Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, David R.; Balasubramanian, Shankar; Swerdlow, Harold P.; Smith, Geoffrey P.; Milton, John; Brown, Clive G.; Hall, Kevin P.; Evers, Dirk J.; Barnes, Colin L.; Bignell, Helen R.; Boutell, Jonathan M.; Bryant, Jason; Carter, Richard J.; Keira Cheetham, R.; Cox, Anthony J.; Ellis, Darren J.; Flatbush, Michael R.; Gormley, Niall A.; Humphray, Sean J.; Irving, Leslie J.; Karbelashvili, Mirian S.; Kirk, Scott M.; Li, Heng; Liu, Xiaohai; Maisinger, Klaus S.; Murray, Lisa J.; Obradovic, Bojan; Ost, Tobias; Parkinson, Michael L.; Pratt, Mark R.; Rasolonjatovo, Isabelle M. J.; Reed, Mark T.; Rigatti, Roberto; Rodighiero, Chiara; Ross, Mark T.; Sabot, Andrea; Sankar, Subramanian V.; Scally, Aylwyn; Schroth, Gary P.; Smith, Mark E.; Smith, Vincent P.; Spiridou, Anastassia; Torrance, Peta E.; Tzonev, Svilen S.; Vermaas, Eric H.; Walter, Klaudia; Wu, Xiaolin; Zhang, Lu; Alam, Mohammed D.; Anastasi, Carole; Aniebo, Ify C.; Bailey, David M. D.; Bancarz, Iain R.; Banerjee, Saibal; Barbour, Selena G.; Baybayan, Primo A.; Benoit, Vincent A.; Benson, Kevin F.; Bevis, Claire; Black, Phillip J.; Boodhun, Asha; Brennan, Joe S.; Bridgham, John A.; Brown, Rob C.; Brown, Andrew A.; Buermann, Dale H.; Bundu, Abass A.; Burrows, James C.; Carter, Nigel P.; Castillo, Nestor; Chiara E. Catenazzi, Maria; Chang, Simon; Neil Cooley, R.; Crake, Natasha R.; Dada, Olubunmi O.; Diakoumakos, Konstantinos D.; Dominguez-Fernandez, Belen; Earnshaw, David J.; Egbujor, Ugonna C.; Elmore, David W.; Etchin, Sergey S.; Ewan, Mark R.; Fedurco, Milan; Fraser, Louise J.; Fuentes Fajardo, Karin V.; Scott Furey, W.; George, David; Gietzen, Kimberley J.; Goddard, Colin P.; Golda, George S.; Granieri, Philip A.; Green, David E.; Gustafson, David L.; Hansen, Nancy F.; Harnish, Kevin; Haudenschild, Christian D.; Heyer, Narinder I.; Hims, Matthew M.; Ho, Johnny T.; Horgan, Adrian M.; Hoschler, Katya; Hurwitz, Steve; Ivanov, Denis V.; Johnson, Maria Q.; James, Terena; Huw Jones, T. A.; Kang, Gyoung-Dong; Kerelska, Tzvetana H.; Kersey, Alan D.; Khrebtukova, Irina; Kindwall, Alex P.; Kingsbury, Zoya; Kokko-Gonzales, Paula I.; Kumar, Anil; Laurent, Marc A.; Lawley, Cynthia T.; Lee, Sarah E.; Lee, Xavier; Liao, Arnold K.; Loch, Jennifer A.; Lok, Mitch; Luo, Shujun; Mammen, Radhika M.; Martin, John W.; McCauley, Patrick G.; McNitt, Paul; Mehta, Parul; Moon, Keith W.; Mullens, Joe W.; Newington, Taksina; Ning, Zemin; Ling Ng, Bee; Novo, Sonia M.; O'Neill, Michael J.; Osborne, Mark A.; Osnowski, Andrew; Ostadan, Omead; Paraschos, Lambros L.; Pickering, Lea; Pike, Andrew C.; Pike, Alger C.; Chris Pinkard, D.; Pliskin, Daniel P.; Podhasky, Joe; Quijano, Victor