¤ OpenAccess: Hybrid

This work has “Hybrid” OA status. This means it is free under an open license in a toll-access journal.

Accurate whole human genome sequencing using reversible terminator chemistry

David Bentley,Shankar Balasubramanian,Harold Swerdlow,Geoffrey Smith,John Milton,Clive Brown,Kevin P. Hall,Dirk Evers,Colin L. Barnes,Helen Bignell,Jonathan M. Boutell,Jason Bryant,Richard J. Carter,R. Keira Cheetham,Anthony J. Cox,Darren J. Ellis,Michael R. Flatbush,Niall Gormley,Sean Humphray,Leslie J. Irving,Mirian Karbelashvili,Scott Kirk,Heng Li,Xiaohai Liu,Klaus S. Maisinger,Lisa Murray,Bojan Obradović,Tobias W B Ost,Michael L. Parkinson,M. R. Pratt,Isabelle Rasolonjatovo,Mark T. Reed,Roberto Rigatti,Chiara Rodighiero,Mark T. Ross,Andrea Sabot,S. V. Sankar,Aylwyn Scally,Gary P. Schroth,Mark E. Smith,Vincent P. Smith,Anastassia Spiridou,Peta E. Torrance,Svilen Tzonev,Eric H. Vermaas,Klaudia Walter,Xiaolin Wu,Lu Zhang,Mohammed D. Alam,Carole Anastasi,Ify C. Aniebo,David M. Bailey,Iain Bancarz,Subhankar Banerjee,Selena G. Barbour,Primo Baybayan,Vincent A. Benoit,Kevin F. Benson,Claire Bevis,Phillip J. Black,Asha Boodhun,Joe S. Brennan,John A. Bridgham,Rob Brown,Andrew Brown,Dale H. Buermann,Abass A. Bundu,James C. Burrows,Nigel P. Carter,Néstor Castillo,Maria Chiara E. Catenazzi,Simon Chang,R. Neil Cooley,Natasha R. Crake,Olubunmi O. Dada,Konstantinos D. Diakoumakos,Belen Dominguez‐Fernandez,David Earnshaw,Ugonna C. Egbujor,David W. Elmore,Sergey S. Etchin,Mark Ewan,Milan Fedurco,Louise Fraser,Karin V. Fuentes Fajardo,W. Scott Furey,David George,Kimberley J. Gietzen,Colin Goddard,George S. Golda,Philip A. Granieri,David E. Green,David Gustafson,Nancy F. Hansen,Kevin Harnish,Christian Haudenschild,Narinder I. Heyer,Matthew M. Hims,Johnny T. Ho,Adrian Horgan,Katya Hoschler,Steve Hurwitz,Д. Иванов,Maria Q. Johnson,Terena James,Ted Jones,Gyoung Dong Kang,Tzvetana H. Kerelska,Alan D. Kersey,Irina Khrebtukova,Alex Kindwall,Zoya Kingsbury,Paula Kokko-Gonzales,Anil Kumar,Marc Laurent,Cindy Lawley,Sarah E. Lee,Xavier Lee,Arnold Liao,Jennifer A. Loch,Mitch Lok,Shujun Luo,Radhika M. Mammen,J. W. Martin,Patrick G. McCauley,Paul McNitt,Parul Mehta,Keith Moon,Joe W. Mullens,Taksina Newington,Zemin Ning,Bee Ling Ng,Sonia M. Novo,Michael O’Neill,Mark A. Osborne,Andrew P. 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 Roe,J. H. Rogers,M. Candelaria Rogert Bacigalupo,Н. С. Романов,Anthony Romieu,Rithy K. Roth,Natalie J. Rourke,Silke T. Ruediger,Eli Rusman,Raquel M. Sanches-Kuiper,Martin Schenker,Josefina M. Seoane,Richard J. Shaw,Mitch K. Shiver,S. 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 Tregidgo,Gerardo Turcatti,Stephanie Vandevondele,Yuli Verhovsky,Selene 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 West,Frank Oaks,Peter L. Lundberg,David Klenerman,Richard Durbin,Anthony J. Smith

DNA sequencing

Genome

Human genome

2008

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. The power of the latest massively parallel synthetic DNA sequencing technologies is demonstrated in two major collaborations that shed light on the nature of genomic variation with ethnicity. The first describes the genomic characterization of an individual from the Yoruba ethnic group of west Africa. The second reports a personal genome of a Han Chinese, the group comprising 30% of the world's population. These new resources can now be used in conjunction with the Venter, Watson and NIH reference sequences. A separate study looked at genetic ethnicity on the continental scale, based on data from 1,387 individuals from more than 30 European countries. Overall there was little genetic variation between countries, but the differences that do exist correspond closely to the geographic map. Statistical analysis of the genome data places 50% of the individuals within 310 km of their reported origin. As well as its relevance for testing genetic ancestry, this work has implications for evaluating genome-wide association studies that link genes with diseases.

