Accurate whole human genome sequencing using reversible terminator chemistry

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

doi:10.1038/nature07517

Accurate whole human genome sequencing using reversible terminator chemistry

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

Research output: Contribution to journal › Article › peer-review

2746 Citations (Scopus)

Abstract

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30× average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

Original language	English
Pages (from-to)	53-59
Number of pages	7
Journal	Nature
Volume	456
Issue number	7218
DOIs	https://doi.org/10.1038/nature07517
Publication status	Published - 6 Nov 2008
Externally published	Yes

Bibliographical note

Funding Information:
Acknowledgements The authors acknowledge the advice of A. Williamson, T. Rink, S. Benkovic, J. Berriman, J. Todd, R. Waterston, S. Eletr, W. Jack, M. Cooper, T. Brown, C. Reece and R. Cook during this work; E. Margulies for assistance with data analysis; M. Shumway for assistance with data submission; and the contributions of the administrative and support staff at all the institutions. This research was supported in part by The Wellcome Trust (to H.L., A.Sc., K.W., N.P.C, B.N.L., J.R., M.E.H. and R.D.), the Biotechnology and Biological Sciences Research Council (BBSRC) (to S.B. and D.K.), the BBSRC Applied Genomics LINK Programme (to A.Sp. and C.L.B.) and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (to N.F.H. and J.C.M.). S. Balasubramanian and D. Klenerman are inventors and founders of Solexa Ltd.

Access to Document

10.1038/nature07517

Cite this

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., Boutell, J. M., Bryant, J., Carter, R. J., Keira Cheetham, R., Cox, A. J., Ellis, D. J., Flatbush, M. R., Gormley, N. A., Humphray, S. J., ... Smith, A. J. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456(7218), 53-59. https://doi.org/10.1038/nature07517

@article{91a3c4d38b114c8fa2aeafe61c70360c,

title = "Accurate whole human genome sequencing using reversible terminator chemistry",

abstract = "DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30× average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.",

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

note = "Funding Information: Acknowledgements The authors acknowledge the advice of A. Williamson, T. Rink, S. Benkovic, J. Berriman, J. Todd, R. Waterston, S. Eletr, W. Jack, M. Cooper, T. Brown, C. Reece and R. Cook during this work; E. Margulies for assistance with data analysis; M. Shumway for assistance with data submission; and the contributions of the administrative and support staff at all the institutions. This research was supported in part by The Wellcome Trust (to H.L., A.Sc., K.W., N.P.C, B.N.L., J.R., M.E.H. and R.D.), the Biotechnology and Biological Sciences Research Council (BBSRC) (to S.B. and D.K.), the BBSRC Applied Genomics LINK Programme (to A.Sp. and C.L.B.) and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (to N.F.H. and J.C.M.). S. Balasubramanian and D. Klenerman are inventors and founders of Solexa Ltd.",

