千人基因組計劃

千人基因組計劃(英語:1000 Genomes Project, 1KGP)啟動於2008年1月,是一項國際研究工作,目標是迄今建立最詳盡的人類遺傳變異英語Human genetic variation目錄。科學家們計劃在隨後三年內,利用新開發的、更快、更便宜的技術,測定來自不同族群的數量至少一千名的匿名參與者的基因組序列。在2010年,該項目完成了前導研究階段,數據結果發表在《自然 (期刊)》雜誌(Nature)上[1]。在2012年10月,1092個基因組的測序結果公佈在《自然》雜誌上[2]。2015年,兩篇關於項目結果和未來展望的論文發表在了《自然》雜誌上。項目識別出許多限於密切相關群體的罕見變異和八種結構類變異[3]

基因數量和順序的變化(A-D)在群體內和種群之間產生遺傳多樣性。

該項目集結來自世界各地機構的多學科研究團隊,包括中國意大利日本肯雅尼日利亞秘魯英國美國。每一個團隊將貢獻巨大的測序數據集以完善人類基因組計劃。最終收集數據建立公共數據庫,免費向科學界和社會公眾開放。[2]

通過提供所有人類遺傳變異的概述,該聯盟將為生物科學的所有領域,特別是在遺傳學醫學藥理學生物化學生物信息學學科打造有價值的科研工具[4]

背景

人類基因組計劃完成後,人類群體遺傳學比較基因組學的進步使得有可能越來越多地洞察遺傳多樣性的性質[5]。然而,我們剛剛才開始明白如何隨機取樣配子結構變異(插入/刪除(indel),拷貝數變異英語Copy-number variation(CNV),反轉錄轉座子),單核苷酸多態性(SNP)和自然選擇等過程的塑造了物種內部以及物種之間變化的水平和模式[6][7][8][9]

人類遺傳變異

有性生殖期間配子的隨機抽樣導致遺傳漂變 - 後代中種群頻率的隨機波動 - 並且在沒有外部影響的情況下會導致所有變異的喪失。 據推測,遺傳漂移率與種群規模成反比,並且可能在特定情況下加速,例如種群瓶頸,種群規模減少一段時間,以及奠基者效應(英語:founder effect,指個體在一群人追溯到少數創始人)[6]

項目介紹

目標

千人基因組計劃計劃旨在彌補對簡單特徵產生嚴重影響的罕見遺傳變異(例如囊腫性纖維化亨廷頓病)與對複雜特徵產生輕微影響且與之有關的常見遺傳變異(例如認知糖尿病心臟病)之間的知識差距。[4]

該項目的主要目標是創建一個完整而詳細的人類遺傳變異目錄,可用於將遺傳變異與疾病聯繫起來的關聯研究。該聯盟旨在發現>95% 的變異(例如 SNP、CNV、插入/缺失),其中次要等位基因頻率在整個基因組中低至 1%,在基因區域中低至 0.1-0.5%,以及估計變異等位基因的種群頻率、單倍型背景和連鎖不平衡模式。[10]

次要目標包括為未來研究中的基因型分型平台提供更好的 SNP 和探針選擇支持,以及改進人類參考序列。完整的數據庫有望成為研究選擇區域、多個種群中的變異以及了解突變和重組的潛在過程的有用工具。[10]

概要

人類基因組由大約30億個DNA鹼基對組成,估計攜帶約20,000個蛋白質編碼基因。在設計研究時,該聯盟需要解決與項目指標有關的幾個關鍵問題,例如技術挑戰、數據質量標準和序列覆蓋率。[10]

在接下來的三年裏[需要解釋]維康桑格研究所深圳華大基因國家人類基因組研究所大規模測序網絡的科學家計劃對至少 1,000 個人類基因組進行測序。由於需要大量的序列數據,因此繼續招募更多參與者。[4]

在為期兩年的生產階段,每天將測序近 100 億個鹼基,相當於每 24 小時測序兩個以上的人類基因組。預期的序列數據集包含 6 萬億個 DNA 鹼基,比當時在 DNA 數據庫中發佈的序列數據多 60 倍。[4]

