之個人帳號密碼來做為保護資料。所有收集資料包含了病人之臨床資料及基因檢測結果目前都已經分別輸入系統並妥善管理。 | zh_TW |
| dc.description.abstract | Tuberous sclerosis complex (TSC) is an autosomal dominant disease due to causative variants at either TSC1 or TSC2. The disease-causating mutations are highly variable and 10–20% of TSC individuals have no causative variants identified after thorough conventional molecular diagnostic assessment. In this study, 110 definite TSC probands were studied using next-generation sequencing (NGS) to search for pathogenic variants at TSC1 and TSC2 genes. “Pathogenic” or “likely pathogenic” variants were identified in 96 (87%) probands; however, 14 (13%) probands could not be assigned causative variants. Among the 96 identified causative variants, 58 (60%) were single nucleotide substitutions, 28 (29%) were small indels, and 10 (10%) were large deletions/duplications. Fourteen (15%) probands were found to have variants at TSC1 and 82 (85%) were found to have variants at TSC2. Seven individuals were mosaic regarding to their causative variants, including 5 probands and parents of other two non-mosaic probands. A splicing site variant “TSC2, c.138+5G>T” was identified in one TSC family co-segregated in 2 affected family members.
With the intent to investigate the genetic etiology in those TSC patients without identifiable causative variants at TSC1 or TSC2, we conducted sequencing using focal lesion DNA. A total of 10 focal lesions obtained from 3 no-mutation-identified probands and 2 probands with one germline mutation (positive control) were studied. One pathogenic mutation at TSC2 with 0.6% of allele percentage was detected in the focal lesion DNA of one no-mutation-identified proband. This variant was considered as the second-hit mutation and indicated that the germline mutation in this patient is located in TSC2 gene as well. However, no potential second-hit mutation was identified in the positive control samples. These findings concluded and suggested that there were several possible reasons for no-mutation-identified status in TSC patients: 1) mosaicism with very low allele percentage for variants at TSC1 or TSC2; 2) variants in introns that affect splicing, or in promoter and enhancer regions of TSC1 and TSC2; 3) variants detection failure due to technical issues; 4) variants at a yet-unknown third TSC gene. Furthermore, to manage the clinical research data collected from TSC Genetic Research, a user-friendly online clinical research database - Clinical Study Information System (CSIS) was established. The study-specified data entry forms were designed for TSC Genetic Research and the system was under security protection by personal ID and password for researchers who were delegated to this study. All the available data including the clinical information from subjects and genetic test results were entered and managed by our study team accordingly. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-15T11:51:50Z (GMT). No. of bitstreams: 1 ntu-105-P03448011-1.pdf: 2112354 bytes, checksum: 09b656012bcad314f6db5388ad631a3f (MD5) Previous issue date: 2016 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