year = "2008",

month = nov,

day = "6",

doi = "10.1038/nature07517",

language = "English",

volume = "456",

pages = "53--59",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7218",

}

Bentley, DR, Balasubramanian, S, Swerdlow, HP, Smith, GP, Milton, J, Brown, CG, Hall, KP, Evers, DJ, Barnes, CL, Bignell, HR, Boutell, JM, Bryant, J, Carter, RJ, Keira Cheetham, R, Cox, AJ, Ellis, DJ, Flatbush, MR, Gormley, NA, Humphray, SJ, Irving, LJ, Karbelashvili, MS, Kirk, SM, Li, H, Liu, X, Maisinger, KS, Murray, LJ, Obradovic, B, Ost, T, Parkinson, ML, Pratt, MR, Rasolonjatovo, IMJ, Reed, MT, Rigatti, R, Rodighiero, C, Ross, MT, Sabot, A, Sankar, SV, Scally, A, Schroth, GP, Smith, ME, Smith, VP, Spiridou, A, Torrance, PE, Tzonev, SS, Vermaas, EH, Walter, K, Wu, X, Zhang, L, Alam, MD, Anastasi, C, Aniebo, IC, Bailey, DMD, Bancarz, IR, Banerjee, S, Barbour, SG, Baybayan, PA, Benoit, VA, Benson, KF, Bevis, C, Black, PJ, Boodhun, A, Brennan, JS, Bridgham, JA, Brown, RC, Brown, AA, Buermann, DH, Bundu, AA, Burrows, JC, Carter, NP, Castillo, N, Catenazzi, MCE, Chang, S, Neil Cooley, R, Crake, NR, Dada, OO, Diakoumakos, KD, Dominguez-Fernandez, B, Earnshaw, DJ, Egbujor, UC, Elmore, DW, Etchin, SS, Ewan, MR, Fedurco, M, Fraser, LJ, Fuentes Fajardo, KV, Scott Furey, W, George, D, Gietzen, KJ, Goddard, CP, Golda, GS, Granieri, PA, Green, DE, Gustafson, DL, Hansen, NF, Harnish, K, Haudenschild, CD, Heyer, NI, Hims, MM, Ho, JT, Horgan, AM, Hoschler, K, Hurwitz, S, Ivanov, DV, Johnson, MQ, James, T, Huw Jones, TA, Kang, GD, Kerelska, TH, Kersey, AD, Khrebtukova, I, Kindwall, AP, Kingsbury, Z, Kokko-Gonzales, PI, Kumar, A, Laurent, MA, Lawley, CT, Lee, SE, Lee, X, Liao, AK, Loch, JA, Lok, M, Luo, S, Mammen, RM, Martin, JW, McCauley, PG, McNitt, P, Mehta, P, Moon, KW, Mullens, JW, Newington, T, Ning, Z, Ling Ng, B, Novo, SM, O'Neill, MJ, Osborne, MA, Osnowski, A, Ostadan, O, Paraschos, LL, Pickering, L, Pike, AC, Pike, AC, Chris Pinkard, D, Pliskin, DP, Podhasky, J, Quijano, VJ, Raczy, C, Rae, VH, Rawlings, SR, Chiva Rodriguez, A, Roe, PM, Rogers, J, Rogert Bacigalupo, MC, Romanov, N, Romieu, A, Roth, RK, Rourke, NJ, Ruediger, ST, Rusman, E, Sanches-Kuiper, RM, Schenker, MR, Seoane, JM, Shaw, RJ, Shiver, MK, Short, SW, Sizto, NL, Sluis, JP, Smith, MA, Ernest Sohna Sohna, J, Spence, EJ, Stevens, K, Sutton, N, Szajkowski, L, Tregidgo, CL, Turcatti, G, Vandevondele, S, Verhovsky, Y, Virk, SM, Wakelin, S, Walcott, GC, Wang, J, Worsley, GJ, Yan, J, Yau, L, Zuerlein, M, Rogers, J, Mullikin, JC, Hurles, ME, McCooke, NJ, West, JS, Oaks, FL, Lundberg, PL, Klenerman, D, Durbin, R & Smith, AJ 2008, 'Accurate whole human genome sequencing using reversible terminator chemistry', Nature, vol. 456, no. 7218, pp. 53-59. https://doi.org/10.1038/nature07517

TY - JOUR

T1 - Accurate whole human genome sequencing using reversible terminator chemistry

AU - Bentley, David R.

AU - Balasubramanian, Shankar

AU - Swerdlow, Harold P.

AU - Smith, Geoffrey P.

AU - Milton, John

AU - Brown, Clive G.

AU - Hall, Kevin P.

AU - Evers, Dirk J.

AU - Barnes, Colin L.

AU - Bignell, Helen R.

AU - Boutell, Jonathan M.

AU - Bryant, Jason

AU - Carter, Richard J.

AU - Keira Cheetham, R.

AU - Cox, Anthony J.

AU - Ellis, Darren J.

