Accurate whole human genome sequencing using reversible terminator chemistry View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-11

AUTHORS

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

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. More... »

PAGES

53-59

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  • Journal

    TITLE

    Nature

    ISSUE

    7218

    VOLUME

    456

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  • Nucleic Acid Sequencing
  • Methods For Synchronizing Nucleic Acid Molecules
  • Methods And Systems For Associating Physical And Genetic Properties Of Biological Particles
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Polymers And Dna Copolymer Coatings
  • Microbial Strain Improvement By A Htp Genomic Engineering Platform
  • Microarray Fabrication System And Method
  • Distinguishing Methylation Levels In Complex Biological Samples
  • Methods For Profiling The T Cell Repertoire
  • Shared Neoantigens
  • Methods For Accurate Sequence Data And Modified Base Position Determination
  • Methods Of Sequencing Nucleic Acids In Mixtures And Compositions Related Thereto
  • Synthesis Of Four-Color 3′-O-Allyl Modified Photocleavable Fluorescent Nucleotides And Related Methods
  • Labelled Nucleotides
  • Modified Archaeal Family B Polymerases
  • Method For Detecting Enteritis Pathogenic Bacteria
  • Spatially Encoded Biological Assays
  • Promoters From Corynebacterium Glutamicum
  • Systems, Methods, And Apparatuses To Image A Sample For Biological Or Chemical Analysis
  • Monitoring Health And Disease Status Using Clonotype Profiles
  • Methods, Apparatuses And Systems For Analyzing Microorganism Strains From Complex Heterogeneous Communities, Predicting And Identifying Functional Relationships And Interactions Thereof, And Selecting And Synthesizing Microbial Ensembles Based Thereon
  • System And Method For Cleaning Noisy Genetic Data And Determining Chromosome Copy Number
  • Engineering Monoclonal Antibodies To Improve Stability And Production Titer
  • Direct Capture, Amplification And Sequencing Of Target Dna Using Immobilized Primers
  • Massive Parallel Method For Decoding Dna And Rna
  • Nucleic Acid Amplification
  • Amplicon Preparation And Sequencing On Solid Supports
  • Nucleic Acid Amplification
  • Methods For Simultaneous Amplification Of Target Loci
  • System And Method For Cleaning Noisy Genetic Data And Determining Chromosome Copy Number
  • Mutant Rb69 Dna Polymerase
  • Nucleotide Analogues
  • Spatially Encoded Biological Assays
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Method For Genotyping Clonotype Profiles Using Sequence Tags
  • Methods For Non-Invasive Prenatal Ploidy Calling
  • Reversible Surface Functionalization
  • Dna Sequencing With Non-Fluorescent Nucleotide Reversible Terminators And Cleavable Label Modified Nucleotide Terminators
  • Methods Of Lowering The Error Rate Of Massively Parallel Dna Sequencing Using Duplex Consensus Sequencing
  • Compositions And Method For Measuring And Calibrating Amplification Bias In Multiplexed Pcr Reactions
  • Methods Of Lowering The Error Rate Of Massively Parallel Dna Sequencing Using Duplex Consensus Sequencing
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Methods And Systems For Sequencing Long Nucleic Acids
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Methods For Nested Pcr Amplification Of Cell-Free Dna
  • Spatially Distinguished, Multiplex Nucleic Acid Analysis Of Biological Specimens
  • Sequencing Methods And Compositions For Prenatal Diagnoses
  • Nucleotide Transient Binding For Sequencing Methods
  • Methods For Generating A Glucose Permease Library And Uses Thereof
  • Device And Method For Determining The Fluorescence And The Number Of Antibodies On Exosomes.
  • Flow Cell Array And Uses Thereof
  • Adaptive Immunity Profiling And Methods For Generation Of Monoclonal Antibodies
  • Spatially Encoded Biological Assays
  • Methods And Apparatus For Sorting Data
  • Compositions And Method For Measuring And Calibrating Amplification Bias In Multiplexed Pcr Reactions
  • Nucleic Acid Amplification
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Method For Determining Copy Number Variations
  • Methods For Accurate Sequence Data And Modified Base Position Determination
