全基因組定序

完全確定某生物的基因組的過程
(重定向自基因组测序

全基因組定序(Whole genome sequencing,WGS)是將一個生物的基因組完整(或接近完整)定序的流程。1990年代起陸續有生物的基因組被完整定序,最早被定序完成的生物為流感嗜血桿菌(1995年),1996年首次有真核生物釀酒酵母)被完整定序。2014年以後全基因組定序逐漸開始被用於臨床用途[2][3][4],以病人基因組資訊決定其療法,即個人化醫療[5]。2000年全基因體定序技術獲《科學》期刊選為該年的年度突破英语Breakthrough of the Year[6]

霰彈槍定序法的流程圖
顯示基因定序結果的電泳圖譜英语Electropherogram[1]

歷史

 
流感嗜血桿菌為第一個被全基因組定序的生物
 
秀麗隱桿線蟲為第一個被全基因組定序的多細胞生物(動物)
 
阿拉伯芥為第一個被全基因組定序的植物

1977年,弗雷德里克·桑格的團隊將ΦX174噬菌體英语Phi X 174的基因組完整定序,長5368bp,是第一個被完整定序的基因組[7][8][9]。1990年代起測序技術逐漸成熟,開始被用於定序生物的完整基因組[10]。第一個被完整定序的生物為流感嗜血桿菌,共長183萬bp,於1995年由霰彈槍定序法完成[11],隨後有其他細菌古菌的基因組陸續被以相同方法定序。真核生物的基因組大小則大的多,因此定序較為困難,1996年釀酒酵母的基因組定序完成,約長1200萬bp,為第一個被完整定序的真核生物[12];1998年秀麗隱桿線蟲的基因組被完整定序,為第一個完成定序的多細胞真核生物[13]。真核生物定序的方式除使用霰彈槍定序法外,還用到了細菌人工染色體(BAC)、酵母菌人工染色體(YAC)等基因文庫[14]



1999年人類22號染色體(最短的體染色體)被定序發表[15];2000年黑腹果蠅的基因組被完整定序,為第二種被完整定序的動物[16],同年阿拉伯芥的基因組定序也告完成,是第一個被完整定序的植物[17]。2001年人類基因組計劃發表人類基因組的定序草圖(draft)[18],2003年宣告真染色質的序列皆定序完成[19][20],2021年發表定序程度達「完整」的基因組[21][22];2002年小鼠的基因組也被定序發表[23]。目前已有上千種生物的基因組被完整定序。2005年起桑格测序等傳統的定序方法逐漸被Illumina染料定序英语Illumina dye sequencing焦磷酸測序SMRT定序英语Single-molecule real-time sequencing奈米孔洞測序次世代定序英语Massive parallel sequencing(NGS)技術取代(但仍使用霰彈槍定序法的策略,將基因組打碎成許多片段後分別完成定序,再進行組裝)。[24][25]

商業化

 
2001年至2019年一次人類全基因組定序的費用變化

已有許多公司嘗試將全基因組定序商業化以作研究或臨床用途[26],包括Illumina[27]Knome英语Knome[28]Sequenom英语Sequenom[29]454生物科学[30]Pacific Biosciences英语Pacific Biosciences[31]Complete Genomics英语Complete Genomics[32]Helicos Biosciences英语Helicos Biosciences[33]GE Global Research英语GE Global Research通用电气的研發部門)、Affymetrix英语AffymetrixIBM、Intelligent Bio-Systems[34]、Life Technologies、Oxford Nanopore Technologies英语Oxford Nanopore Technologies[35]华大基因[36][37][38]。2010年代晚期全基因組定序一次約要價1000美元,許多公司正試圖將成本進一步降低[39],2017年華大基因的全基因組定序收費已降為一人600美元[40],2019年Veritas Genetics英语Veritas Genetics也將費用降至一人599美元[41]

應用

 
全基因組關聯分析(GWAS)的結果(曼哈頓圖英语Manhattan plot)示意圖

在生醫研究中,全基因組定序可被用於全基因組關聯分析(GWAS)以尋找基因組中與特定疾病相關的單核苷酸多態性(SNP)位點[42]

全基因組定序在醫療上也有很大的應用價值,2009年Illumina即推出了用於臨床醫療的全基因組分析套件,供醫師在不知病人病因、傳統療法均效果不彰時使用[43]。因近年來全基因組定序的費用大幅下降,其應用潛力也大幅增加。2011年布萊根婦女醫院哈佛醫學院創立了Genomes2People(G2P)計畫,旨在將基因定序整合進臨床醫療[44]

