A window into third-generation sequencing

被引：566

作者：

Schadt, Eric E. ^{[1
]}

Turner, Steve ^{[1
]}

Kasarskis, Andrew ^{[1
]}

机构：

[1] Pacific Biosci, Menlo Pk, CA 94025 USA

来源：

HUMAN MOLECULAR GENETICS | 2010年 / 19卷

关键词：

SINGLE-MOLECULE; DNA METHYLATION; GENOME; QUANTIFICATION; READS;

D O I：

10.1093/hmg/ddq416

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：

First- and second-generation sequencing technologies have led the way in revolutionizing the field of genomics and beyond, motivating are astonishing number of scientific advances, including enabling a more complete understanding of whole genome sequences and the information encoded therein, a more complete characterization of the methylome and transcriptome and a better understanding of interactions between proteins and DNA. Nevertheless, there are sequencing applications and aspects of genome biology that are presently beyond the reach of current sequencing technologies, leaving fertile ground for additional innovation in this space. In this review, we describe a new generation of single-molecule sequencing technologies (third-generation sequencing) that is emerging to fill this space, with the potential for dramatically longer read lengths, shorter time to result and lower overall cost.

引用

页码：R227 / R240

页数：14

共 62 条

[11] Nanopore DNA sequencing with MspA [J].

Derrington, Ian M. ;

Butler, Tom Z. ;

Collins, Marcus D. ;

Manrao, Elizabeth ;

Pavlenok, Mikhail ;

Niederweis, Michael ;

Gundlach, Jens H. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (37) :16060-16065

[12] SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing [J].

Dohm, Juliane C. ;

Lottaz, Claudio ;

Borodina, Tatiana ;

Himmelbauer, Heinz .

GENOME RESEARCH, 2007, 17 (11) :1697-1706

[13] Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays [J].

Drmanac, Radoje ;

Sparks, Andrew B. ;

Callow, Matthew J. ;

Halpern, Aaron L. ;

Burns, Norman L. ;

Kermani, Bahram G. ;

Carnevali, Paolo ;

Nazarenko, Igor ;

Nilsen, Geoffrey B. ;

Yeung, George ;

Dahl, Fredrik ;

Fernandez, Andres ;

Staker, Bryan ;

Pant, Krishna P. ;

Baccash, Jonathan ;

Borcherding, Adam P. ;

Brownley, Anushka ;

Cedeno, Ryan ;

Chen, Linsu ;

Chernikoff, Dan ;

Cheung, Alex ;

Chirita, Razvan ;

Curson, Benjamin ;

Ebert, Jessica C. ;

Hacker, Coleen R. ;

Hartlage, Robert ;

Hauser, Brian ;

Huang, Steve ;

Jiang, Yuan ;

Karpinchyk, Vitali ;

Koenig, Mark ;

Kong, Calvin ;

Landers, Tom ;

Le, Catherine ;

Liu, Jia ;

McBride, Celeste E. ;

Morenzoni, Matt ;

Morey, Robert E. ;

Mutch, Karl ;

Perazich, Helena ;

Perry, Kimberly ;

Peters, Brock A. ;

Peterson, Joe ;

Pethiyagoda, Charit L. ;

Pothuraju, Kaliprasad ;

Richter, Claudia ;

Rosenbaum, Abraham M. ;

Roy, Shaunak ;

Shafto, Jay ;

Sharanhovich, Uladzislau .

SCIENCE, 2010, 327 (5961) :78-81

[14] Real-Time DNA Sequencing from Single Polymerase Molecules [J].

Eid, John ;

Fehr, Adrian ;

Gray, Jeremy ;

Luong, Khai ;

Lyle, John ;

Otto, Geoff ;

Peluso, Paul ;

Rank, David ;

Baybayan, Primo ;

Bettman, Brad ;

Bibillo, Arkadiusz ;

Bjornson, Keith ;

Chaudhuri, Bidhan ;

Christians, Frederick ;

Cicero, Ronald ;

Clark, Sonya ;

Dalal, Ravindra ;

deWinter, Alex ;

Dixon, John ;

Foquet, Mathieu ;

Gaertner, Alfred ;

Hardenbol, Paul ;

Heiner, Cheryl ;

Hester, Kevin ;

Holden, David ;

Kearns, Gregory ;

Kong, Xiangxu ;

Kuse, Ronald ;

Lacroix, Yves ;

Lin, Steven ;

Lundquist, Paul ;

Ma, Congcong ;

Marks, Patrick ;

Maxham, Mark ;

Murphy, Devon ;

Park, Insil ;

Pham, Thang ;

Phillips, Michael ;

Roy, Joy ;

Sebra, Robert ;

Shen, Gene ;

Sorenson, Jon ;

Tomaney, Austin ;

Travers, Kevin ;

Trulson, Mark ;

Vieceli, John ;

Wegener, Jeffrey ;

Wu, Dawn ;

Yang, Alicia ;

Zaccarin, Denis .

SCIENCE, 2009, 323 (5910) :133-138

[15] Base-calling of automated sequencer traces using phred.: II.: Error probabilities [J].

Ewing, B ;

Green, P .

GENOME RESEARCH, 1998, 8 (03) :186-194

[16] Base-calling of automated sequencer traces using phred.: I.: Accuracy assessment [J].

Ewing, B ;

Hillier, L ;

Wendl, MC ;

Green, P .

GENOME RESEARCH, 1998, 8 (03) :175-185

[17]

Flusberg BA, 2010, NAT METHODS, V7, P461, DOI [10.1038/NMETH.1459, 10.1038/nmeth.1459]

[18]

Goren A, 2010, NAT METHODS, V7, P47, DOI [10.1038/NMETH.1404, 10.1038/nmeth.1404]

[19] Single-molecule DNA sequencing of a viral genome [J].

Harris, Timothy D. ;

Buzby, Phillip R. ;

Babcock, Hazen ;

Beer, Eric ;

Bowers, Jayson ;

Braslavsky, Ido ;

Causey, Marie ;

Colonell, Jennifer ;

DiMeo, James ;

Efcavitch, J. William ;

Giladi, Eldar ;

Gill, Jaime ;

Healy, John ;

Jarosz, Mirna ;

Lapen, Dan ;

Moulton, Keith ;

Quake, Stephen R. ;

Steinmann, Kathleen ;

Thayer, Edward ;

Tyurina, Anastasia ;

Ward, Rebecca ;

Weiss, Howard ;

Xie, Zheng .

SCIENCE, 2008, 320 (5872) :106-109

[20] De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer [J].

Hernandez, David ;

Francois, Patrice ;

Farinelli, Laurent ;

Osteras, Magne ;

Schrenzel, Jacques .

GENOME RESEARCH, 2008, 18 (05) :802-809

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