跳到主要內容

臺灣博碩士論文加值系統

(44.212.99.208) 您好!臺灣時間:2024/04/17 20:30
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

: 
twitterline
研究生:李宛萱
研究生(外文):Lee, WAN-HSUAN
論文名稱:使用納米孔測序同時定相單核苷酸多態性和表觀遺傳甲基化
論文名稱(外文):Simultaneous phasing of single-nucleotide polymorphisms and epigenetic methylations using Nanopore sequencing
指導教授:黃耀廷
指導教授(外文):Huang, Yao-Ting
口試委員:蔡懷寬莊樹諄陳璿宇
口試委員(外文):Tsai, Huai-KuangChuang, Trees-JuenChen, Hsuan-Yu
口試日期:2022-07-28
學位類別:碩士
校院名稱:國立中正大學
系所名稱:資訊工程研究所
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2022
畢業學年度:110
語文別:英文
論文頁數:30
外文關鍵詞:Oxford nanopore sequencing,allele-specific methylationgenome phasing
相關次數:
  • 被引用被引用:0
  • 點閱點閱:114
  • 評分評分:
  • 下載下載:9
  • 收藏至我的研究室書目清單書目收藏:0
牛津納米孔技術(ONT) 是一種第三代測序技術,已廣泛用於新生兒和傳染病的快速
診斷。除了速度之外,ONT 還可以對超長DNA 片段進行測序,這對於基因組組裝和定
相項目至關重要。特別是,ONT 能夠同時對任何生物體的基因組和表觀基因組進行測
序。在本論文中,我們旨在通過從一開始就考慮ONT 提供的基因組和表觀基因組信息
來解決相位問題。我們實施了一個名為Modphase 的新程序,它同時對ONT 的單核酸多
態性和等位基因特異性甲基化進行定相。結果表明,Modphase 以略微降低精度為代價
產生了更大的相位塊。