為了確定整個項目的最終設計,將在項目的第一年進行三項前導階段(Pilot phase)研究。第一項前導計劃以低覆蓋率(2x)對 3 個主要地理群體中的 180 人進行基因分型。對於第二項前導研究,將以深度覆蓋率(每個基因組 20x)對兩個核心家庭(父母和成年子女)的基因組進行測序。第三項前導研究涉及以深度覆蓋率(20x)對 1,000 人的 1,000 個基因的編碼區(外顯子)進行測序。[4][10]

人類基因組樣本

 
千人基因組計劃人口樣本的位置。[11] 每個圓圈代表最終版本中的序列數。

根據項目的總體目標,將選擇樣本為正在進行常見疾病關聯研究的人群提供依據。此外,樣本不需要有醫學或表型信息,因為擬議的目錄將成為人類變異的基本資源。[10]

對於前導階段研究,將對來自國際人類基因組單體型圖計劃(HapMap)集合的人類基因組樣本進行測序。重點關注具有其他可用數據的樣本(例如ENCODE序列、全基因組基因型、fosmid-end 序列、結構變異分析和基因表達)將很有用,以便能夠將結果與其他項目的結果進行比較。[10]

千人基因組計劃將遵循嚴格的道德程序,使用來自志願捐贈者的樣本。該研究將納入以下人群:尼日利亞伊巴丹約魯巴人(YRI);東京的日本人(JPT);北京的中國人(CHB);具有北歐和西歐血統的猶他州居民(CEU);肯雅韋布耶盧希亞人(LWK);肯雅基尼亞瓦的馬賽人(MKK);意大利的托斯卡尼人(TSI);秘魯利馬的秘魯人(PEL);休斯頓的古吉拉特人印第安人(GIH);丹佛大都市區的中國人(CHD);洛杉磯的墨西哥血統人士(MXL);以及美國西南部非洲血統人士(ASW)。[4]

項目發現

前導階段

前導階段(Pilot phase)包括三個項目:

  • 來自4個群體的179個個體的低覆蓋度全基因組測序
  • 2個三人組(母親-父親-孩子)的高覆蓋率排序
  • 來自7個群體的697個個體的外顯子靶向測序

結果發現,平均而言,每個人在註釋基因中攜帶約250-300個功能喪失變體,並且先前涉及遺傳性疾病的50-100個變體。 基於這2個三人組,估計每個新的種系的從頭開始生殖系突變率約為每一對每一代有10−8[1]