AU - Flatbush, Michael R.

AU - Gormley, Niall A.

AU - Humphray, Sean J.

AU - Irving, Leslie J.

AU - Karbelashvili, Mirian S.

AU - Kirk, Scott M.

AU - Li, Heng

AU - Liu, Xiaohai

AU - Maisinger, Klaus S.

AU - Murray, Lisa J.

AU - Obradovic, Bojan

AU - Ost, Tobias

AU - Parkinson, Michael L.

AU - Pratt, Mark R.

AU - Rasolonjatovo, Isabelle M.J.

AU - Reed, Mark T.

AU - Rigatti, Roberto

AU - Rodighiero, Chiara

AU - Ross, Mark T.

AU - Sabot, Andrea

AU - Sankar, Subramanian V.

AU - Scally, Aylwyn

AU - Schroth, Gary P.

AU - Smith, Mark E.

AU - Smith, Vincent P.

AU - Spiridou, Anastassia

AU - Torrance, Peta E.

AU - Tzonev, Svilen S.

AU - Vermaas, Eric H.

AU - Walter, Klaudia

AU - Wu, Xiaolin

AU - Zhang, Lu

AU - Alam, Mohammed D.

AU - Anastasi, Carole

AU - Aniebo, Ify C.

AU - Bailey, David M.D.

AU - Bancarz, Iain R.

AU - Banerjee, Saibal

AU - Barbour, Selena G.

AU - Baybayan, Primo A.

AU - Benoit, Vincent A.

AU - Benson, Kevin F.

AU - Bevis, Claire

AU - Black, Phillip J.

AU - Boodhun, Asha

AU - Brennan, Joe S.

AU - Bridgham, John A.

AU - Brown, Rob C.

AU - Brown, Andrew A.

AU - Buermann, Dale H.

AU - Bundu, Abass A.

AU - Burrows, James C.

AU - Carter, Nigel P.

AU - Castillo, Nestor

AU - Catenazzi, Maria Chiara E.

AU - Chang, Simon

AU - Neil Cooley, R.

AU - Crake, Natasha R.

AU - Dada, Olubunmi O.

AU - Diakoumakos, Konstantinos D.

AU - Dominguez-Fernandez, Belen

AU - Earnshaw, David J.

AU - Egbujor, Ugonna C.

AU - Elmore, David W.

AU - Etchin, Sergey S.

AU - Ewan, Mark R.

AU - Fedurco, Milan

AU - Fraser, Louise J.

AU - Fuentes Fajardo, Karin V.

AU - Scott Furey, W.

AU - George, David

AU - Gietzen, Kimberley J.

AU - Goddard, Colin P.

AU - Golda, George S.

AU - Granieri, Philip A.

AU - Green, David E.

AU - Gustafson, David L.

AU - Hansen, Nancy F.

AU - Harnish, Kevin

AU - Haudenschild, Christian D.

AU - Heyer, Narinder I.

AU - Hims, Matthew M.

AU - Ho, Johnny T.

AU - Horgan, Adrian M.

AU - Hoschler, Katya

AU - Hurwitz, Steve

AU - Ivanov, Denis V.

AU - Johnson, Maria Q.

AU - James, Terena

AU - Huw Jones, T. A.

AU - Kang, Gyoung Dong

AU - Kerelska, Tzvetana H.

AU - Kersey, Alan D.

AU - Khrebtukova, Irina

AU - Kindwall, Alex P.

AU - Kingsbury, Zoya

AU - Kokko-Gonzales, Paula I.

AU - Kumar, Anil

AU - Laurent, Marc A.

AU - Lawley, Cynthia T.

AU - Lee, Sarah E.

AU - Lee, Xavier

AU - Liao, Arnold K.

AU - Loch, Jennifer A.

AU - Lok, Mitch

AU - Luo, Shujun

AU - Mammen, Radhika M.

AU - Martin, John W.

