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Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry

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      Most cited references 37

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      Genome sequencing in microfabricated high-density picolitre reactors.

      The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.
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        High-resolution profiling of histone methylations in the human genome.

        Histone modifications are implicated in influencing gene expression. We have generated high-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology. Typical patterns of histone methylations exhibited at promoters, insulators, enhancers, and transcribed regions are identified. The monomethylations of H3K27, H3K9, H4K20, H3K79, and H2BK5 are all linked to gene activation, whereas trimethylations of H3K27, H3K9, and H3K79 are linked to repression. H2A.Z associates with functional regulatory elements, and CTCF marks boundaries of histone methylation domains. Chromosome banding patterns are correlated with unique patterns of histone modifications. Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations. Our data provide new insights into the function of histone methylation and chromatin organization in genome function.
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          Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

          We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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            Author and article information

            Affiliations
            [1 ] Illumina Cambridge Ltd., (Formerly Solexa Ltd) Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex. CB10 1XL, UK
            [2 ] Department of Chemistry, University of Cambridge, The University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
            [3 ] Illumina Hayward, (Formerly Solexa Inc) 23851 Industrial Bvld, Hayward, CA 94343, USA
            [4 ] The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
            [5 ] Manteia Predictive Medicine S.A. Zone Industrielle, Coinsins, CH-1267, Switzerland
            [6 ] Illumina Inc. ,Corporate Headquarters, 9883 Towne Centre Drive, San Diego, CA 92121, USA
            [7 ] National Human Genome Research Institute, National Institutes of Health, 41 Center Drive, MSC 2132, 9000 Rockville Pike, Bethesda, MD 20892-2132, USA
            Author notes
            [*]

            Inventors and founders of Solexa Ltd

            [†]

            Present addresses

            The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

            [§]

            Oxford Nanopore Technologies, Begbroke Science Park, Sandy Lane, Kidlington. OX5 1PF

            [‡]

            Pronota, NV, VIB Bio-Incubator, Technologiepark 4, B-9052 Zwijnaarde / Ghent, Belgium

            All authors at Illumina (see affiliations) are employees of Illumina Inc., a public company that develops and markets systems for genetic analysis.

            Correspondence and requests for materials should be addressed to David.R. Bentley ( dbentley@ 123456illumina.com ).
            Journal
            0410462
            6011
            Nature
            Nature
            Nature
            0028-0836
            1476-4687
            27 October 2008
            6 November 2008
            08 December 2012
            : 456
            : 7218
            : 53-59
            18987734
            2581791
            10.1038/nature07517
            EMS2586
            Funding
            Funded by: Biotechnology and Biological Sciences Research Council :
            Award ID: MOL04534 || BB_
            Funded by: Biotechnology and Biological Sciences Research Council :
            Award ID: B05823 || BB_
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