參見

參考文獻

  1. ^ 1.0 1.1 Durbin, R. M.; Abecasis, G. R.; Altshuler, R. M.; Auton, A.; Brooks, D. R.; Durbin, A.; Gibbs, A. G.; Hurles, F. S.; McVean, F. M.; Donnelly, P.; Egholm, M.; Flicek, P.; Gabriel, S. B.; Gibbs, R. A.; Knoppers, B. M.; Lander, E. S.; Lehrach, H.; Mardis, E. R.; McVean, G. A.; Nickerson, D. A.; Peltonen, L.; Schafer, A. J.; Sherry, S. T.; Wang, J.; Wilson, R. K.; Gibbs, R. A.; Deiros, D.; Metzker, M.; Muzny, D.; Reid, J. A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061–1073. PMC 3042601 . PMID 20981092. doi:10.1038/nature09534. 
  2. ^ 2.0 2.1 Gil A. McVean, David M. Altshuler (Co-Chair), Richard M. Durbin (Co-Chair), Gonçalo R. Abecasis, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Peter Donnelly, Evan E. Eichler, Paul Flicek, Stacey B. Gabriel, Richard A. Gibbs, Eric D. Green, Matthew E. Hurles, Bartha M. Knoppers, Jan O. Korbel, Eric S. Lander, Charles Lee, Hans Lehrach, Elaine R. Mardis, Gabor T. Marth, Deborah A. Nickerson, Jeanette P. Schmidt, Stephen T. Sherry, Jun Wang, Richard K. Wilson, Richard A. Gibbs (Principal Investigator), Huyen Dinh, Christie Kovar, Sandra Lee, Lora Lewis, Donna Muzny, Jeff Reid, Min Wang, Jun Wang (Principal Investigator), Xiaodong Fang, Xiaosen Guo, Min Jian, Hui Jiang, Xin Jin, Guoqing Li, Jingxiang Li, Yingrui Li, Zhuo Li, Xiao Liu, Yao Lu, Xuedi Ma, Zhe Su, Shuaishuai Tai, Meifang Tang, Bo Wang, Guangbiao Wang, Honglong Wu, Renhua Wu, Ye Yin, Wenwei Zhang, Jiao Zhao, Meiru Zhao, Xiaole Zheng, Yan Zhou, Eric S. Lander (Principal Investigator), David M. Altshuler, Stacey B. Gabriel (Co-Chair), Namrata Gupta, Paul Flicek (Principal Investigator), Laura Clarke, Rasko Leinonen, Richard E. Smith, Xiangqun Zheng-Bradley, David R. Bentley (Principal Investigator), Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Hans Lehrach (Principal Investigator), Ralf Sudbrak (Project Leader), Marcus W. Albrecht, Vyacheslav S. Amstislavskiy, Tatiana A. Borodina, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie-Laure Yaspo, Stephen T. Sherry (Principal Investigator), Gil A. McVean (Principal Investigator), Elaine R. Mardis (Co-Principal Investigator) (Co-Chair), Richard K. Wilson (Co-Principal Investigator), Lucinda Fulton, Robert Fulton, George M. Weinstock, Richard M. Durbin (Principal Investigator), Senduran Balasubramaniam, John Burton, Petr Danecek, Thomas M. Keane, Anja Kolb-Kokocinski, Shane McCarthy, James Stalker, Michael Quail, Jeanette P. Schmidt (Principal Investigator), Christopher J. Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Adam Auton (Principal Investigator), Richard A. Gibbs (Principal Investigator), Fuli Yu (Project Leader), Matthew Bainbridge, Danny Challis, Uday S. Evani, James Lu, Donna Muzny, Uma Nagaswamy, Jeff Reid, Aniko Sabo, Yi Wang, Jin Yu, Jun Wang (Principal Investigator), Lachlan J. M. Coin, Lin Fang, Xiaosen Guo, Xin Jin, Guoqing Li, Qibin Li, Yingrui Li, Zhenyu Li, Haoxiang Lin, Binghang Liu, Ruibang Luo, Nan Qin, Haojing Shao, Bingqiang Wang, Yinlong Xie, Chen Ye, Chang Yu, Fan Zhang, Hancheng Zheng, Hongmei Zhu, Gabor T. Marth (Principal Investigator), Erik P. Garrison, Deniz Kural, Wan-Ping Lee, Wen Fung Leong, Alistair N. Ward, Jiantao Wu, Mengyao Zhang, Charles Lee (Principal Investigator), Lauren Griffin, Chih-Heng Hsieh, Ryan E. Mills, Xinghua Shi, Marcin von Grotthuss, Chengsheng Zhang, Mark J. Daly (Principal Investigator), Mark A. DePristo (Project Leader), David