An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

被引：48

作者：

Cho, Yun Sung ^{[1
,2
,3
]}

Kim, Hyunho ^{[4
]}

Kim, Hak-Min ^{[1
,2
]}

Jho, Sungwoong ^{[3
]}

Jun, JeHoon ^{[3
,4
]}

Lee, Yong Joo ^{[4
]}

Chae, Kyun Shik ^{[5
]}

Kim, Chang Geun ^{[5
]}

Kim, Sangsoo ^{[6
]}

Eriksson, Anders ^{[7
]}

Edwards, Jeremy S. ^{[8
]}

Lee, Semin ^{[1
,2
]}

Kim, Byung Chul ^{[1
,2
]}

Manica, Andrea ^{[7
]}

Oh, Tae-Kwang ^{[9
]}

Church, George M. ^{[10
]}

Bhak, Jong ^{[1
,2
,3
,4
]}

机构：

[1] UNIST, TGI, Ulsan 44919, South Korea

[2] UNIST, Sch Life Sci, Dept Biomed Engn, Ulsan 44919, South Korea

[3] Genome Res Fdn, Personal Genom Inst, Cheongju 28160, South Korea

[4] UNIST, Gerom Inc, Ulsan 44919, South Korea

[5] Korea Res Inst Stand & Sci, Natl Standard Reference Ctr, Daejeon 34113, South Korea

[6] Soongsil Univ, Sch Syst Biomed Sci, Seoul 06978, South Korea

[7] Univ Cambridge, Dept Zool, Downing St, Cambridge CB2 3EJ, England

[8] Univ New Mexico, Ctr Comprehens Canc, Chem & Chem Biol, Albuquerque, NM 87131 USA

[9] Korea Res Inst Biosci & Biotechnol, Infect & Immun Res Ctr, Daejeon 34141, South Korea

[10] Harvard Med Sch, Dept Genet, New Res Bldg NRB,77 Ave Louis Pasteur,Room 238, Boston, MA 02115 USA

来源：

NATURE COMMUNICATIONS | 2016年 / 7卷

关键词：

STRUCTURAL VARIATION; SEQUENCE; DATABASE; TOOL; POLYMORPHISMS; ARCHITECTURE; NEANDERTHAL; GENERATION; FRAMEWORK; ALIGNMENT;

D O I：

10.1038/ncomms13637

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

引用

页数：12

共 69 条

[21] Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence [J].

Dewey, Frederick E. ;

Chen, Rong ;

Cordero, Sergio P. ;

Ormond, Kelly E. ;

Caleshu, Colleen ;

Karczewski, Konrad J. ;

Whirl-Carrillo, Michelle ;

Wheeler, Matthew T. ;

Dudley, Joel T. ;

Byrnes, Jake K. ;

Cornejo, Omar E. ;

Knowles, Joshua W. ;

Woon, Mark ;

Sangkuhl, Katrin ;

Gong, Li ;

Thorn, Caroline F. ;

Hebert, Joan M. ;

Capriotti, Emidio ;

David, Sean P. ;

Pavlovic, Aleksandra ;

West, Anne ;

Thakuria, Joseph V. ;

Ball, Madeleine P. ;

Zaranek, Alexander W. ;

Rehm, Heidi L. ;

Church, George M. ;

West, John S. ;

Bustamante, Carlos D. ;

Snyder, Michael ;

Altman, Russ B. ;

Klein, Teri E. ;

Butte, Atul J. ;

Ashley, Euan A. .

PLOS GENETICS, 2011, 7 (09)

[22] Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) [J].

Dong, Yang ;

Xie, Min ;

Jiang, Yu ;

Xiao, Nianqing ;

Du, Xiaoyong ;

Zhang, Wenguang ;

Tosser-Klopp, Gwenola ;

Wang, Jinhuan ;

Yang, Shuang ;

Liang, Jie ;

Chen, Wenbin ;

Chen, Jing ;

Zeng, Peng ;

Hou, Yong ;

Bian, Chao ;

Pan, Shengkai ;

Li, Yuxiang ;

Liu, Xin ;

Wang, Wenliang ;

Servin, Bertrand ;

Sayre, Brian ;

Zhu, Bin ;

Sweeney, Deacon ;

Moore, Rich ;

Nie, Wenhui ;

Shen, Yongyi ;

Zhao, Ruoping ;

Zhang, Guojie ;

Li, Jinquan ;

Faraut, Thomas ;

Womack, James ;

Zhang, Yaping ;

Kijas, James ;

Cockett, Noelle ;

Xu, Xun ;

Zhao, Shuhong ;

Wang, Jun ;

Wang, Wen .

NATURE BIOTECHNOLOGY, 2013, 31 (02) :135-141

[23] Alignathon: a competitive assessment of whole-genome alignment methods [J].

Earl, Dent ;

Nguyen, Ngan ;

Hickey, Glenn ;

Harris, Robert S. ;

Fitzgerald, Stephen ;

Beal, Kathryn ;

Seledtsov, Igor ;

Molodtsov, Vladimir ;

Raney, Brian J. ;

Clawson, Hiram ;

Kim, Jaebum ;

Kemena, Carsten ;

Chang, Jia-Ming ;

Erb, Ionas ;

Poliakov, Alexander ;

Hou, Minmei ;

Herrero, Javier ;

Kent, William James ;

Solovyev, Victor ;

Darling, Aaron E. ;

Ma, Jian ;

Notredame, Cedric ;

Brudno, Michael ;

Dubchak, Inna ;

Haussler, David ;

Paten, Benedict .

