Next-generation sequencing: applications beyond genomes

被引：71

作者：

Marguerat, Samuel ^{[1
]}

Wilhelm, Brian T. ^{[1
]}

Baehler, Juerg ^{[1
]}

机构：

[1] UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England

来源：

BIOCHEMICAL SOCIETY TRANSACTIONS | 2008年 / 36卷

基金：

英国惠康基金;

关键词：

ChiP-Seq; high-throughput sequencing; massively parallel sequencing; microarray; RNA-Seq; transcriptome; yeast;

D O I：

10.1042/BST0361091

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：

The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. in the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.

引用

页码：1091 / 1096

页数：6

共 55 条

[1] A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis [J].

Andries, K ;

Verhasselt, P ;

Guillemont, J ;

Göhlmann, HWH ;

Neefs, JM ;

Winkler, H ;

Van Gestel, J ;

Timmerman, P ;

Zhu, M ;

Lee, E ;

Williams, P ;

de Chaffoy, D ;

Huitric, E ;

Hoffner, S ;

Cambau, E ;

Truffot-Pernot, C ;

Lounis, N ;

Jarlier, V .

SCIENCE, 2005, 307 (5707) :223-227

[2] The marine viromes of four oceanic regions [J].

Angly, Florent E. ;

Felts, Ben ;

Breitbart, Mya ;

Salamon, Peter ;

Edwards, Robert A. ;

Carlson, Craig ;

Chan, Amy M. ;

Haynes, Matthew ;

Kelley, Scott ;

Liu, Hong ;

Mahaffy, Joseph M. ;

Mueller, Jennifer E. ;

Nulton, Jim ;

Olson, Robert ;

Parsons, Rachel ;

Rayhawk, Steve ;

Suttle, Curtis A. ;

Rohwer, Forest .

PLOS BIOLOGY, 2006, 4 (11) :2121-2131

[3] Primer: Sequencing - the next generation [J].

不详 .

NATURE METHODS, 2008, 5 (01) :15-15

[4] Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach [J].

Bainbridge, Matthew N. ;

Warren, Rene L. ;

Hirst, Martin ;

Romanuik, Tammy ;

Zeng, Thomas ;

Go, Anne ;

Delaney, Allen ;

Griffith, Malachi ;

Hickenbotham, Matthew ;

Magrini, Vincent ;

Mardis, Elaine R. ;

Sadar, Marianne D. ;

Siddiqui, Asim S. ;

Marra, Marco A. ;

Jones, Steven J. M. .

BMC GENOMICS, 2006, 7 (1)

[5] High-resolution profiling of histone methylations in the human genome [J].

Barski, Artern ;

Cuddapah, Suresh ;

Cui, Kairong ;

Roh, Tae-Young ;

Schones, Dustin E. ;

Wang, Zhibin ;

Wei, Gang ;

Chepelev, Iouri ;

Zhao, Keji .

CELL, 2007, 129 (04) :823-837

[6] High-resolution mapping and characterization of open chromatin across the genome [J].

Boyle, Alan P. ;

Davis, Sean ;

Shulha, Hennady P. ;

Meltzer, Paul ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Furey, Terrence S. ;

Crawford, Gregory E. .

CELL, 2008, 132 (02) :311-322

[7] Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays [J].

Brenner, S ;

Johnson, M ;

Bridgham, J ;

Golda, G ;

Lloyd, DH ;

Johnson, D ;

Luo, SJ ;

McCurdy, S ;

Foy, M ;

Ewan, M ;

Roth, R ;

George, D ;

Eletr, S ;

Albrecht, G ;

Vermaas, E ;

Williams, SR ;

Moon, K ;

Burcham, T ;

Pallas, M ;

DuBridge, RB ;

Kirchner, J ;

Fearon, K ;

Mao, J ;

Corcoran, K .

NATURE BIOTECHNOLOGY, 2000, 18 (06) :630-634

[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] A metagenomic survey of microbes in honey bee colony collapse disorder [J].

Cox-Foster, Diana L. ;

Conlan, Sean ;

Holmes, Edward C. ;

Palacios, Gustavo ;

Evans, Jay D. ;

Moran, Nancy A. ;

Quan, Phenix-Lan ;

Briese, Thomas ;

Hornig, Mady ;

Geiser, David M. ;

Martinson, Vince ;

vanEngelsdorp, Dennis ;

Kalkstein, Abby L. ;

Drysdale, Andrew ;

Hui, Jeffrey ;

Zhai, Junhui ;

Cui, Liwang ;

Hutchison, Stephen K. ;

Simons, Jan Fredrik ;

Egholm, Michael ;

Pettis, Jeffery S. ;

Lipkin, W. Ian .

SCIENCE, 2007, 318 (5848) :283-287

[10] Using pyrosequencing to shed light on deep mine microbial ecology [J].

Edwards, Robert A. ;

Rodriguez-Brito, Beltran ;

Wegley, Linda ;

Haynes, Matthew ;

Breitbart, Mya ;

Peterson, Dean M. ;

Saar, Martin O. ;

Alexander, Scott ;

Alexander, E. Calvin, Jr. ;

Rohwer, Forest .

BMC GENOMICS, 2006, 7 (1)

← 1 2 3 4 5 6 →