M. Altshuler, Eric Banks, Gaurav Bhatia, Mauricio O. Carneiro, Guillermo del Angel, Stacey B. Gabriel, Giulio Genovese, Namrata Gupta, Robert E. Handsaker, Chris Hartl, Eric S. Lander, Steven A. McCarroll, James C. Nemesh, Ryan E. Poplin, Stephen F. Schaffner, Khalid Shakir, Seungtai C. Yoon (Principal Investigator), Jayon Lihm, Vladimir Makarov, Hanjun Jin (Principal Investigator), Wook Kim, Ki Cheol Kim, Jan O. Korbel (Principal Investigator), Tobias Rausch, Paul Flicek (Principal Investigator), Kathryn Beal, Laura Clarke, Fiona Cunningham, Javier Herrero, William M. McLaren, Graham R. S. Ritchie, Richard E. Smith, Xiangqun Zheng-Bradley, Andrew G. Clark (Principal Investigator), Srikanth Gottipati, Alon Keinan, Juan L. Rodriguez-Flores, Pardis C. Sabeti (Principal Investigator), Sharon R. Grossman, Shervin Tabrizi, Ridhi Tariyal, David N. Cooper (Principal Investigator), Edward V. Ball, Peter D. Stenson, David R. Bentley (Principal Investigator), Bret Barnes, Markus Bauer, R. Keira Cheetham, Tony Cox, Michael Eberle, Sean Humphray, Scott Kahn, Lisa Murray, John Peden, Richard Shaw, Kai Ye (Principal Investigator), Mark A. Batzer (Principal Investigator), Miriam K. Konkel, Jerilyn A. Walker, Daniel G. MacArthur (Principal Investigator), Monkol Lek, Sudbrak (Project Leader), Vyacheslav S. Amstislavskiy, Ralf Herwig, Mark D. Shriver (Principal Investigator), Carlos D. Bustamante (Principal Investigator), Jake K. Byrnes, Francisco M. De La Vega, Simon Gravel, Eimear E. Kenny, Jeffrey M. Kidd, Phil Lacroute, Brian K. Maples, Andres Moreno-Estrada, Fouad Zakharia, Eran Halperin (Principal Investigator), Yael Baran, David W. Craig (Principal Investigator), Alexis Christoforides, Nils Homer, Tyler Izatt, Ahmet A. Kurdoglu, Shripad A. Sinari, Kevin Squire, Stephen T. Sherry (Principal Investigator), Chunlin Xiao, Jonathan Sebat (Principal Investigator), Vineet Bafna, Kenny Ye, Esteban G. Burchard (Principal Investigator), Ryan D. Hernandez (Principal Investigator), Christopher R. Gignoux, David Haussler (Principal Investigator), Sol J. Katzman, W. James Kent, Bryan Howie, Andres Ruiz-Linares (Principal Investigator), Emmanouil T. Dermitzakis (Principal Investigator), Tuuli Lappalainen, Scott E. Devine (Principal Investigator), Xinyue Liu, Ankit Maroo, Luke J. Tallon, Jeffrey A. Rosenfeld (Principal Investigator), Leslie P. Michelson, Gonçalo R. Abecasis (Principal Investigator) (Co-Chair), Hyun Min Kang (Project Leader), Paul Anderson, Andrea Angius, Abigail Bigham, Tom Blackwell, Fabio Busonero, Francesco Cucca, Christian Fuchsberger, Chris Jones, Goo Jun, Yun Li, Robert Lyons, Andrea Maschio, Eleonora Porcu, Fred Reinier, Serena Sanna, David Schlessinger, Carlo Sidore, Adrian Tan, Mary Kate Trost, Philip Awadalla (Principal Investigator), Alan Hodgkinson, Gerton Lunter (Principal Investigator), Gil A. McVean (Principal Investigator) (Co-Chair), Jonathan L. Marchini (Principal Investigator), Simon Myers (Principal Investigator), Claire Churchhouse, Olivier Delaneau, Anjali Gupta-Hinch, Zamin Iqbal, Iain Mathieson, Andy Rimmer, Dionysia K. Xifara, Taras K. Oleksyk (Principal Investigator), Yunxin Fu (Principal Investigator), Xiaoming Liu, Momiao Xiong, Lynn Jorde (Principal Investigator), David Witherspoon, Jinchuan Xing, Evan E. Eichler (Principal Investigator), Brian L. Browning (Principal Investigator), Can Alkan, Iman Hajirasouliha, Fereydoun Hormozdiari, Arthur Ko, Peter