Cite this:

Generate Citation

“Accurate whole human genome sequencing using reversible terminator chemistry” is a paper by David Bentley Shankar Balasubramanian Harold Swerdlow Geoffrey Smith John Milton Clive Brown Kevin P. Hall Dirk Evers Colin L. Barnes Helen Bignell Jonathan M. Boutell Jason Bryant Richard J. Carter R. Keira Cheetham Anthony J. Cox Darren J. Ellis Michael R. Flatbush Niall Gormley Sean Humphray Leslie J. Irving Mirian Karbelashvili Scott Kirk Heng Li Xiaohai Liu Klaus S. Maisinger Lisa Murray Bojan Obradović Tobias W B Ost Michael L. Parkinson M. R. Pratt Isabelle Rasolonjatovo Mark T. Reed Roberto Rigatti Chiara Rodighiero Mark T. Ross Andrea Sabot S. V. Sankar Aylwyn Scally Gary P. Schroth Mark E. Smith Vincent P. Smith Anastassia Spiridou Peta E. Torrance Svilen Tzonev Eric H. Vermaas Klaudia Walter Xiaolin Wu Lu Zhang Mohammed D. Alam Carole Anastasi Ify C. Aniebo David M. Bailey Iain Bancarz Subhankar Banerjee Selena G. Barbour Primo Baybayan Vincent A. Benoit Kevin F. Benson Claire Bevis Phillip J. Black Asha Boodhun Joe S. Brennan John A. Bridgham Rob Brown Andrew Brown Dale H. Buermann Abass A. Bundu James C. Burrows Nigel P. Carter Néstor Castillo Maria Chiara E. Catenazzi Simon Chang R. Neil Cooley Natasha R. Crake Olubunmi O. Dada Konstantinos D. Diakoumakos Belen Dominguez‐Fernandez David Earnshaw Ugonna C. Egbujor David W. Elmore Sergey S. Etchin Mark Ewan Milan Fedurco Louise Fraser Karin V. Fuentes Fajardo W. Scott Furey David George Kimberley J. Gietzen Colin Goddard George S. Golda Philip A. Granieri David E. Green David Gustafson Nancy F. Hansen Kevin Harnish Christian Haudenschild Narinder I. Heyer Matthew M. Hims Johnny T. Ho Adrian Horgan Katya Hoschler Steve Hurwitz Д. Иванов Maria Q. Johnson Terena James Ted Jones Gyoung Dong Kang Tzvetana H. Kerelska Alan D. Kersey Irina Khrebtukova Alex Kindwall Zoya Kingsbury Paula Kokko-Gonzales Anil Kumar Marc Laurent Cindy Lawley Sarah E. Lee Xavier Lee Arnold Liao Jennifer A. Loch Mitch Lok Shujun Luo Radhika M. Mammen J. W. Martin Patrick G. McCauley Paul McNitt Parul Mehta Keith Moon Joe W. Mullens Taksina Newington Zemin Ning Bee Ling Ng Sonia M. Novo Michael O’Neill Mark A. Osborne Andrew P. 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 Roe J. H. Rogers M. Candelaria Rogert Bacigalupo Н. С. Романов Anthony Romieu Rithy K. Roth Natalie J. Rourke Silke T. Ruediger Eli Rusman Raquel M. Sanches-Kuiper Martin Schenker Josefina M. Seoane Richard J. Shaw Mitch K. Shiver S. 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 Tregidgo Gerardo Turcatti Stephanie Vandevondele Yuli Verhovsky Selene 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 West Frank Oaks Peter L. Lundberg David Klenerman Richard Durbin Anthony J. Smith published in 2008. It has an Open Access status of “hybrid”. You can read and download a PDF Full Text of this paper here.