致謝 ii 中文摘要 iii 英文摘要 v 目錄 vii 圖目錄 x 表目錄 xi 第一章 研究背景與動機 1 1.1 結節硬化症疾病介紹 1 1.2 結節硬化症的歷史演進 1 1.3 結節硬化症的臨床特徵 3 1.3.1 皮膚表徵 3 1.3.2 眼部表徵 4 1.3.3 神經表徵 4 1.3.4 心臟表徵 4 1.3.5 腎臟表徵 4 1.3.6 肺臟表徵 4 1.3.7 牙齒表徵 4 1.3.8 其他器官表現 5 1.4 結節硬化症臨床診斷及檢查 5 1.4.1 臨床診斷 5 1.4.1.1 主要表徵 5 1.4.1.2 次要表徵 6 1.4.2 臨床診斷檢查 6 1.5 結節硬化症基因診斷及檢測方式 6 1.5.1 基因診斷 6 1.5.2 基因檢測方式 7 1.6 臨床研究資訊系統（Clinical study information system） 7 1.7 遺傳諮詢 8 1.8 研究目的 8 第二章 研究方法 10 2.1 研究對象來源及條件 10 2.1.1 受試者來源 10 2.1.2 受試者條件 10 2.1.3 檢體來源與取得 10 2.2 次世代定序基因檢測 10 2.2.1 DNA的萃取與定量分析 10 2.2.1.1 周邊血液檢體 10 2.2.1.2 局部病灶組織檢體 10 2.2.2 次世代定序及檢體配置 11 2.2.3 次世代定序結果判讀 12 2.2.3.1 軟體判讀 12 2.2.3.2 資料過濾 12 2.2.3.3 圖像化判讀 12 2.2.4 聚合酶連鎖反應（PCR）與Sanger定序分析 13 2.2.5 實驗試劑及器材 13 2.2.5.1 實驗試劑 13 2.2.5.2 實驗器材 13 2.2.6 變異點致病性判定 14 2.3 臨床研究資訊系統建立與管理 14 2.3.1 表單建立 14 2.3.2 帳號管理 14 2.4 遺傳諮詢 16 第三章 研究結果 19 3.1 次世代定序結果統計及分析 19 3.1.1 結節硬化症基因研究 19 3.1.2 結節硬化症局部病灶研究 19 3.1.2.1 局部病灶檢體 19 3.1.2.2 局部病灶檢體之次世代定序結果 19 3.2 結節硬化症基因變異型態 20 3.2.1 鑲嵌型 20 3.2.2 剪接位點（splicing site）變異 20 3.2.3 全基因大片段缺失或重複 21 3.2.4 Second-Hit變異現象 21 3.2.4.1 Small Indel 21 3.2.4.2 點突變（point mutation） 21 3.3 遺傳諮詢案例 23 3.3.1 案例一 23 3.3.2 案例二 24 3.4 臨床研究資訊系統 25 3.4.1 線上資料庫統計 25 第四章 討論 35 4.1 鑲嵌型突變 35 4.2 病灶檢體之變異點偵測 35 4.2.1 陽性對照個案檢體 35 4.2.2 過去未發現致病變異點個案之檢體 36 4.3 剪接位點（splicing site）突變 37 第五章 結論 38 參考文獻 39 附錄一 42 附錄二 46 | |
| dc.language.iso | zh-TW | |
| dc.subject | 臨床研究資訊系統 | zh_TW |
| dc.subject | 結節硬化症 | zh_TW |
| dc.subject | 次世代定序 | zh_TW |
| dc.subject | 未找到致病變異點 | zh_TW |
| dc.subject | 鑲嵌型 | zh_TW |
| dc.subject | 局部病灶 | zh_TW |
| dc.subject | 線上臨床研究資料庫 | zh_TW |
| dc.subject | Tuberous sclerosis complex (TSC) | en |
| dc.subject | clinical study information system | en |
| dc.subject | online clinical research database | en |
| dc.subject | focal lesion | en |
| dc.subject | mosaicism | en |
| dc.subject | no mutation identified | en |
| dc.subject | next generation sequencing | en |
| dc.title | 結節硬化症之次世代定序基因檢測 - 強調局部病灶檢體定序及臨床研究資料庫 | zh_TW |
| dc.title | Next-generation Sequencing (NGS)-based Genetic Testing for Tuberous Sclerosis Complex (TSC) - Highlighting on Focal Lesion Sequencing & Clinical Research Database | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 104-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 楊偉勛(Wei-Shiung Yang),謝豐舟(Fon-Jou, HSIEH),廖怡華(Yi-Hua Liao) | |
| dc.subject.keyword | 結節硬化症,次世代定序,未找到致病變異點,鑲嵌型,局部病灶,線上臨床研究資料庫,臨床研究資訊系統, | zh_TW |
| dc.subject.keyword | Tuberous sclerosis complex (TSC),next generation sequencing,no mutation identified,mosaicism,focal lesion,online clinical research database,clinical study information system, | en |
| dc.relation.page | 57 | |
| dc.identifier.doi | 10.6342/NTU201602307 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2016-08-11 | |
| dc.contributor.author-college | 醫學院 | zh_TW |
| dc.contributor.author-dept | 分子醫學研究所 | zh_TW |
| 顯示於系所單位： | 分子醫學研究所 | |
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