H. Sudmant, Elaine R. Mardis (Co-Principal Investigator), Ken Chen, Asif Chinwalla, Li Ding, David Dooling, Daniel C. Koboldt, Michael D. McLellan, John W. Wallis, Michael C. Wendl, Qunyuan Zhang, Richard M. Durbin (Principal Investigator), Matthew E. Hurles (Principal Investigator), Cornelis A. Albers, Qasim Ayub, Senduran Balasubramaniam, Yuan Chen, Alison J. Coffey, Vincenza Colonna, Petr Danecek, Ni Huang, Luke Jostins, Thomas M. Keane, Heng Li, Shane McCarthy, Aylwyn Scally, James Stalker, Klaudia Walter, Yali Xue, Yujun Zhang, Mark B. Gerstein (Principal Investigator), Alexej Abyzov, Suganthi Balasubramanian, Jieming Chen, Declan Clarke, Yao Fu, Lukas Habegger, Arif O. Harmanci, Mike Jin, Ekta Khurana, Xinmeng Jasmine Mu, Cristina Sisu, Yingrui Li, Ruibang Luo, Hongmei Zhu, Charles Lee (Principal Investigator) (Co-Chair), Lauren Griffin, Chih-Heng Hsieh, Ryan E. Mills, Xinghua Shi, Marcin von Grotthuss, Chengsheng Zhang, Gabor T. Marth (Principal Investigator), Erik P. Garrison, Deniz Kural, Wan-Ping Lee, Alistair N. Ward, Jiantao Wu, Mengyao Zhang, Steven A. McCarroll (Project Leader), David M. Altshuler, Eric Banks, Guillermo del Angel, Giulio Genovese, Robert E. Handsaker, Chris Hartl, James C. Nemesh, Khalid Shakir, Seungtai C. Yoon (Principal Investigator), Jayon Lihm, Vladimir Makarov, Jeremiah Degenhardt, Paul Flicek (Principal Investigator), Laura Clarke, Richard E. Smith, Xiangqun Zheng-Bradley, Jan O. Korbel (Principal Investigator) (Co-Chair), Tobias Rausch, Adrian M. Stütz, David R. Bentley (Principal Investigator), Bret Barnes, R. Keira Cheetham, Michael Eberle, Sean Humphray, Scott Kahn, Lisa Murray, Richard Shaw, Kai Ye (Principal Investigator), Mark A. Batzer (Principal Investigator), Miriam K. Konkel, Jerilyn A. Walker, Phil Lacroute, David W. Craig (Principal Investigator), Nils Homer, Deanna Church, Chunlin Xiao, Jonathan Sebat (Principal Investigator), Vineet Bafna, Jacob J. Michaelson, Kenny Ye, Scott E. Devine (Principal Investigator), Xinyue Liu, Ankit Maroo, Luke J. Tallon, Gerton Lunter (Principal Investigator), Gil A. McVean (Principal Investigator), Zamin Iqbal, David Witherspoon, Jinchuan Xing, Evan E. Eichler (Principal Investigator) (Co-Chair), Can Alkan, Iman Hajirasouliha, Fereydoun Hormozdiari, Arthur Ko, Peter H. Sudmant, Ken Chen, Asif Chinwalla, Li Ding, Michael D. McLellan, John W. Wallis, Matthew E. Hurles (Principal Investigator) (Co-Chair), Ben Blackburne, Heng Li, Sarah J. Lindsay, Zemin Ning, Aylwyn Scally, Klaudia Walter, Yujun Zhang, Mark B. Gerstein (Principal Investigator), Alexej Abyzov, Jieming Chen, Declan Clarke, Ekta Khurana, Xinmeng Jasmine Mu, Cristina Sisu, Richard A. Gibbs (Principal Investigator) (Co-Chair), Fuli Yu (Project Leader), Matthew Bainbridge, Danny Challis, Uday S. Evani, Christie Kovar, Lora Lewis, James Lu, Donna Muzny, Uma Nagaswamy, Jeff Reid, Aniko Sabo, Jin Yu, Xiaosen Guo, Yingrui Li, Renhua Wu, Gabor T. Marth (Principal Investigator) (Co-Chair), Erik P. Garrison, Wen Fung Leong, Alistair N. Ward, Guillermo del Angel, Mark A. DePristo, Stacey B. Gabriel, Namrata Gupta, Chris Hartl, Ryan E. Poplin, Andrew G. Clark (Principal Investigator), Juan L. Rodriguez-Flores, Paul Flicek (Principal Investigator), Laura Clarke, Richard E. Smith, Xiangqun Zheng-Bradley, Daniel G. MacArthur (Principal Investigator), Carlos D. Bustamante (Principal Investigator), Simon Gravel, David W. Craig (Principal Investigator), Alexis