倫理爭議

人類全基因組定序可能伴隨一些倫理議題,此技術雖有診斷出疾病的潛力[45],但也有造成基因歧視英语Genetic discrimination、隱私外洩(特別是未成年人的隱私[46])與心理上負面影響之風險[47]。另外當一個人接受全基因組定序時,除了自己基因組的資訊外,還可能得知其近親的基因組資訊,進而推得他們過去、現在或未來的健康狀況[48],因此接受定序者是否應與近親分享定序的結果也是一倫理議題,若其帶有一與某疾病相關的突變,卻不願與近親分享此資訊,則醫療人員可能面臨預防醫療與病人隱私的兩難[45]。科學研究中的全基因組定序也可能有隱私外洩的疑慮,因學術研究發表時通常需要將病人的基因型的資訊發表到公開資料庫,此資訊雖為匿名,但在疾病或突變相當罕見的情況下仍有可能使病人被認出[45]

被全基因組定序的名人

最早被全基因組定序完成的人是克萊格·凡特[49][50][51]詹姆斯·杜威·沃森[52][53][54],於2007年完成(覆蓋度英语Coverage (genetics)分別為7.5與7.4),2008年又有一名匿名的中國漢族人(覆蓋度為36)[55]奈及利亞約魯巴人(覆蓋度為30)[56]、荷蘭的女性遺傳學家玛乔琳·克里克(為首位基因組被完整定序的女性,覆蓋度7至8)[57][58]與一高加索人種白血病女性患者基因組被定序完成[59]史蒂夫·賈伯斯為最早被全基因組定序的20人之一,有消息指其花費高達10萬美元[60]。截至2012年6月共有69個人接近完整的基因組序列資料向大眾公開[61]。2013年11月有一西班牙家庭在接受23andMe與華大基因定序後,將全家的全基因組序列以創用CC公有領域授權條款公開,是第一個公開的家族全基因組序列資料[62]

