Accurate whole human genome sequencing using reversible terminator chemistry

Nature

Volumn 456, Issue 7218, 2008, Pages 53-59

  Bentley, David R ^a   Balasubramanian, Shankar ^b   Swerdlow, Harold P ^a,c   Smith, Geoffrey P ^a   Milton, John ^a,f   Brown, Clive G ^a,f   Hall, Kevin P ^a   Evers, Dirk J ^a   Barnes, Colin L ^a,b   Bignell, Helen R ^a   Boutell, Jonathan M ^a   Bryant, Jason ^a   Carter, Richard J ^a   Keira Cheetham, R ^a   Cox, Anthony J ^a   Ellis, Darren J ^a   Flatbush, Michael R ^a   Gormley, Niall A ^a   Humphray, Sean J ^a   Irving, Leslie J ^a   Karbelashvili, Mirian S ^a   Kirk, Scott M ^a   Li, Heng ^c   Liu, Xiaohai ^a,b   Maisinger, Klaus S ^a   Murray, Lisa J ^a   Obradovic, Bojan ^a   Ost, Tobias ^a   Parkinson, Michael L ^a   Pratt, Mark R ^a   Rasolonjatovo, Isabelle M J ^a   Reed, Mark T ^a   Rigatti, Roberto ^a   Rodighiero, Chiara ^a   Ross, Mark T ^a   Sabot, Andrea ^a   Sankar, Subramanian V ^a   Scally, Aylwyn ^c   Schroth, Gary P ^a   Smith, Mark E ^a   Smith, Vincent P ^a   Spiridou, Anastassia ^a   Torrance, Peta E ^a   Tzonev, Svilen S ^a   Vermaas, Eric H ^a   Walter, Klaudia ^c   Wu, Xiaolin ^a   Zhang, Lu ^a   Alam, Mohammed D ^a   Anastasi, Carole ^a   Aniebo, Ify C ^a   Bailey, David M D ^a   Bancarz, Iain R ^a   Banerjee, Saibal ^a   Barbour, Selena G ^a   Baybayan, Primo A ^a   Benoit, Vincent A ^a   Benson, Kevin F ^a   Bevis, Claire ^a   Black, Phillip J ^a   Boodhun, Asha ^a   Brennan, Joe S ^a   Bridgham, John A ^a   Brown, Rob C ^a   Brown, Andrew A ^a   Buermann, Dale H ^a   Bundu, Abass A ^a   Burrows, James C ^a   Carter, Nigel P ^c   Castillo, Nestor ^a   Catenazzi, Maria Chiara E ^a   Chang, Simon ^a   Neil Cooley, R ^a   Crake, Natasha R ^a   Dada, Olubunmi O ^a   Diakoumakos, Konstantinos D ^a   Dominguez Fernandez, Belen ^a   Earnshaw, David J ^a,b   Egbujor, Ugonna C ^a   Elmore, David W ^a   Etchin, Sergey S ^a   Ewan, Mark R ^a   Fedurco, Milan ^d   Fraser, Louise J ^a   Fuentes Fajardo, Karin V ^a   Scott Furey, W ^b   George, David ^a   Gietzen, Kimberley J ^a   Goddard, Colin P ^a   Golda, George S ^a   Granieri, Philip A ^a   Green, David E ^a   Gustafson, David L ^a   Hansen, Nancy F ^e   Harnish, Kevin ^a   Haudenschild, Christian D ^a   Heyer, Narinder I ^a   Hims, Matthew M ^a   Ho, Johnny T ^a   Horgan, Adrian M ^a   Hoschler, Katya ^a   Hurwitz, Steve ^a   Ivanov, Denis V ^a   Johnson, Maria Q ^a   James, Terena ^a   Huw Jones, T A ^a   Kang, Gyoung Dong ^a   Kerelska, Tzvetana H ^a   Kersey, Alan D ^a   Khrebtukova, Irina ^a   Kindwall, Alex P ^a   Kingsbury, Zoya ^a   Kokko Gonzales, Paula I ^a   Kumar, Anil ^a   Laurent, Marc A ^a   Lawley, Cynthia T ^a   Lee, Sarah E ^a   Lee, Xavier ^a   Liao, Arnold K ^a   Loch, Jennifer A ^a   Lok, Mitch ^a   Luo, Shujun ^a   Mammen, Radhika M ^a   Martin, John W ^a   McCauley, Patrick G ^a   McNitt, Paul ^a   Mehta, Parul ^a   Moon, Keith W ^a   Mullens, Joe W ^a   Newington, Taksina ^a   Ning, Zemin ^c   Ling Ng, Bee ^c   Novo, Sonia M ^a   O'Neill, Michael J ^a   Osborne, Mark A ^a,b   Osnowski, Andrew ^a   Ostadan, Omead ^a   Paraschos, Lambros L ^a   Pickering, Lea ^a   Pike, Andrew C ^a   Pike, Alger C ^a   Chris Pinkard, D ^a   Pliskin, Daniel P ^a   Podhasky, Joe ^a   Quijano, Victor J ^a   Raczy, Come ^a   Rae, Vicki H ^a   Rawlings, Stephen R ^a   Chiva Rodriguez, Ana ^a   Roe, Phyllida M ^a   Rogers, John ^a   Rogert Bacigalupo, Maria C ^a   Romanov, Nikolai ^a   Romieu, Anthony ^d   Roth, Rithy K ^a   Rourke, Natalie J ^a   Ruediger, Silke T ^a   Rusman, Eli ^a   Sanches Kuiper, Raquel M ^a   Schenker, Martin R ^a   Seoane, Josefina M ^a   Shaw, Richard J ^a   Shiver, Mitch K ^a   Short, Steven W ^a   Sizto, Ning L ^a   Sluis, Johannes P ^a   Smith, Melanie A ^a   Ernest Sohna Sohna, Jean ^a   Spence, Eric J ^a   Stevens, Kim ^a   Sutton, Neil ^a   Szajkowski, Lukasz ^a   Tregidgo, Carolyn L ^a   Turcatti, Gerardo ^d   Vandevondele, Stephanie ^a   Verhovsky, Yuli ^a   Virk, Selene M ^a   Wakelin, Suzanne ^a   Walcott, Gregory C ^a   Wang, Jingwen ^a   Worsley, Graham J ^a   Yan, Juying ^a   Yau, Ling ^a   Zuerlein, Mike ^a   Rogers, Jane ^c,g   Mullikin, James C ^e   Hurles, Matthew E ^c   McCooke, Nick J ^a,h   West, John S ^a   Oaks, Frank L ^a   Lundberg, Peter L ^a   Klenerman, David ^b   Durbin, Richard ^c   Smith, Anthony J ^a   more..