Christoforides, Nils Homer, Tyler Izatt, Stephen T. Sherry (Principal Investigator), Chunlin Xiao, Emmanouil T. Dermitzakis (Principal Investigator), Gonçalo R. Abecasis (Principal Investigator), Hyun Min Kang, Gil A. McVean (Principal Investigator), Elaine R. Mardis (Principal Investigator), David Dooling, Lucinda Fulton, Robert Fulton, Daniel C. Koboldt, Richard M. Durbin (Principal Investigator), Senduran Balasubramaniam, Thomas M. Keane, Shane McCarthy, James Stalker, Mark B. Gerstein (Principal Investigator), Suganthi Balasubramanian, Lukas Habegger, Erik P. Garrison, Richard A. Gibbs (Principal Investigator), Matthew Bainbridge, Donna Muzny, Fuli Yu, Jin Yu, Guillermo del Angel, Robert E. Handsaker, Vladimir Makarov, Juan L. Rodriguez-Flores, Hanjun Jin (Principal Investigator), Wook Kim, Ki Cheol Kim, Paul Flicek (Principal Investigator), Kathryn Beal, Laura Clarke, Fiona Cunningham, Javier Herrero, William M. McLaren, Graham R. S. Ritchie, Xiangqun Zheng-Bradley, Shervin Tabrizi, Daniel G. MacArthur (Principal Investigator), Monkol Lek, Carlos D. Bustamante (Principal Investigator), Francisco M. De La Vega, David W. Craig (Principal Investigator), Ahmet A. Kurdoglu, Tuuli Lappalainen, Jeffrey A. Rosenfeld (Principal Investigator), Leslie P. Michelson, Philip Awadalla (Principal Investigator), Alan Hodgkinson, Gil A. McVean (Principal Investigator), Ken Chen, Yuan Chen, Vincenza Colonna, Adam Frankish, Jennifer Harrow, Yali Xue, Mark B. Gerstein (Principal Investigator) (Co-Chair), Alexej Abyzov, Suganthi Balasubramanian, Jieming Chen, Declan Clarke, Yao Fu, Arif O. Harmanci, Mike Jin, Ekta Khurana, Xinmeng Jasmine Mu, Cristina Sisu, Richard A. Gibbs (Principal Investigator), Gerald Fowler, Walker Hale, Divya Kalra, Christie Kovar, Donna Muzny, Jeff Reid, Jun Wang (Principal Investigator), Xiaosen Guo, Guoqing Li, Yingrui Li, Xiaole Zheng, David M. Altshuler, Paul Flicek (Principal Investigator) (Co-Chair), Laura Clarke (Project Leader), Jonathan Barker, Gavin Kelman, Eugene Kulesha, Rasko Leinonen, William M. McLaren, Rajesh Radhakrishnan, Asier Roa, Dmitriy Smirnov, Richard E. Smith, Ian Streeter, Iliana Toneva, Brendan Vaughan, Xiangqun Zheng-Bradley, David R. Bentley (Principal Investigator), Tony Cox, Sean Humphray, Scott Kahn, Ralf Sudbrak (Project Leader), Marcus W. Albrecht, Matthias Lienhard, David W. Craig (Principal Investigator), Tyler Izatt, Ahmet A. Kurdoglu, Stephen T. Sherry (Principal Investigator) (Co-Chair), Victor Ananiev, Zinaida Belaia, Dimitriy Beloslyudtsev, Nathan Bouk, Chao Chen, Deanna Church, Robert Cohen, Charles Cook, John Garner, Timothy Hefferon, Mikhail Kimelman, Chunlei Liu, John Lopez, Peter Meric, Chris O』Sullivan, Yuri Ostapchuk, Lon Phan, Sergiy Ponomarov, Valerie Schneider, Eugene Shekhtman, Karl Sirotkin, Douglas Slotta, Chunlin Xiao, Hua Zhang, David Haussler (Principal Investigator), Gonçalo R. Abecasis (Principal Investigator), Gil A. McVean (Principal Investigator), Can Alkan, Arthur Ko, David Dooling, Richard M. Durbin (Principal Investigator), Senduran Balasubramaniam, Thomas M. Keane, Shane McCarthy, James Stalker, Aravinda Chakravarti (Co-Chair), Bartha M. Knoppers (Co-Chair), Gonçalo R. Abecasis, Kathleen C. Barnes, Christine Beiswanger, Esteban G. Burchard, Carlos D. Bustamante, Hongyu Cai, Hongzhi Cao, Richard M. Durbin, Neda Gharani, Richard A. Gibbs, Christopher R. 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