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Methods And Systems For Processing Polynucleotides
  • Complex Surface-Bound Transposome Complexes
  • Sequence Tag Directed Subassembly Of Short Sequencing Reads Into Long Sequencing Reads
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Method For Immobilizing A Nucleic Acid Molecule On A Solid Support
  • 3′-Oh Unblocked, Fast Photocleavable Terminating Nucleotides And Methods For Nucleic Acid Sequencing
  • Next-Generation Sequencing Libraries
  • Detection And Quantification Of Sample Contamination In Immune Repertoire Analysis
  • Methods For Simultaneous Amplification Of Target Loci
  • Methods For Detecting Modification Resistant Nucleic Acids
  • Methods Of Lowering The Error Rate Of Massively Parallel Dna Sequencing Using Duplex Consensus Sequencing
  • Methods And Systems For Processing Polynucleotides
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Biosensors For Biological Or Chemical Analysis And Methods Of Manufacturing The Same
  • Markers For Detecting Microsatellite Instability In Cancer And Determining Synthetic Lethality With Inhibition Of The Dna Base Excision Repair Pathway
  • A Library Of Polynucleotides
  • Massive Parallel Method For Decoding Dna And Rna
  • Spatially Encoded Biological Assays
  • Avapritinib Resistance Of Kit Mutants
  • Methods For Non-Invasive Prenatal Ploidy Calling
  • Compositions And Methods For Diagnosing, Evaluating And Treating Cancer
  • Labelled Nucleotides
  • Novel Protocol For Preparing Sequencing Libraries
  • Methods For Non-Invasive Prenatal Ploidy Calling
  • Non-Invasive Prenatal Diagnosis Of Fetal Genetic Condition Using Cellular Dna And Cell Free Dna
  • Chemically Cleavable 3′-O-Allyl-Dntp-Allyl-Fluorophore Fluorescent Nucleotide Analogues And Related Methods
  • Sequencing Method For In-Situ Copying High-Flux Sequencing Template And Increasing Reading Length Thereof
  • Nucleotide Analogs
  • Identification Of Immunogenic Mutant Peptides Using Genomic, Transcriptomic And Proteomic Information
  • Detection And Measurement Of Tissue-Infiltrating Lymphocytes
  • Method For Immobilizing A Nucleic Acid Molecule On A Solid Support
  • Nucleotide Analogs
  • Reversible Modifications Of Nucleotides
  • Massive Parallel Method For Decoding Dna And Rna
  • Systems And Methods For Visualizing Structural Variation And Phasing Information
  • Analyte Sequencing With Nanopores
  • Microbial Strain Improvement By A Htp Genomic Engineering Platform
  • Methods And Systems For Determining Spatial Patterns Of Biological Targets In A Sample
  • Methods And Systems For Detecting Genetic Variants
  • Methods Of Targeted Sequencing
  • Polymers And Dna Copolymer Coatings
  • Error Detection In Sequence Tag Directed Subassemblies Of Short Sequencing Reads
  • Method For Determining A Measure Correlated To The Probability That Two Mutated Sequence Reads Derive From The Same Sequence Comprising Mutations
  • Nucleic Acid Sample Enrichment For Sequencing Applications
  • Methods For Sequencing Nucleic Acids
  • Massive Parallel Method For Decoding Dna And Rna
  • Systems And Methods For Determining The Integrity Of Test Strings With Respect To A Ground Truth String
  • Massive Parallel Method For Decoding Dna And Rna
  • Clonal Amplification Of Nucleic Acid On Solid Surface With Template Walking
  • Massive Parallel Method For Decoding Dna And Rna
  • Methods For Simultaneous Amplifications Of Target Loci
  • Massive Parallel Method For Decoding Dna And Rna
  • Spatially Encoded Biological Assays
  • Labelled Nucleotides
  • Methods And Systems For Processing Polynucleotides
  • Methods For Simultaneous Amplification Of Target Loci
  • Methods And Systems For Sequencing Nucleic Acids
  • Random Array Sequencing Of Low-Complexity Libraries
  • Methods For Selecting And Amplifying Polynucleotides
  • Entangled Mate Sequencing
  • Microarray Fabrication System And Method
  • Analyzing Copy Number Variation In The Detection Of Cancer
  • Methods And Systems For Determining Spatial Patterns Of Biological Targets In A Sample
  • Dna Sequencing
  • Nucleic Acid Amplification
  • Systems And Methods For Host Cell Improvement Utilizing Epistatic Effects
  • Flow Cell Array And Uses Thereof
  • Spatially Distinguished, Multiplex Nucleic Acid Analysis Of Biological Specimens