J.; Raczy, Come; Rae, Vicki H.; Rawlings, Stephen R.; Chiva Rodriguez, Ana; Roe, Phyllida M.; Rogers, John; Rogert Bacigalupo, Maria C.; Romanov, Nikolai; Romieu, Anthony; Roth, Rithy K.; Rourke, Natalie J.; Ruediger, Silke T.; Rusman, Eli; Sanches-Kuiper, Raquel M.; Schenker, Martin R.; Seoane, Josefina M.; Shaw, Richard J.; Shiver, Mitch K.; Short, Steven W.; Sizto, Ning L.; Sluis, Johannes P.; Smith, Melanie A.; Ernest Sohna Sohna, Jean; Spence, Eric J.; Stevens, Kim; Sutton, Neil; Szajkowski, Lukasz; Tregidgo, Carolyn L.; Turcatti, Gerardo; Vandevondele, Stephanie; Verhovsky, Yuli; Virk, Selene M.; Wakelin, Suzanne; Walcott, Gregory C.; Wang, Jingwen; Worsley, Graham J.; Yan, Juying; Yau, Ling; Zuerlein, Mike; Rogers, Jane; Mullikin, James C.; Hurles, Matthew E.; McCooke, Nick J.; West, John S.; Oaks, Frank L.; Lundberg, Peter L.; Klenerman, David; Durbin, Richard; Smith, Anthony J.
2008
Résumé
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 >30x 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.
Détails
Titre
Accurate whole human genome sequencing using reversible terminator chemistry
Auteur(s)
Bentley, David R. ; Balasubramanian, Shankar ; Swerdlow, Harold P. ; Smith, Geoffrey P. ; Milton, John ; Brown, Clive G. ; Hall, Kevin P. ; Evers, Dirk J. ; Barnes, Colin L. ; Bignell, Helen R. ; Boutell, Jonathan M. ; Bryant, Jason ; Carter, Richard J. ; Keira Cheetham, R. ; Cox, Anthony J. ; Ellis, Darren J. ; Flatbush, Michael R. ; Gormley, Niall A. ; Humphray, Sean J. ; Irving, Leslie J. ; Karbelashvili, Mirian S. ; Kirk, Scott M. ; Li, Heng ; Liu, Xiaohai ; Maisinger, Klaus S. ; Murray, Lisa J. ; Obradovic, Bojan ; Ost, Tobias ; Parkinson, Michael L. ; Pratt, Mark R. ; Rasolonjatovo, Isabelle M. J. ; Reed, Mark T. ; Rigatti, Roberto ; Rodighiero, Chiara ; Ross, Mark T. ; Sabot, Andrea ; Sankar, Subramanian V. ; Scally, Aylwyn ; Schroth, Gary P. ; Smith, Mark E. ; Smith, Vincent P. ; Spiridou, Anastassia ; Torrance, Peta E. ; Tzonev, Svilen S. ; Vermaas, Eric H. ; Walter, Klaudia ; Wu, Xiaolin ; Zhang, Lu ; Alam, Mohammed D. ; Anastasi, Carole ; Aniebo, Ify C. ; Bailey, David M. D. ; Bancarz, Iain R. ; Banerjee, Saibal ; Barbour, Selena G. ; Baybayan, Primo A. ; Benoit, Vincent A. ; Benson, Kevin F. ; Bevis, Claire ; Black, Phillip J. ; Boodhun, Asha ; Brennan, Joe S. ; Bridgham, John A. ; Brown, Rob C. ; Brown, Andrew A. ; Buermann, Dale H. ; Bundu, Abass A. ; Burrows, James C. ; Carter, Nigel P. ; Castillo, Nestor ; Chiara E. Catenazzi, Maria ; Chang, Simon ; Neil Cooley, R. ; Crake, Natasha R. ; Dada, Olubunmi O. ; Diakoumakos, Konstantinos D. ; Dominguez-Fernandez, Belen ; Earnshaw, David J. ; Egbujor, Ugonna C. ; Elmore, David