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研究生: 賴俊吉
Lai, Chun Chi
論文名稱: 以家譜基因型方法找尋全外顯體測序結果中符合孟德爾遺傳疾病的候選突變
The pedigree-genotype method to find candidate variants of Mendelian disease with whole exome sequencing
指導教授: 唐傳義
Tang, Chuan Yi
謝文萍
Hsieh, Wen Ping
口試委員: 唐傳義
謝文萍
許隆安
葉勇信
林俊淵
王雯靜
盧錦隆
韓永楷
Hsieh, Wen Ping
學位類別: 博士
Doctor
系所名稱: 電機資訊學院 - 資訊工程學系
Computer Science
論文出版年: 2014
畢業學年度: 102
語文別: 英文
論文頁數: 50
中文關鍵詞: 病竇症候群全外顯體測序LMNA 基因短序列排比變異點呼叫變異點註解連鎖分析蛋白結構模擬
外文關鍵詞: Sick Sinus Syndrome, whole exome sequencing, LMNA gene, short reads alignment, variants calling, variants annotation, linkage analysis, protein structure modeling
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  • 摘要

    追獵疾病的致病基因以找尋病痛的本質然後治癒是我們的目標。全外顯子體測序是一個強大的工具,可以比全基因體測序技術較低的成本來得到周圍目標區域的DNA序列。序列排比和變異點呼叫這些工具幫助我們從龐大的原始 DNA 數據進行分析找出單核苷酸變異( SNV )和插入/缺失(INDEL)的變異。病竇症候群的特點是竇性停搏,房顫和房室傳導干擾。我們使用譜系基因型的方法來研究一個有病竇症候群包含3代成員的家庭。我們以此譜系基因型的方法縮減可能相關變異至很小一部份。經由變異點註解和聚合酶鏈反應(PCR )驗證後,我們發現了一個新的SNV位於LMNA基因,它是內核膜蛋白纖層蛋白 A/C 的基因。蛋白結構模擬預測此突變點可能會影響LMNA功能。


    ABSTRACT

    The Mendelian disease genes’ hunting is our goal to discover the nature of the illness and try to find a way to cure it. Exome sequencing is a powerful tool to characterize DNA sequences surrounding target regions at a much lower cost compared to the whole genome sequencing technique. The Single Nucleotide Variation (SNV) and insertion/deletion (Indel) variants called with the sequence alignment tools and variants calling tools are big raw data for the analysis. We use the pedigree-genotype method to investigate 3 generations of a Chinese family with SSS that was characterized by sinus arrest, atrial fibrillation and atrioventricular conduction disturbance. We narrowed down the variants to a small set with the pedigree-genotype method. Following with the annotation and the polymerase chain reaction (PCR) verification, we identified a novel SNV located in LMNA gene, which encodes the inner nuclear membrane protein lamin A/C. Structural modeling predicts the mutation may affect LMNA function.

    TABLE OF CONTENTS ABSTRACT …………………………………………………………I Acknowledgement誌謝 ………………………………………………II CHAPTER 1 Introduction …………………………………………1 1-1 Whole Exome Sequencing ………………………………………………1 1-2 Sequence Alignment ………………………………………………1 1-3 Variant Calling ………………………………………………2 1-4 The Pedigree-Genotype Analysis …………………………………………3 1-5 Annotation ………………………………………………4 1-6 Finding Candidate Variants and Verification ………………………………5 1-7 The Cardiac Conduction Disease …………………………………………6 CHAPTER 2 Methods ……………………………………………9 2-1 Exome Sequencing ……………………………………………………9 2-2 The Workflow of Finding Candidate Disease-Related Variants ………10 2-2.1 Total SNVs and Indels sites from combing 5 samples ………10 2-2.2 Bi-allelic analysis ……………………………………10 2-2.3 Matching genotypes with pedigree analysis …………………10 2-2.4 Annotation analysis ………………………………………11 2-3 Mutation Validation …………………………………………………12 2-4 LMNA Wild-Type/Mutation Structural Modeling ………………………13 2-5 Expression Analysis …………………………………………………13 CHAPTER 3 Results ………………………………………………15 3-1 Exome sequencing, Sequence Alignment and Variant Calling ………15 3-2 Variant Filtration and Prioritization According to Inheritance Models …15 3-3 Annotation Analysis ………………………………………………………16 3-4 Candidate Genes ………………………………………………………17 3-5 Validation of Candidate Genes ………………………………………17 3-6 LMNA Wild-Type/Mutation Structural Modeling ………………………18 3-7 Expression of the p.Gly232Val Mutation in the HL-1 Cell Line ………19 CHAPTER 4 Discussion …………………………………………20 Bibliography ………………………………………………………27 Tables ……………………………………………………………31 Figures ……………………………………………………………43

