Advances in Whole Genome Sequencing Technology

被引：49

作者：

Zhao, Jianhua ^{[1
]}

Grant, Struan F. A. ^{[1
,2
,3
]}

机构：

[1] Childrens Hosp Philadelphia, Div Human Genet, Philadelphia, PA 19104 USA

[2] Univ Penn, Sch Med, Dept Pediat, Philadelphia, PA 19104 USA

[3] Childrens Hosp Philadelphia, Ctr Appl Genom, Abramson Res Ctr, Philadelphia, PA 19104 USA

来源：

CURRENT PHARMACEUTICAL BIOTECHNOLOGY | 2011年 / 12卷 / 02期

关键词：

Genome; sequencing; technology; applications; WIDE ASSOCIATION SCAN; SUSCEPTIBILITY LOCI; GENETIC-VARIANTS; COMMON VARIANTS; DNA-POLYMERASE; CROHN-DISEASE; RISK LOCI; RNA-SEQ; TRANSCRIPTOME; REVEALS;

D O I：

10.2174/138920111794295729

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Sanger sequencing revolutionized the field of genetics by becoming the standard approach to appraise a given region of the genome at base-level resolution. However, the relatively recent need to sequence entire genomes has driven innovative developments within the market-place to allow for sequencing technology to be faster, cheaper and more accurate. In this review, we will cover these recent developments from both a technical and cost perspective. Firstly, we will place sequencing in a historical context by describing how it first came to the attention of the scientific community. Next, we will address the current high-throughput technologies generally available, including Roche's 454, Illumina's Genome Analyzer, Applied BioSystem's SOLiD, Complete Genomics, Helios, Pacific Biosciences and IonTorrent. These 'next-generation' technologies also allow for applications related to target region deep sequencing, epigenetics(ChIP-seq), transcriptome sequencing (RNA-seq), megagenomics. Thus, these technologies offer unprecedented opportunities to increase our understanding of the functions and dynamics of the human genome in the near future.

引用

页码：293 / 305

页数：13

共 100 条

[1] A haplotype map of the human genome [J].

Altshuler, D ;

Brooks, LD ;

Chakravarti, A ;

Collins, FS ;

Daly, MJ ;

Donnelly, P ;

Gibbs, RA ;

Belmont, JW ;

Boudreau, A ;

Leal, SM ;

Hardenbol, P ;

Pasternak, S ;

Wheeler, DA ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Zeng, CQ ;

Gao, Y ;

Hu, HR ;

Hu, WT ;

Li, CH ;

Lin, W ;

Liu, SQ ;

Pan, H ;

Tang, XL ;

Wang, J ;

Wang, W ;

Yu, J ;

Zhang, B ;

Zhang, QR ;

Zhao, HB ;

Zhao, H ;

Zhou, J ;

Gabriel, SB ;

Barry, R ;

Blumenstiel, B ;

Camargo, A ;

Defelice, M ;

Faggart, M ;

Goyette, M ;

Gupta, S ;

Moore, J ;

Nguyen, H ;

Onofrio, RC ;

Parkin, M ;

Roy, J ;

Stahl, E ;

Winchester, E ;

Ziaugra, L ;

Shen, Y .

NATURE, 2005, 437 (7063) :1299-1320

[2] Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease [J].

Barrett, Jeffrey C. ;

Hansoul, Sarah ;

Nicolae, Dan L. ;

Cho, Judy H. ;

Duerr, Richard H. ;

Rioux, John D. ;

Brant, Steven R. ;

Silverberg, Mark S. ;

Taylor, Kent D. ;

Barmada, M. Michael ;

Bitton, Alain ;

Dassopoulos, Themistocles ;

Datta, Lisa Wu ;

Green, Todd ;

Griffiths, Anne M. ;

Kistner, Emily O. ;

Murtha, Michael T. ;

Regueiro, Miguel D. ;

Rotter, Jerome I. ;

Schumm, L. Philip ;

Steinhart, A. Hillary ;

Targan, Stephan R. ;

Xavier, Ramnik J. ;

Libioulle, Cecile ;

Sandor, Cynthia ;

Lathrop, Mark ;

Belaiche, Jacques ;

Dewit, Olivier ;

Gut, Ivo ;

Heath, Simon ;

Laukens, Debby ;

Mni, Myriam ;

Rutgeerts, Paul ;

Van Gossum, Andre ;

Zelenika, Diana ;

Franchimont, Denis ;

Hugot, Jean-Pierre ;

de Vos, Martine ;

Vermeire, Severine ;

Louis, Edouard ;

Cardon, Lon R. ;

Anderson, Carl A. ;

Drummond, Hazel ;

Nimmo, Elaine ;

Ahmad, Tariq ;

Prescott, Natalie J. ;

Onnie, Clive M. ;

Fisher, Sheila A. ;

Marchini, Jonathan ;

Ghori, Jilur .