W. ; Etchin, Sergey S. ; Ewan, Mark R. ; Fedurco, Milan ; Fraser, Louise J. ; Fuentes Fajardo, Karin V. ; Scott Furey, W. ; George, David ; Gietzen, Kimberley J. ; Goddard, Colin P. ; Golda, George S. ; Granieri, Philip A. ; Green, David E. ; Gustafson, David L. ; Hansen, Nancy F. ; Harnish, Kevin ; Haudenschild, Christian D. ; Heyer, Narinder I. ; Hims, Matthew M. ; Ho, Johnny T. ; Horgan, Adrian M. ; Hoschler, Katya ; Hurwitz, Steve ; Ivanov, Denis V. ; Johnson, Maria Q. ; James, Terena ; Huw Jones, T. A. ; Kang, Gyoung-Dong ; Kerelska, Tzvetana H. ; Kersey, Alan D. ; Khrebtukova, Irina ; Kindwall, Alex P. ; Kingsbury, Zoya ; Kokko-Gonzales, Paula I. ; Kumar, Anil ; Laurent, Marc A. ; Lawley, Cynthia T. ; Lee, Sarah E. ; Lee, Xavier ; Liao, Arnold K. ; Loch, Jennifer A. ; Lok, Mitch ; Luo, Shujun ; Mammen, Radhika M. ; Martin, John W. ; McCauley, Patrick G. ; McNitt, Paul ; Mehta, Parul ; Moon, Keith W. ; Mullens, Joe W. ; Newington, Taksina ; Ning, Zemin ; Ling Ng, Bee ; Novo, Sonia M. ; O'Neill, Michael J. ; Osborne, Mark A. ; Osnowski, Andrew ; Ostadan, Omead ; Paraschos, Lambros L. ; Pickering, Lea ; Pike, Andrew C. ; Pike, Alger C. ; Chris Pinkard, D. ; Pliskin, Daniel P. ; Podhasky, Joe ; Quijano, Victor J. ; Raczy, Come ; Rae, Vicki H. ; Rawlings, Stephen R. ; Chiva Rodriguez, Ana ; Roe, Phyllida M. ; Rogers, John ; Rogert Bacigalupo, Maria C. ; Romanov, Nikolai ; Romieu, Anthony ; Roth, Rithy K. ; Rourke, Natalie J. ; Ruediger, Silke T. ; Rusman, Eli ; Sanches-Kuiper, Raquel M. ; Schenker, Martin R. ; Seoane, Josefina M. ; Shaw, Richard J. ; Shiver, Mitch K. ; Short, Steven W. ; Sizto, Ning L. ; Sluis, Johannes P. ; Smith, Melanie A. ; Ernest Sohna Sohna, Jean ; Spence, Eric J. ; Stevens, Kim ; Sutton, Neil ; Szajkowski, Lukasz ; Tregidgo, Carolyn L. ; Turcatti, Gerardo ; Vandevondele, Stephanie ; Verhovsky, Yuli ; Virk, Selene M. ; Wakelin, Suzanne ; Walcott, Gregory C. ; Wang, Jingwen ; Worsley, Graham J. ; Yan, Juying ; Yau, Ling ; Zuerlein, Mike ; Rogers, Jane ; Mullikin, James C. ; Hurles, Matthew E. ; McCooke, Nick J. ; West, John S. ; Oaks, Frank L. ; Lundberg, Peter L. ; Klenerman, David ; Durbin, Richard ; Smith, Anthony J.
Publié dans
Nature
Volume
456
Numéro
7218
Pages
53-9
Date
2008
Laboratoires
PTCB
Le document apparaît dans
Production scientifique et compétences > SV - Faculté des sciences de la vie > PTECH - Plateformes technologiques > PTCB - Plateforme technologique de criblage biomoléculaire
Publications validées par des pairs
Travail produit à l'EPFL
Articles de journaux
Publié
Publications validées par des pairs
Travail produit à l'EPFL
Articles de journaux
Publié
Date de création de la notice
2008-11-10