AU - McCauley, Patrick G.

AU - McNitt, Paul

AU - Mehta, Parul

AU - Moon, Keith W.

AU - Mullens, Joe W.

AU - Newington, Taksina

AU - Ning, Zemin

AU - Ling Ng, Bee

AU - Novo, Sonia M.

AU - O'Neill, Michael J.

AU - Osborne, Mark A.

AU - Osnowski, Andrew

AU - Ostadan, Omead

AU - Paraschos, Lambros L.

AU - Pickering, Lea

AU - Pike, Andrew C.

AU - Pike, Alger C.

AU - Chris Pinkard, D.

AU - Pliskin, Daniel P.

AU - Podhasky, Joe

AU - Quijano, Victor J.

AU - Raczy, Come

AU - Rae, Vicki H.

AU - Rawlings, Stephen R.

AU - Chiva Rodriguez, Ana

AU - Roe, Phyllida M.

AU - Rogers, John

AU - Rogert Bacigalupo, Maria C.

AU - Romanov, Nikolai

AU - Romieu, Anthony

AU - Roth, Rithy K.

AU - Rourke, Natalie J.

AU - Ruediger, Silke T.

AU - Rusman, Eli

AU - Sanches-Kuiper, Raquel M.

AU - Schenker, Martin R.

AU - Seoane, Josefina M.

AU - Shaw, Richard J.

AU - Shiver, Mitch K.

AU - Short, Steven W.

AU - Sizto, Ning L.

AU - Sluis, Johannes P.

AU - Smith, Melanie A.

AU - Ernest Sohna Sohna, Jean

AU - Spence, Eric J.

AU - Stevens, Kim

AU - Sutton, Neil

AU - Szajkowski, Lukasz

AU - Tregidgo, Carolyn L.

AU - Turcatti, Gerardo

AU - Vandevondele, Stephanie

AU - Verhovsky, Yuli

AU - Virk, Selene M.

AU - Wakelin, Suzanne

AU - Walcott, Gregory C.

AU - Wang, Jingwen

AU - Worsley, Graham J.

AU - Yan, Juying

AU - Yau, Ling

AU - Zuerlein, Mike

AU - Rogers, Jane

AU - Mullikin, James C.

AU - Hurles, Matthew E.

AU - McCooke, Nick J.

AU - West, John S.

AU - Oaks, Frank L.

AU - Lundberg, Peter L.

AU - Klenerman, David

AU - Durbin, Richard

AU - Smith, Anthony J.

N1 - Funding Information: Acknowledgements The authors acknowledge the advice of A. Williamson, T. Rink, S. Benkovic, J. Berriman, J. Todd, R. Waterston, S. Eletr, W. Jack, M. Cooper, T. Brown, C. Reece and R. Cook during this work; E. Margulies for assistance with data analysis; M. Shumway for assistance with data submission; and the contributions of the administrative and support staff at all the institutions. This research was supported in part by The Wellcome Trust (to H.L., A.Sc., K.W., N.P.C, B.N.L., J.R., M.E.H. and R.D.), the Biotechnology and Biological Sciences Research Council (BBSRC) (to S.B. and D.K.), the BBSRC Applied Genomics LINK Programme (to A.Sp. and C.L.B.) and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (to N.F.H. and J.C.M.). S. Balasubramanian and D. Klenerman are inventors and founders of Solexa Ltd.

PY - 2008/11/6

Y1 - 2008/11/6

N2 - DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30× average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

AB - DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30× average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

UR - http://www.scopus.com/inward/record.url?scp=55549089660&partnerID=8YFLogxK

U2 - 10.1038/nature07517

DO - 10.1038/nature07517

M3 - Article

C2 - 18987734

AN - SCOPUS:55549089660

SN - 0028-0836

VL - 456

SP - 53

EP - 59

JO - Nature

JF - Nature

IS - 7218

ER -

Accurate whole human genome sequencing using reversible terminator chemistry

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