NATURE GENETICS, 2008, 40 (08) :955-962

[3] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[4] Genome-wide analysis of histone modifications in human pancreatic islets [J].

Bhandare, Reena ;

Schug, Jonathan ;

Le Lay, John ;

Fox, Alan ;

Smirnova, Olga ;

Liu, Chengyang ;

Naji, Ali ;

Kaestner, Klaus H. .

GENOME RESEARCH, 2010, 20 (04) :428-433

[5]

BLANCO L, 1989, J BIOL CHEM, V264, P8935

[6] Sequence information can be obtained from single DNA molecules [J].

Braslavsky, I ;

Hebert, B ;

Kartalov, E ;

Quake, SR .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (07) :3960-3964

[7] Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls [J].

Burton, Paul R. ;

Clayton, David G. ;

Cardon, Lon R. ;

Craddock, Nick ;

Deloukas, Panos ;

Duncanson, Audrey ;

Kwiatkowski, Dominic P. ;

McCarthy, Mark I. ;

Ouwehand, Willem H. ;

Samani, Nilesh J. ;

Todd, John A. ;

Donnelly, Peter ;

Barrett, Jeffrey C. ;

Davison, Dan ;

Easton, Doug ;

Evans, David ;

Leung, Hin-Tak ;

Marchini, Jonathan L. ;

Morris, Andrew P. ;

Spencer, Chris C. A. ;

Tobin, Martin D. ;

Attwood, Antony P. ;

Boorman, James P. ;

Cant, Barbara ;

Everson, Ursula ;

Hussey, Judith M. ;

Jolley, Jennifer D. ;

Knight, Alexandra S. ;

Koch, Kerstin ;

Meech, Elizabeth ;

Nutland, Sarah ;

Prowse, Christopher V. ;

Stevens, Helen E. ;

Taylor, Niall C. ;

Walters, Graham R. ;

Walker, Neil M. ;

Watkins, Nicholas A. ;

Winzer, Thilo ;

Jones, Richard W. ;

McArdle, Wendy L. ;

Ring, Susan M. ;

Strachan, David P. ;

Pembrey, Marcus ;

Breen, Gerome ;

St Clair, David ;

Caesar, Sian ;

Gordon-Smith, Katherine ;

Jones, Lisa ;

Fraser, Christine ;

Green, Elain K. .

NATURE, 2007, 447 (7145) :661-678

[8] Stem cell transcriptome profiling via massive-scale mRNA sequencing [J].

Cloonan, Nicole ;

Forrest, Alistair R. R. ;

Kolle, Gabriel ;

Gardiner, Brooke B. A. ;

Faulkner, Geoffrey J. ;

Brown, Mellissa K. ;

Taylor, Darrin F. ;

Steptoe, Anita L. ;

Wani, Shivangi ;

Bethel, Graeme ;

Robertson, Alan J. ;

Perkins, Andrew C. ;

Bruce, Stephen J. ;

Lee, Clarence C. ;

Ranade, Swati S. ;

Peckham, Heather E. ;

Manning, Jonathan M. ;

McKernan, Kevin J. ;

Grimmond, Sean M. .

NATURE METHODS, 2008, 5 (07) :613-619

[9] Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning [J].

Cokus, Shawn J. ;

Feng, Suhua ;

Zhang, Xiaoyu ;

Chen, Zugen ;

Merriman, Barry ;

Haudenschild, Christian D. ;

Pradhan, Sriharsa ;

Nelson, Stanley F. ;

Pellegrini, Matteo ;

Jacobsen, Steven E. .

NATURE, 2008, 452 (7184) :215-219

[10] Mutation discovery in the mouse using genetically guided array capture and resequencing [J].

D'Ascenzo, Mark ;

Meacham, Carl ;

Kitzman, Jacob ;

Middle, Christina ;

Knight, Jim ;

Winer, Roger ;

Kukricar, Miroslav ;

Richmond, Todd ;

Albert, Thomas J. ;

Czechanski, Anne ;

Donahue, Leah Rae ;

Affourtit, Jason ;

Jeddeloh, Jeffrey A. ;

Reinholdt, Laura .

MAMMALIAN GENOME, 2009, 20 (07) :424-436

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