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.
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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.