Next-generation sequencing: applications beyond genomes.
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.
Marguerat
Samuel
S
Cancer Research UK, Fission Yeast Functional Genomics Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK. jurg@sanger.ac.uk
Wilhelm
Brian T
BT
Bähler
Jürg
J
D001483:Base Sequence; D002843:Chromatin / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016678:Genome; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D002843:Chromatin; D004268:DNA-Binding Proteins
Nat Methods. 2008 Feb;5(2):183-8
18204455
Proc Natl Acad Sci U S A. 2006 May 23;103(21):8107-12
16707573
Cell. 2006 Dec 15;127(6):1193-207
17174894
Cell. 2008 May 2;133(3):523-36
18423832
Nat Methods. 2008 Jan;5(1):19-21
18165803
Nat Biotechnol. 2007 Aug;25(8):878-80
17687366
Nature. 2005 Sep 15;437(7057):376-80
16056220
Genome Res. 2006 Oct;16(10):1276-88
16954541
Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9999-10004
16788065
Nat Biotechnol. 2000 Jun;18(6):630-4
10835600
Nucleic Acids Res. 2007;35(13):e91
17576693
Genes Dev. 2008 Jan 1;22(1):26-36
18172163
Nature. 2008 Apr 17;452(7189):872-6
18421352
Biotechniques. 2008 Jul;45(1):81-94
18611170
Nat Rev Genet. 2005 Nov;6(11):805-14
16304596
Science. 2008 Aug 15;321(5891):956-60
18599741
Nature. 2006 Oct 26;443(7114):950-5
16980956
Genome Res. 2008 Jan;18(1):172-7
18032722
Genome Res. 2007 Aug;17(8):1195-201
17600086
Nat Rev Genet. 2007 Jun;8(6):413-23
17486121
Nature. 2001 Jan 25;409(6819):533-8
11206552
Nature. 2007 Aug 2;448(7153):553-60
17603471
Nat Methods. 2008 Jan;5(1):15
18175411
BMC Genomics. 2006 Mar 20;7:57
16549033
Nature. 2008 Jun 26;453(7199):1239-43
18488015
BMC Genomics. 2006 Sep 29;7:246
17010196
Science. 2005 Jan 14;307(5707):223-7
15591164
Nucleic Acids Res. 2006 Jul 13;34(12):e84
16840528
Science. 2000 Dec 22;290(5500):2306-9
11125145
Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
16880384
Nat Methods. 2008 Jul;5(7):613-9
18516046
Genes Dev. 2008 Jan 1;22(1):8-13
18172160
Nat Genet. 2007 Mar;39(3):347-51
17293865
Nature. 2007 Nov 22;450(7169):560-5
18033299
Science. 1995 Oct 20;270(5235):484-7
7570003
Science. 2006 Nov 17;314(5802):1113-8
17110569
Cell. 2007 May 18;129(4):823-37
17512414
Science. 2008 Jun 6;320(5881):1344-9
18451266
Science. 2006 Jan 20;311(5759):392-4
16368896
Science. 2007 Oct 5;318(5847):97-100
17916733
Science. 2007 Jun 8;316(5830):1481-4
17556586
Nat Methods. 2008 Jul;5(7):621-8
18516045
Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7
271968
Science. 2007 Oct 19;318(5849):441-4
17901299
Nat Methods. 2007 Aug;4(8):651-7
17558387
Nat Methods. 2008 Jan;5(1):16-8
18165802
Science. 2007 Oct 19;318(5849):420-6
17901297
Science. 2007 Oct 12;318(5848):283-7
17823314
Science. 2007 Jun 8;316(5830):1497-502
17540862
PLoS Biol. 2006 Nov;4(11):e368
17090214
Infect Immun. 2006 Aug;74(8):4694-707
16861657
Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3521-6
18303113
Science. 2005 Sep 9;309(5741):1728-32
16081699
Nature. 2006 Nov 16;444(7117):330-6
17108958
Cell. 2008 Jan 25;132(2):311-22
18243105