Accurate whole human genome sequencing using reversible terminator chemistry
Open accessAbstract
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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Over the last two years, Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model and non-model organisms.
“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [15]
The paper’s opening section reports successful Illumina sequencing of a human genome, and its Concluding remarks say paired reads enabled de novo assembly of some structural variants. But it describes the whole-genome work as reference-based re-sequencing, not de novo assembly of a whole genome or transcriptome; it also does not document use across model and non-model organisms. (LLM, conf=0.87)
Experimental — accuracy not yet measuredNGS is a powerful and cost-efficient tool for advanced research in many areas, including de novo transcriptome sequencing for non-model organisms.
“The newly developed high throughput sequencing technology, i.e. Next Generation Sequencing (NGS), including the Roche/454 Genome Sequencer FLX Instrument, the ABI SOLiD System, and the Illumina Genome Analyser, is a powerful and cost-efficient tool for advanced research in many areas, including re-sequencing, microRNA expression profiling, DNA methylation, especially de novo transcriptome”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [15]
The paper’s opening section reports high-throughput, low-cost sequencing and demonstrates human-genome re-sequencing; its Concluding remarks also mention applications to transcriptional activity and epigenetic modification. Our copy does not establish de novo transcriptome sequencing in non-model organisms. Page numbers were not provided for these passages. (LLM, conf=0.88)
Experimental — accuracy not yet measured
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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
- Published
- 2008-11
- Volume
- 456
- Issue
- 7218
- Pages
- 53-59
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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
- 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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