參見

參考文獻

  1. ^ Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter. Chapter 8. Molecular biology of the cell 5th. New York: Garland Science. 2008: 550. ISBN 978-0-8153-4106-2. 
  2. ^ Gilissen. Genome sequencing identifies major causes of severe intellectual disability. Nature. July 2014, 511 (7509): 344–7. Bibcode:2014Natur.511..344G. PMID 24896178. S2CID 205238886. doi:10.1038/nature13394. 
  3. ^ Nones, K; Waddell, N; Wayte, N; Patch, AM; Bailey, P; Newell, F; Holmes, O; Fink, JL; Quinn, MC; et al. Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nature Communications. 2014-10-29, 5: 5224. Bibcode:2014NatCo...5.5224N. PMC 4596003 . PMID 25351503. doi:10.1038/ncomms6224. 
  4. ^ van El, CG; Cornel, MC; Borry, P; Hastings, RJ; Fellmann, F; Hodgson, SV; Howard, HC; Cambon-Thomsen, A; Knoppers, BM; Meijers-Heijboer, H; Scheffer, H; Tranebjaerg, L; Dondorp, W; de Wert, GM. Whole-genome sequencing in health care. Recommendations of the European Society of Human Genetics. European Journal of Human Genetics. June 2013,. 21 Suppl 1: S1–5. PMC 3660957 . PMID 23819146. doi:10.1038/ejhg.2013.46. 
  5. ^ Mooney, Sean. Progress towards the integration of pharmacogenomics in practice. Human Genetics. Sep 2014, 134 (5): 459–65. PMC 4362928 . PMID 25238897. doi:10.1007/s00439-014-1484-7. 
  6. ^ Elizabeth Pennisi. BREAKTHROUGH OF THE YEAR. Genomics Comes of Age. Science. 2000, 290 (5500): 2220–2221. PMID 11188701. S2CID 82676530. doi:10.1126/science.290.5500.2220. 
  7. ^ A History of Genome Sequencing. MB&B 447b3 (747b3) BIOINFORMATICS, Yale University. [2021-12-20]. (原始内容存档于2022-05-01). 
  8. ^ Brownlee, George G. Frederick Sanger CBE CH OM. 13 August 1918 – 19 November 2013. Biographical Memoirs of Fellows of the Royal Society. 2015, 61: 437–466. doi:10.1098/rsbm.2015.0013 . 
  9. ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. February 1977, 265 (5596): 687–95. Bibcode:1977Natur.265..687S. PMID 870828. S2CID 4206886. doi:10.1038/265687a0. 
  10. ^ al.], Bruce Alberts ... [et. Molecular biology of the cell 5th. New York: Garland Science. 2008: 551. ISBN 978-0-8153-4106-2. 
  11. ^ Fleischmann, R.; Adams, M.; White, O; Clayton, R.; Kirkness, E.; Kerlavage, A.; Bult, C.; Tomb, J.; Dougherty, B.; Merrick, J.; al., e. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995-07-28, 269 (5223): 496–512. Bibcode:1995Sci...269..496F. PMID 7542800. doi:10.1126/science.7542800. 
  12. ^ Goffeau, A.; Barrell, B. G.; Bussey, H.; Davis, R. W.; Dujon, B.; Feldmann, H.; Galibert, F.; Hoheisel, J. D.; Jacq, C.; Johnston, M.; Louis, E. J.; Mewes, H. W.; Murakami, Y.; Philippsen, P.; Tettelin, H.; Oliver, S. G. Life with 6000 Genes. Science. 1996-10-25, 274 (5287): 546–567. Bibcode:1996Sci...274..546G. PMID 8849441. S2CID 16763139. doi:10.1126/science.274.5287.546. (原始内容存档 (PDF)于2016-03-07). 
  13. ^ The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science. 1998-12-11, 282 (5396): 2012–2018. Bibcode:1998Sci...282.2012.. PMID 9851916. doi:10.1126/science.282.5396.2012. 
  14. ^ Alberts, Bruce. Molecular Biology of the Cell 5th. New York: Garland Science. 2008: 552. ISBN 978-0-8153-4106-2. 
  15. ^ Dunham, I. The DNA sequence of human chromosome 22. Nature. December 1999, 402 (6761): 489–495. Bibcode:1999Natur.402..489D. PMID 10591208. doi:10.1038/990031 . 
  16. ^ Adams MD; Celniker SE; Holt RA; et al. The Genome Sequence of Drosophila melanogaster. Science. 2000-03-24, 287 (5461): 2185–2195. Bibcode:2000Sci...287.2185.. CiteSeerX 10.1.1.549.8639 . PMID 10731132. doi:10.1126/science.287.5461.2185. 
  17. ^ The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000-12-14, 408 (6814): 796–815. Bibcode:2000Natur.408..796T. PMID 11130711. doi:10.1038/35048692 . 
  18. ^ Venter JC; Adams MD; Myers EW; et al. The Sequence of the Human Genome. Science. 2001-02-16, 291 (5507): 1304–1351. Bibcode:2001Sci...291.1304V. PMID 11181995. doi:10.1126/science.1058040 . 
  19. ^ Human Genome Project Completion: Frequently Asked Questions. National Human Genome Research Institute (NHGRI). [2021-12-10]. (原始内容存档于2019-04-09). 