GENOME RESEARCH, 2014, 24 (12) :2077-2089

[24] Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology [J].

English, Adam C. ;

Richards, Stephen ;

Han, Yi ;

Wang, Min ;

Vee, Vanesa ;

Qu, Jiaxin ;

Qin, Xiang ;

Muzny, Donna M. ;

Reid, Jeffrey G. ;

Worley, Kim C. ;

Gibbs, Richard A. .

PLOS ONE, 2012, 7 (11)

[25] MitoTool: A web server for the analysis and retrieval of human mitochondrial DNA sequence variations [J].

Fan, Long ;

Yao, Yong-Gang .

MITOCHONDRION, 2011, 11 (02) :351-356

[26] Whole-genome sequence variation, population structure and demographic history of the Dutch population [J].

Francioli, Laurent C. ;

Menelaou, Andronild ;

Pulit, Sara L. ;

Van Dijk, Freerk ;

Palamara, Pier Francesco ;

Elbers, Clara C. ;

Neerincx, Pieter B. T. ;

Ye, Kai ;

Guryev, Victor ;

Kloosterman, Wigard P. ;

Deelen, Patrick ;

Abdellaoui, Abdel ;

Van Leeuwen, Elisabeth M. ;

Van Oven, Mannis ;

Vermaat, Martijn ;

Li, Mingkun ;

Laros, Jeroen F. J. ;

Karssen, Lennart C. ;

Kanterakis, Alexandros ;

Amin, Najaf ;

Hottenga, Jouke Jan ;

Lameijer, Eric-Wubbo ;

Kattenberg, Mathijs ;

Dijkstra, Martijn ;

Byelas, Heorhiy ;

Van Settenl, Jessica ;

Van Schaik, Barbera D. C. ;

Bot, Jan ;

Nijman, Isaac J. ;

Renkens, Ivo ;

Marscha, Tobias ;

Schonhuth, Alexander ;

Hehir-Kwa, Jayne Y. ;

Handsaker, Robert E. ;

Polak, Paz ;

Sohail, Mashaal ;

Vuzman, Dana ;

Hormozdiari, Fereydoun ;

Van Enckevort, David ;

Mei, Hailiang ;

Koval, Vyacheslav ;

Moed, Ma-Tthijs H. ;

Van der Velde, K. Joeri ;

Rivadeneira, Fernando ;

Estrada, Karol ;

Medina-Gomez, Carolina ;

Isaacs, Aaron ;

McCarroll, Steven A. ;

Beekrnan, Marian ;

De Craen, Anton J. M. .

NATURE GENETICS, 2014, 46 (08) :818-825

[27] High-quality draft assemblies of mammalian genomes from massively parallel sequence data [J].

Gnerre, Sante ;

MacCallum, Iain ;

Przybylski, Dariusz ;

Ribeiro, Filipe J. ;

Burton, Joshua N. ;

Walker, Bruce J. ;

Sharpe, Ted ;

Hall, Giles ;

Shea, Terrance P. ;

Sykes, Sean ;

Berlin, Aaron M. ;

Aird, Daniel ;

Costello, Maura ;

Daza, Riza ;

Williams, Louise ;

Nicol, Robert ;

Gnirke, Andreas ;

Nusbaum, Chad ;

Lander, Eric S. ;

Jaffe, David B. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (04) :1513-1518

[28] A Draft Sequence of the Neandertal Genome [J].

Green, Richard E. ;

Krause, Johannes ;

Briggs, Adrian W. ;

Maricic, Tomislav ;

Stenzel, Udo ;

Kircher, Martin ;

Patterson, Nick ;

Li, Heng ;

Zhai, Weiwei ;

Fritz, Markus Hsi-Yang ;

Hansen, Nancy F. ;

Durand, Eric Y. ;

Malaspinas, Anna-Sapfo ;

Jensen, Jeffrey D. ;

Marques-Bonet, Tomas ;

Alkan, Can ;

Pruefer, Kay ;

Meyer, Matthias ;

Burbano, Hernan A. ;

Good, Jeffrey M. ;

Schultz, Rigo ;

Aximu-Petri, Ayinuer ;

Butthof, Anne ;

Hoeber, Barbara ;

Hoeffner, Barbara ;

Siegemund, Madlen ;

Weihmann, Antje ;

Nusbaum, Chad ;

Lander, Eric S. ;

Russ, Carsten ;

Novod, Nathaniel ;

Affourtit, Jason ;

Egholm, Michael ;

Verna, Christine ;

Rudan, Pavao ;

Brajkovic, Dejana ;

Kucan, Zeljko ;

Gusic, Ivan ;

Doronichev, Vladimir B. ;

Golovanova, Liubov V. ;

Lalueza-Fox, Carles ;

de la Rasilla, Marco ;

Fortea, Javier ;

Rosas, Antonio ;

Schmitz, Ralf W. ;

Johnson, Philip L. F. ;

Eichler, Evan E. ;

Falush, Daniel ;

Birney, Ewan ;

Mullikin, James C. .

SCIENCE, 2010, 328 (5979) :710-722

[29]

Harris R. S., 2007, THESIS, DOI DOI 10.5555/1414852

[30] Using optical mapping data for the improvement of vertebrate genome assemblies [J].

Howe, Kerstin ;

Wood, Jonathan M. D. .

GIGASCIENCE, 2015, 4

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