    Bibliography

    1. Wolf CM and Berul CI (2006) Inherited conduction system abnormalities--one group of diseases, many genes. J Cardiovasc Electrophysiol 17: 446-455.
    2. Smits JP, Veldkamp MW and Wilde AA (2005) Mechanisms of inherited cardiac conduction disease. Europace 7: 122-137.
    3. Park DS and Fishman GI (2011) The cardiac conduction system. Circulation 123: 904-915.
    4. Gilissen C, Arts HH, Hoischen A, Spruijt L, Mans DA, et al. (2010) Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am J Hum Genet 87: 418-423.
    5. Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, et al. (2010) De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet 42: 483-485.
    6. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636-639.
    7. Norton N, Li D, Rieder MJ, Siegfried JD, Rampersaud E, et al. (2011) Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy. Am J Hum Genet 88: 273-282.
    8. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42: 30-35.
    9. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, et al. (2011) Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 29: 908-914.
    10. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, et al. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12: 745-755.
    11. Stitziel NO, Kiezun A and Sunyaev S (2011) Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol 12: 227.
    12. Li H and Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
    14. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
    15. Wang K, Li M and Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38: e164.
    16. Liu X, Jian X and Boerwinkle E (2011) dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 32: 894-899.
    17. Kumar P, Henikoff S and Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081.
    18. Soding J, Biegert A and Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33: W244-248.
    19. Whitby FG and Phillips GN (2000) Crystal structure of tropomyosin at 7 Angstroms resolution. Proteins 38: 49-59.
    20. Strelkov SV, Schumacher J, Burkhard P, Aebi U and Herrmann H (2004) Crystal structure of the human lamin A coil 2B dimer: implications for the head-to-tail association of nuclear lamins. J Mol Biol 343: 1067-1080.
    21. Strelkov SV HH, Geisler N, Wedig T, Zimbelmann R, Aebi U, Burkhard P. (2002) Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly. EMBO J 21: 1255-1266.
    22. Chernyatina AA and Strelkov SV (2012) Stabilization of vimentin coil2 fragment via an engineered disulfide. J Struct Biol 177: 46-53.
    23. Remmert M, Biegert A, Hauser A and Soding J (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9: 173-175.
    24. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2007) Comparative protein structure modeling using MODELLER. In: John EC, editors. Current protocols in protein science. New York: John Wiley & Sons, Inc. Chapter 2:Unit 2.9, Supplement 50.
    25. Chernyatina AA, Nicolet S, Aebi U, Herrmann H and Strelkov SV (2012) Atomic structure of the vimentin central alpha-helical domain and its implications for intermediate filament assembly. Proc Natl Acad Sci U S A 109: 13620-13625.
    26. Cattin M-E, Muchir A and Bonne G (2013) 'State-of-the-heart'of cardiac laminopathies. Curr Opin Cardiol 28: 297-304
    27. Bonne G, Di Barletta MR, Varnous S, Becane HM, Hammouda EH, et al. (1999) Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy. Nat Genet 21: 285-288.
    28. Fatkin D, MacRae C, Sasaki T, Wolff MR, Porcu M, et al. (1999) Missense mutations in the rod domain of the lamin A/C gene as causes of dilated cardiomyopathy and conduction-system disease. N Engl J Med 341: 1715-1724.
    29. Charniot JC, Pascal C, Bouchier C, Sebillon P, Salama J, et al. (2003) Functional consequences of an LMNA mutation associated with a new cardiac and non?cardiac phenotype. Hum Mutat 21: 473-481.
    30. Taylor MR, Fain PR, Sinagra G, Robinson ML, Robertson AD, et al. (2003) Natural history of dilated cardiomyopathy due to lamin A/C gene mutations. J Am Coll Cardiol 41: 771-780.
    31. Sebillon P, Bouchier C, Bidot LD, Bonne G, Ahamed K, et al. (2003) Expanding the phenotype of LMNA mutations in dilated cardiomyopathy and functional consequences of these mutations. J Med Genet 40: 560-567.
    32. Pan H, Richards AA, Zhu XH, Jogtar JA, Yin HL, et al. (2009) A novel mutation in LAMIN A/C is associated with isolated early-onset atrial fibrillation and progressive atrioventricular block followed by cardiomyopathy and sudden cardiac death. Heart Rhythm 6: 707-710.
    33. Marsman RF, Bardai A, Postma AV, Res JC, Koopmann TT, et al. (2011) A complex double deletion in LMNA underlies progressive cardiac conduction disease, atrial arrhythmias, and sudden death. Circ Cardiovasc Genet 4: 280-287.
    34. Vytopil M, Benedetti S, Ricci E, Galluzzi G, Dello Russo A, et al. (2003) Mutation analysis of the lamin A/C gene (LMNA) among patients with different cardiomuscular phenotypes. J Med Genet 40: e132.
    35. Bonne G, Mercuri E, Muchir A, Urtizberea A, Becane H, et al. (2000) Clinical and molecular genetic spectrum of autosomal dominant Emery?Dreifuss muscular dystrophy due to mutations of the lamin A/C gene. Ann Neurol 48: 170-180.
    36. Rudenskaya GE, Polyakov AV, Tverskaya SM, Zaklyazminskaya EV, Chukhrova AL, et al. (2008) Laminopathies in Russian families. Clin Genet 74: 127-133.
    37. Parry DA and Smith TA (2010) A different conformation for linker L12 in IF molecules in the molecular and filamentous forms: an hypothesis. J Struct Biol 170: 364-368.
    38. Saj M, Dabrowski R, Labib S, Jankowska A, Szperl M, et al. (2012) Variants of the lamin A/C (LMNA) gene in non-valvular atrial fibrillation patients: a possible pathogenic role of the Thr528Met mutation. Mol Diagn Ther 16: 99-107.
    39. Arbustini E, Pilotto A, Repetto A, Grasso M, Negri A, et al. (2002) Autosomal dominant dilated cardiomyopathy with atrioventricular block: a lamin A/C defect-related disease. J Am Coll Cardiol 39: 981-990.
    40. Holaska JM (2008) Emerin and the nuclear lamina in muscle and cardiac disease. Circ Res 103: 16-23.
    41. van Berlo JH, de Voogt WG, van der Kooi AJ, van Tintelen JP, Bonne G, et al. (2005) Meta-analysis of clinical characteristics of 299 carriers of LMNA gene mutations: do lamin A/C mutations portend a high risk of sudden death? J Mol Med 83: 79-83.

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