  20. ^ International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004-09-07, 431 (7011): 931–945. Bibcode:2004Natur.431..931H. PMID 15496913. doi:10.1038/nature03001 . 
  21. ^ CHM13 T2T v1.1 – Genome – Assembly – NCBI. www.ncbi.nlm.nih.gov. [2021-06-16]. (原始内容存档于2021-05-29). 
  22. ^ Genome List – Genome – NCBI. www.ncbi.nlm.nih.gov. [2021-06-16]. (原始内容存档于2015-02-20). 
  23. ^ Waterston RH; Lindblad-Toh K; Birney E; et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002-10-31, 420 (6915): 520–562. Bibcode:2002Natur.420..520W. PMID 12466850. doi:10.1038/nature01262 . 
  24. ^ Mukhopadhyay R. DNA sequencers: the next generation. Anal. Chem. February 2009, 81 (5): 1736–40. PMID 19193124. doi:10.1021/ac802712u. 
  25. ^ Kwong, JC; McCallum, N; Sintchenko, V; Howden, BP. Whole genome sequencing in clinical and public health microbiology.. Pathology. April 2015, 47 (3): 199–210. PMC 4389090 . PMID 25730631. doi:10.1097/pat.0000000000000235. 
  26. ^ Article : Race to Cut Whole Genome Sequencing Costs Genetic Engineering & Biotechnology News — Biotechnology from Bench to Business. Genengnews.com. [2009-02-23]. (原始内容存档于2006-10-17). 
  27. ^ Whole Genome Sequencing Costs Continue to Drop. Eyeondna.com. [2009-02-23]. (原始内容存档于2009-03-25). 
  28. ^ Harmon, Katherine. Genome Sequencing for the Rest of Us. Scientific American. 2010-06-28 [2010-08-13]. (原始内容存档于2011-03-19). 
  29. ^ San Diego/Orange County Technology News. Sequenom to Develop Third-Generation Nanopore-Based Single Molecule Sequencing Technology. Freshnews.com. [2009-02-24]. (原始内容存档于2008-12-05). 
  30. ^ Article : Whole Genome Sequencing in 24 Hours Genetic Engineering & Biotechnology News — Biotechnology from Bench to Business. Genengnews.com. [2009-02-23]. (原始内容存档于2006-10-17). 
  31. ^ Pacific Bio lifts the veil on its high-speed genome-sequencing effort. VentureBeat. 2008-02-10 [2009-02-23]. (原始内容存档于2009-02-20). 
  32. ^ Bio-IT World. Bio-IT World. 2008-10-06 [2009-02-23]. (原始内容存档于2009-02-17). 
  33. ^ With New Machine, Helicos Brings Personal Genome Sequencing A Step Closer. Xconomy. 2008-04-22 [2011-01-28]. (原始内容存档于2011-01-02). 
  34. ^ Whole genome sequencing costs continue to fall: $300 million in 2003, $1 million 2007, $60,000 now, $5000 by year end. Nextbigfuture.com. 2008-03-25 [2011-01-28]. (原始内容存档于2010-12-20). 
  35. ^ Han Cao's nanofluidic chip could cut DNA sequencing costs dramatically. Technology Review. (原始内容存档于2011-03-29). 
  36. ^ Julia Karow. BGI Launches Desktop Sequencer in China; Plans to Register Platform With CFDA. GenomeWeb. 2015-10-26 [2018-12-02]. (原始内容存档于2018-12-02). 
  37. ^ BGI Launches New Desktop Sequencer in China, Registers Larger Version With CFDA. 360Dx. GenomeWeb. 2016-11-11 [2018-12-02]. (原始内容存档于2020-09-19). 
  38. ^ Monica Heger. BGI Launches New Sequencer as Customers Report Data From Earlier Instruments. GenomeWeb. 2018-10-26 [2018-12-02]. (原始内容存档于2021-10-09). 
  39. ^ Sarah Neville. Cheaper DNA sequencing unlocks secrets of rare diseases. Financial Times. 2018-03-05 [2018-12-02]. (原始内容存档于2020-08-19). 
  40. ^ Megan Molteni. A Chinese Genome Giant Sets Its Sights on the Ultimate Sequencer. Wired. 2017-05-18 [2018-12-02]. (原始内容存档于2021-08-10). 
  41. ^ Andrews, Joe. 23andMe competitor Veritas Genetics slashes price of whole genome sequencing 40% to $600. CNBC. 2019-07-01 [2019-09-02]. (原始内容存档于2022-02-24). 
  42. ^ Yano, K; Yamamoto, E; Aya, K; Takeuchi, H; Lo, PC; Hu, L; Yamasaki, M; Yoshida, S; Kitano, H; Hirano, K; Matsuoka, M. Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice.. Nature Genetics. August 2016, 48 (8): 927–34. PMID 27322545. S2CID 22427006. doi:10.1038/ng.3596. 
  43. ^ Abbott, Phil. US clinics quietly embrace whole-genome sequencing : Nature News. Nature. 2010 [2016-11-11]. doi:10.1038/news.2010.465. (原始内容存档于2017-04-16). 
  44. ^ Genomes2People: A Roadmap for Genomic Medicine. www.frontlinegenomics.com. [2018-04-29]. (原始内容存档于2017-02-14). 
  45. ^ 45.0 45.1 45.2 Sijmons, R.H.; Van Langen, I.M. A clinical perspective on ethical issues in genetic testing. Accountability in Research: Policies and Quality Assurance. 2011, 18 (3): 148–162. Bibcode:2013ARPQ...20..143D. PMID 21574071. S2CID 24935558. doi:10.1080/08989621.2011.575033. 