  • Functionalized Gel Beads
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Methods And Apparatus For Synthesizing Nucleic Acids
  • Fluidic Devices, Systems, And Methods For Encapsulating And Partitioning Reagents, And Applications Of Same
  • Functionalized Gel Beads
  • Imaging Multiple Chemical Reactions In A Flow Cell Array
  • Methods For Accurate Sequence Data And Modified Base Position Determination
  • Labelled Nucleotides
  • Microarray Fabrication System And Method
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Massive Parallel Method For Decoding Dna And Rna
  • Labelled Nucleotides
  • Microbial Compositions For Improving Milk Production In Ruminants
  • Methods For Non-Invasive Prenatal Ploidy Calling
  • Systems And Methods For Visualizing Structural Variation And Phasing Information
  • Spatially Encoded Biological Assays
  • Systems And Methods For Nucleic Acid Sequence Assembly
  • Compositions And Methods For Screening Aptamers
  • Reaction Carrier For A Microfluidic Device And Method For Determining A Nucleotide Sequence
  • Method For Generating Clonotype Profiles Using Sequence Tags
  • Methods Of Detecting Analytes
  • Monitoring Immunoglobulin Heavy Chain Evolution In B-Cell Acute Lymphoblastic Leukemia
  • Method Of Sequence Determination Using Sequence Tags
  • Sequencing And High Resolution Imaging
  • Fetal Genomic Analysis From A Maternal Biological Sample
  • Massive Parallel Method For Decoding Dna And Rna
  • Microbial Compositions And Methods Of Use For Improving Milk Production
  • Flow Cell Array And Uses Thereof
  • Prenatal Paternity Testing Using Maternal Blood, Free Floating Fetal Dna And Snp Genotyping
  • Microbial Compositions And Methods Of Use For Improving Fowl Production
  • Methods Of Lowering The Error Rate Of Massively Parallel Dna Sequencing Using Duplex Consensus Sequencing
  • Sequence Analysis Of Complex Amplicons
  • Detecting And Classifying Copy Number Variation
  • Nucleotide Cleavable Linkers And Uses Thereof
  • Patterned Flow-Cells Useful For Nucleic Acid Analysis
  • Methods For Detecting Modification Resistant Nucleic Acids
  • Detecting Mutations And Ploidy In Chromosomal Segments
  • Methods And Compositions For Stabilizing Nucleic Acid-Nucleotide-Polymerase Complexes
  • Methods For Simultaneous Amplification Of Target Loci
  • Modified Nucleosides Or Nucleotides
  • Methods And Systems For Detecting Genetic Variants
  • Methods For Simultaneous Amplification Of Target Loci
  • Detecting And Classifying Copy Number Variation
  • Spatially Encoded Biological Assays
  • Analyzing Copy Number Variation In The Detection Of Cancer
  • Methods For Detecting Modification Resistant Nucleic Acids
  • Labelled Nucleotides
  • Compositions And Methods For Single Molecular Placement On A Substrate
  • Method For Synthesis Of Polynucleotides Using A Diverse Library Of Oligonucleotides
  • Assay Instrument For Detecting Optical Signals From Samples Having A Controlled Optics Adjustment System Based On The Priority Statuses Of The Samples
  • Methods And Systems For Detecting Genetic Variants
  • Paired End Bead Amplification And High Throughput Sequencing
  • Massive Parallel Method For Decoding Dna And Rna
  • Methods And Compositions Using One-Sided Transposition
  • Methods For Simultaneous Amplification Of Target Loci
  • Assay For Exo-Site Binding Molecules
  • Methods Of Lowering The Error Rate Of Massively Parallel Dna Sequencing Using Duplex Consensus Sequencing
  • Systems And Methods To Detect Rare Mutations And Copy Number Variation
  • Dna Sequencing
  • Fabrication Of Patterned Arrays
  • Amplification Of Cell-Free Dna Using Nested Pcr
  • Methods And Compositions For Capping Nucleic Acids
  • Mutant Rb69 Dna Polymerase
  • Methods For Non-Invasive Prenatal Ploidy Calling
  • Rare Clonotypes And Uses Thereof
  • Determining Fetal Genomes For Multiple Fetus Pregnancies
  • Four-Color Dna Sequencing By Synthesis Using Cleavable Fluorescent Nucleotide Reversible Terminators
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature07517

    DOI

    http://dx.doi.org/10.1038/nature07517

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1052925719

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/18987734


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