^a ILLUMINA INC   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d Manteia Predictive Medicine SA Zone Industrielle   (Switzerland)

^e NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^f Oxford Nanopore Technologies Ltd   (United Kingdom)

^g JOHN INNES CENTRE   (United Kingdom)

^h Pronota NV   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEOTIDE; GENOMIC DNA;

CHROMOSOME; DNA; GENETIC VARIATION; GENOMICS; HOMINID; IMAGE ANALYSIS; POLYMORPHISM;

ARTICLE; COST CONTROL; FLUORESCENCE ANALYSIS; GENE AMPLIFICATION; GENOME ANALYSIS; HOMOZYGOSITY; HUMAN; HUMAN GENOME; MUTATIONAL ANALYSIS; NIGERIA; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME; Y CHROMOSOME;

CHROMOSOMES, HUMAN, X; CONSENSUS SEQUENCE; GENOME, HUMAN; GENOMICS; GENOTYPE; HUMANS; MALE; NIGERIA; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 55549089660     PISSN: 00280836     EISSN: 14764679     Source Type: Journal    
DOI: 10.1038/nature07517     Document Type: Article

References (33)

1. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
2. Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
3. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
4. Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728-1732 (2005).
5. Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science 320, 106-109 (2008).
6. Lundquist, P. M. et al. Parallel confocal detection of single molecules in real time. Opt. Lett. 33, 1026-1028 (2008).
7. Wheeler, D. A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (2008).
8. Milton, J. et al. Modified nucleotides. World Intellectual Property Organization WO/2004/018497 (2004).
9. Smith, G. P. et al. Modified polymerases for improved incorporation of nucleotide analogues. World Intellectual Property Organization WO/2005/024010 (2005).
10. Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194 (1998).
11. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res.. doi:10.1101/gr.078212.108 (25 September 2008).
12. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 (2001).
13. Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet. 37, 727-732 (2005).
14. Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007).
15. Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genet. 40, 722-729 (2008).
16. Hubbard, T. et al. The Ensembl genome database project. Nucleic Acids Res. 30, 38-41 (2002).
17. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
18. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007).
19. The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
20. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
21. Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444-454 (2006).
22. Cargill, M. et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genet. 22, 231-238 (1999).
23. Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64 (2008).
24. Hillier, L. W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods 5, 183-188 (2008).
25. Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nature Genet. 39, 1522-1527 (2007).
26. Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nature Methods 4, 931-936 (2007).
27. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
28. Johnson, D. S., Mortazavi, A., Myers, R. M.&Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
29. Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
30. Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008).
31. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
32. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 585-587 (2008).
33. Fedurco, M., Romieu, A., Williams, S., Lawrence, I. & Turcatti, G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res. 34, e22 (2006).