The Oxford Nanopore Technology (ONT) is a third-generation sequencing that has been
widely used for rapid diagnosis of newborn and infectious diseases. In addition to its speed,
ONT can sequence ultra-long DNA fragments, which is essential for genome assembly and
phasing projects. In particular, ONT is capable of sequencing both the genome and epigenome
of any organism simultaneously. In this thesis, we aim to solve the phasing problem by con-
sidering genomic and epigenomic information provided by ONT from the beginning. We im-
plemented a new program, called Modphase, which simultaneously phase the single-nucleotide
polymorphisms and allele-specific methylations for ONT. The results indicated that Modphase
produced larger phasing blocks at the cost of slightly decreasing the accuracy.
Abstract
Introduction
Related Work
Method
Results
Conclusion
Bibliography
Appendix
[1] M. Martin, M. Patterson, S. Garg, S. Fischer, N. Pisanti, G. Klau, A. Sch ̈oenhuth, and
T. Marschall, “WhatsHap: fast and accurate read-based phasing,” bioRxiv, 11 2016.
[2] J. Ebler, M. Haukness, T. Pesout, T. Marschall, and B. Paten, “Haplotype-aware diplotyp-
ing from noisy long reads,” Genome Biol., vol. 20, no. 1, p. 116, Jun. 2019.
[3] K. Shafin, T. Pesout, P.-C. Chang, M. Nattestad, A. Kolesnikov, S. Goel, G. Baid, J. M.
Eizenga, K. H. Miga, P. Carnevali, M. Jain, A. Carroll, and B. Paten, “Haplotype-aware
variant calling enables high accuracy in nanopore long-reads using deep neural networks,”
Mar. 2021.
[4] J.-H. Lin, L.-C. Chen, S.-C. Yu, and Y.-T. Huang, “Longphase: an ultra-fast chromosome-
scale phasing algorithm for small and large variants.” Bioinformatics (Oxford, England),
no. 4, 02 2022.
[5] A. Rhoads and K. F. Au, “Pacbio sequencing and its applications,” Genomics,
Proteomics Bioinformatics, vol. 13, no. 5, pp. 278–289, 2015, sI: Metagenomics of
Marine Environments. [Online]. Available: https://www.sciencedirect.com/science/articl
e/pii/S1672022915001345
[6] Y. Wang, Y. Zhao, A. Bollas, Y. Wang, and K. F. Au, “Nanopore sequencing technology,
bioinformatics and applications,” Nature Biotechnology, vol. 39, 11 2021.
[7] N. J. Loman, J. Quick, and J. T. Simpson, “A complete bacterial genome assembled de
novo using only nanopore sequencing data,” Nature Methods, vol. 12, no. 8, 08 2015.
[Online]. Available: https://doi.org/10.1038/nmeth.3444
[8] D. Anastasiadi, A. Esteve-Codina, and F. Piferrer, “Consistent inverse correlation between
DNA methylation of the first intron and gene expression across tissues and species,” Epi-
genetics Chromatin, vol. 11, 06 2018.
[9] M. Mahmoud, H. Doddapaneni, W. Timp, and F. J. Sedlazeck, “A complete
bacterial genome assembled de novo using only nanopore sequencing data,” Genome
Biology, vol. 22, no. 1, Sep. 2021. [Online]. Available: https://doi.org/10.1186/
s13059-021-02486-w
[10] V. Akbari, J.-M. Garant, K. O’Neill, P. Pandoh, R. Moore, M. Marra, M. Hirst,
and S. Jones, “Megabase-scale methylation phasing using nanopore long reads and
nanomethphase,” Genome Biology, vol. 22, no. 3, 02 2021. [Online]. Available:
https://doi.org/10.1186/s13059-021-02283-5
[11] M. C. Benton, R. A. Lea, D. Macartney-Coxson, H. G. Sutherland, N. White, D. Kennedy,
K. Mengersen, L. M. Haupt, and L. R. Griffiths, “Genome-wide allele-specific
methylation is enriched at gene regulatory regions in a multi-generation pedigree from the
Norfolk Island isolate,” Epigenetics Chromatin, vol. 12, 10 2019. [Online]. Available:
https://doi.org/10.1186/s13072-019-0304-7
[12] C. C. Glenn, S. Saitoh, M. T. Jong, M. M. Filbrandt, U. Surti, D. J. Driscoll, and R. D.
Nicholls, “Gene structure, DNA methylation, and imprinted expression of the human
SNRPN gene.” American journal of human genetics, vol. 58, 02 1996.
[13] S. B. Cassidy, S. Schwartz, J. L. Miller, and D. J. Driscoll, “Prader-Willi syndrome,” Ge-
netics in Medicine, vol. 14, 1 2012.
[14] B. E. Madsen, P. Villesen, and C. Wiuf, “A periodic pattern of snps in the human genome,”
Genome research, vol. 17, no. 10, pp. 1414–1419, 2007.
[15] C. L ̈ovkvist, I. B. Dodd, K. Sneppen, and J. O. Haerter, “DNA methylation in human
epigenomes depends on local topology of CpG sites,” Nucleic Acids Research, vol. 44,
no. 11, pp. 5123–5132, 02 2016. [Online]. Available: https://doi.org/10.1093/nar/gkw124
[16] H. Li, “Minimap2: pairwise alignment for nucleotide sequences,” Bioinformatics, vol. 34,
no. 18, pp. 3094–3100, 05 2018. [Online]. Available: https://doi.org/10.1093/bioinformati
cs/bty191
[17] J. K. Bonfield, J. Marshall, P. Danecek, H. Li, V. Ohan, A. Whitwham,
T. Keane, and R. M. Davies, “HTSlib: C library for reading/writing high-throughput
sequencing data,” GigaScience, vol. 10, no. 2, 02 2021, giab007. [Online]. Available:
https://doi.org/10.1093/gigascience/giab007
[18] Z. Zheng, S. Li, J. Su, A. Leung, T.-W. Lam, and R. Luo, “Symphonizing pileup and
full-alignment for deep learning-based long-read variant calling,” biorxiv, 12 2021.
[19] P. Danecek, J. K. Bonfield, J. Liddle, J. Marshall, V. Ohan, M. O. Pollard, A. Whitwham,
T. Keane, S. A. McCarthy, R. M. Davies, and H. Li, “Twelve years of SAMtools
and BCFtools,” GigaScience, vol. 10, no. 2, 02 2021, giab008. [Online]. Available:
https://doi.org/10.1093/gigascience/giab008
[20] K. Shafin, T. Pesout, P.-C. Chang, M. Nattestad, A. Kolesnikov, S. Goel,
G. Baid, M. Kolmogorov, J. M. Eizenga, K. H. Miga, P. Carnevali, M. Jain,A. Carroll, and B. Paten, “DNA methylation in human epigenomes depends on local
topology of CpG sites,” Nature Methods, vol. 18, 11 2021. [Online]. Available:
https://doi.org/10.1038/s41592-021-01299-w
[21] J. T. Robinson, H. Thorvaldsd ́ottir, A. M. Wenger, A. Zehir, and J. P. Mesirov, “Variant
Review with the Integrative Genomics Viewer,” Cancer Research, vol. 77, no. 21, pp.
e31–e34, 10 2017. [Online]. Available: https://doi.org/10.1158/0008-5472.CAN-17-0337
[22] J. T. Robinson, H. Thorvaldsd ́ottir, D. Turner, and J. P. Mesirov, “igv.js: an embeddable
javascript implementation of the integrative genomics viewer (igv),” bioRxiv, no. 7,
2022. [Online]. Available: https://www.biorxiv.org/content/early/2022/06/10/2020.05.03.
075499
[23] R. Shoemaker, J. Deng, W. Wang, and K. Zhang, “Allele-specific methylation is prevalent
and is contributed by cpg-snps in the human genome.” Genome research, no. 5, 07 2010.
[24] J. Stanurova, A. Neureiter, M. Hiber, H. de Oliveira Kessler, K. Stolp, R. Goetzke,
D. Klein, A. Bankfalvi, H. Klump, and L. Steenpass, “Angelman syndrome-derived neu-
rons display late onset of paternal ube3a silencing,” Scientific Reports, no. 6, 08 2016.

QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top