Cited by 3,684Genomics and Phylogenetic StudiesGenomics and Rare DiseasesGenomic variations and chromosomal abnormalities

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Accurate whole human genome sequencing using reversible terminator chemistry

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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·Nature

DOI 10.1038/nature07517PMC PMC2581791

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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. 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.

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Authors: 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., Irving, L. J., Karbelashvili, M. S., Kirk, S. M., Li, H., Liu, X., Maisinger, K. S., Murray, L. J., Obradovic, B., Ost, T., Parkinson, M. L., Pratt, M. R., Rasolonjatovo, I. M. J., Reed, M. T., Rigatti, R., Rodighiero, C., Ross, M. T., Sabot, A., Sankar, S. V., Scally, A., Schroth, G. P., Smith, M. E., Smith, V. P., Spiridou, A., Torrance, P. E., Tzonev, S. S., Vermaas, E. H., Walter, K., Wu, X., Zhang, L., Alam, M. D., Anastasi, C., Aniebo, I. C., Bailey, D. M. D., Bancarz, I. R., Banerjee, S., Barbour, S. G., Baybayan, P. A., Benoit, V. A., Benson, K. F., Bevis, C., Black, P. J., Boodhun, A., Brennan, J. S., Bridgham, J. A., Brown, R. C., Brown, A. A., Buermann, D. H., Bundu, A. A., Burrows, J. C., Carter, N. P., Castillo, N., Chiara E. Catenazzi, M., Chang, S., Neil Cooley, R., Crake, N. R., Dada, O. O., Diakoumakos, K. D., Dominguez-Fernandez, B., Earnshaw, D. J., Egbujor, U. C., Elmore, D. W., Etchin, S. S., Ewan, M. R., Fedurco, M., Fraser, L. J., Fuentes Fajardo, K. V., Scott Furey, W., George, D., Gietzen, K. J., Goddard, C. P., Golda, G. S., Granieri, P. A., Green, D. E., Gustafson, D. L., Hansen, N. F., Harnish, K., Haudenschild, C. D., Heyer, N. I., Hims, M. M., Ho, J. T., Horgan, A. M., Hoschler, K., Hurwitz, S., Ivanov, D. V., Johnson, M. Q., James, T., Huw Jones, T. A., Kang, G.-D., Kerelska, T. H., Kersey, A. D., Khrebtukova, I., Kindwall, A. P., Kingsbury, Z., Kokko-Gonzales, P. I., Kumar, A., Laurent, M. A., Lawley, C. T., Lee, S. E., Lee, X., Liao, A. K., Loch, J. A., Lok, M., Luo, S., Mammen, R. M., Martin, J. W., McCauley, P. G., McNitt, P., Mehta, P., Moon, K. W., Mullens, J. W., Newington, T., Ning, Z., Ling Ng, B., Novo, S. M., O’Neill, M. J., Osborne, M. A., Osnowski, A., Ostadan, O., Paraschos, L. L., Pickering, L., Pike, A. C., Pike, A. C., Chris Pinkard, D., Pliskin, D. P., Podhasky, J., Quijano, V. J., Raczy, C., Rae, V. H., Rawlings, S. R., Chiva Rodriguez, A., Roe, P. M., Rogers, J., Rogert Bacigalupo, M. C., Romanov, N., Romieu, A., Roth, R. K., Rourke, N. J., Ruediger, S. T., Rusman, E., Sanches-Kuiper, R. M., Schenker, M. R., Seoane, J. M., Shaw, R. J., Shiver, M. K., Short, S. W., Sizto, N. L., Sluis, J. P., Smith, M. A., Ernest Sohna Sohna, J., Spence, E. J., Stevens, K., Sutton, N., Szajkowski, L., Tregidgo, C. L., Turcatti, G., vandeVondele, S., Verhovsky, Y., Virk, S. M., Wakelin, S., Walcott, G. C., Wang, J., Worsley, G. J., Yan, J., Yau, L., Zuerlein, M., Rogers, J., Mullikin, J. C., Hurles, M. E., McCooke, N. J., West, J. S., Oaks, F. L., Lundberg, P. L., Klenerman, D., Durbin, R., & Smith, A. J.
Affiliations: Illumina (United Kingdom) (GB)
University of Cambridge (GB)
Wellcome Sanger Institute (GB)
Illumina (United States) (US)
National Institutes of Health (US)
Corresponding author: Bentley, David R.
ORCID: Balasubramanian, Shankar
Swerdlow, Harold P.
Hall, Kevin P.
Humphray, Sean J.
Li, Heng
Liu, Xiaohai
Ross, Mark T.
Scally, Aylwyn
Schroth, Gary P.
Spiridou, Anastassia
Walter, Klaudia
Wu, Xiaolin
Bailey, David M. D.
Brown, Andrew A.
Fraser, Louise J.
Gustafson, David L.
Hansen, Nancy F.
Horgan, Adrian M.
Ivanov, Denis V.
James, Terena
Kang, Gyoung-Dong
Kumar, Anil
Lee, Sarah E.
Luo, Shujun
Martin, John W.
Mehta, Parul
Ning, Zemin
O’Neill, Michael J.
Rogers, John
Romieu, Anthony
Sanches-Kuiper, Raquel M.
Shaw, Richard J.
Smith, Melanie A.
Turcatti, Gerardo
Wang, Jingwen
Yan, Juying
Mullikin, James C.
Hurles, Matthew E.
Klenerman, David
Durbin, Richard
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2008-11
Volume: 456
Issue: 7218
Pages: 53-59
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature07517
PMC: PMC2581791
OpenAlex: W2012016911
Cited by: 3,684
References: 36
Citations by year: 2026: 95 · 2025: 110 · 2024: 150 · 2023: 122 · 2022: 127 · 2021: 165 · 2020: 175 · 2019: 157 · 2018: 183 · 2017: 194 · 2016: 233 · 2015: 235 · 2014: 260 · 2013: 307 · 2012: 330
FWCI: 115.18
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc-sa
creativecommons.org/licenses/by-nc-sa/3.0/ (tdm)
Locations: Nature (publishedVersion, cc-by-nc-sa)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
DMU Open Research Archive (De Montfort University) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
Funders: Wellcome Trust
National Institutes of Health
Directorate for Biological Sciences
Goddard Space Flight Center
Biotechnology and Biological Sciences Research Council (B05823, MOL04534)
National Human Genome Research Institute (Z01HG200330)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords: whole-genome resequencing, single-molecule DNA sequencing, single nucleotide polymorphisms, structural variants, genetic ancestry, population genetic variation, X chromosome, consensus sequence, genome-wide association study
MeSH terms: Genotype, Humans, Male, Nigeria, Sensitivity and Specificity, Genome, Human, Consensus Sequence, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics, Chromosomes, Human, X

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