  46. ^ Borry, P.; Evers-Kiebooms, G.; Cornel, MC; Clarke, A; Dierickx, K; Public Professional Policy Committee (PPPC) of the European Society of Human Genetics (ESHG)英语European Society of Human Genetics. Genetic testing in asymptomatic minors Background considerations towards ESHG Recommendations. Eur J Hum Genet. 2009, 17 (6): 711–9. PMC 2947094 . PMID 19277061. doi:10.1038/ejhg.2009.25. 
  47. ^ Ayday E; De Cristofaro E; Hubaux JP; Tsudik G. The Chills and Thrills of Whole Genome Sequencing. 2015. arXiv:1306.1264  [cs.CR]. 
  48. ^ McGuire, Amy, L; Caulfield, Timothy. Science and Society: Research ethics and the challenge of whole-genome sequencing. Nature Reviews Genetics. 2008, 9 (2): 152–156. PMC 2225443 . PMID 18087293. doi:10.1038/nrg2302. 
  49. ^ Wade, Nicholas. In the Genome Race, the Sequel Is Personal. New York Times. 2007-09-04 [2009-02-22]. (原始内容存档于2009-04-11). 
  50. ^ Ledford, Heidi. Access : All about Craig: the first 'full' genome sequence. Nature. 2007, 449 (7158): 6–7. Bibcode:2007Natur.449....6L. PMID 17805257. doi:10.1038/449006a . 
  51. ^ Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC. The diploid genome sequence of an individual human. PLOS Biol. September 2007, 5 (10): e254. PMC 1964779 . PMID 17803354. doi:10.1371/journal.pbio.0050254 . 
  52. ^ Wade, Wade. DNA pioneer Watson gets own genome map. International Herald Tribune. 2007-06-01 [2009-02-22]. (原始内容存档于2008-09-27). 
  53. ^ Wade, Nicholas. Genome of DNA Pioneer Is Deciphered. New York Times. 2007-05-31 [2009-02-21]. (原始内容存档于2011-06-20). 
  54. ^ Wheeler DA; Srinivasan M; Egholm M; Shen Y; Chen L; McGuire A; He W; Chen YJ; Makhijani V; Roth GT; Gomes X; Tartaro K; Niazi F; Turcotte CL; Irzyk GP; Lupski JR; Chinault C; Song XZ; Liu Y; Yuan Y; Nazareth L; Qin X; Muzny DM; Margulies M; Weinstock GM; Gibbs RA; Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008, 452 (7189): 872–6. Bibcode:2008Natur.452..872W. PMID 18421352. doi:10.1038/nature06884 . 
  55. ^ Wang J; Wang, Wei; Li, Ruiqiang; Li, Yingrui; Tian, Geng; Goodman, Laurie; Fan, Wei; Zhang, Junqing; Li, Jun; Zhang, Juanbin, Juanbin; Guo, Yiran, Yiran; Feng, Binxiao, Binxiao; Li, Heng, Heng; Lu, Yao, Yao; Fang, Xiaodong, Xiaodong; Liang, Huiqing, Huiqing; Du, Zhenglin, Zhenglin; Li, Dong, Dong; Zhao, Yiqing, Yiqing; Hu, Yujie, Yujie; Yang, Zhenzhen, Zhenzhen; Zheng, Hancheng, Hancheng; Hellmann, Ines, Ines; Inouye, Michael, Michael; Pool, John, John; Yi, Xin, Xin; Zhao, Jing, Jing; Duan, Jinjie, Jinjie; Zhou, Yan, Yan; et al. The diploid genome sequence of an Asian individual. Nature. 2008, 456 (7218): 60–65. Bibcode:2008Natur.456...60W. PMC 2716080 . PMID 18987735. doi:10.1038/nature07484. 
  56. ^ Bentley DR; Balasubramanian S; et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008, 456 (7218): 53–9. Bibcode:2008Natur.456...53B. PMC 2581791 . PMID 18987734. doi:10.1038/nature07517. 
  57. ^ Coats, Christopher. Dr. Marjolein Kriek, First Woman to Have Her DNA Sequence Determined. 2009-12-27 [2012-01-03]. (原始内容存档于2021-08-13). 
  58. ^ First Female DNA Sequenced. ScienceDaily. 2008-05-26. (原始内容存档于2021-02-05). 
  59. ^ Ley TJ; Mardis ER; Ding L; Fulton B; McLellan MD; Chen K; Dooling D; Dunford-Shore BH; McGrath S; Hickenbotham M; Cook L; Abbott R; Larson DE; Koboldt DC; Pohl C; Smith S; Hawkins A; Abbott S; Locke D; Hillier LW; Miner T; Fulton L; Magrini V; Wylie T; Glasscock J; Conyers J; Sander N; Shi X; Osborne JR; et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008, 456 (7218): 66–72. Bibcode:2008Natur.456...66L. PMC 2603574 . PMID 18987736. doi:10.1038/nature07485. 
  60. ^ Lohr, Steve. New Book Details Jobs's Fight Against Cancer. The New York Times. 2011-10-20. (原始内容存档于2017-09-28). 
  61. ^ Complete Human Genome Sequencing Datasets to its Public Genomic Repository. (原始内容存档于2012-06-10). 
  62. ^ Corpas, Manuel; Cariaso, Mike; Coletta, Alain; Weiss, David; Harrison, Andrew P; Moran, Federico; Yang, Huanming. A Complete Public Domain Family Genomics Dataset. 2013-11-12. bioRxiv 10.1101/000216 . 

外部連結