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Genome sequencing in microfabricated high-density picolitre reactors View Full Text

Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2005-09

AUTHORS

Marcel Margulies, Michael Egholm, William E. Altman, Said Attiya, Joel S. Bader, Lisa A. Bemben, Jan Berka, Michael S. Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B. Dewell, Lei Du, Joseph M. Fierro, Xavier V. Gomes, Brian C. Godwin, Wen He, Scott Helgesen, Chun He Ho, Gerard P. Irzyk, Szilveszter C. Jando, Maria L. I. Alenquer, Thomas P. Jarvie, Kshama B. Jirage, Jong-Bum Kim, James R. Knight, Janna R. Lanza, John H. Leamon, Steven M. Lefkowitz, Ming Lei, Jing Li, Kenton L. Lohman, Hong Lu, Vinod B. Makhijani, Keith E. McDade, Michael P. McKenna, Eugene W. Myers, Elizabeth Nickerson, John R. Nobile, Ramona Plant, Bernard P. Puc, Michael T. Ronan, George T. Roth, Gary J. Sarkis, Jan Fredrik Simons, John W. Simpson, Maithreyan Srinivasan, Karrie R. Tartaro, Alexander Tomasz, Kari A. Vogt, Greg A. Volkmer, Shally H. Wang, Yong Wang, Michael P. Weiner, Pengguang Yu, Richard F. Begley, Jonathan M. Rothberg

ABSTRACT

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. More... »

PAGES

376

References to SciGraph publications

  • 1998-07. Man-made cell-like compartments for molecular evolution in NATURE BIOTECHNOLOGY

    • Journal

    TITLE

    Nature

    ISSUE

    7057

    VOLUME

    437

    Subjects

  • FOR: Genetics
  • FOR: Biological Sciences
  • MESH: Electrophoresis, Capillary
  • MESH: Emulsions
  • MESH: Fiber Optic Technology
  • MESH: Genome, Bacterial
  • MESH: Genomics
  • MESH: Microchemistry
  • MESH: Mycoplasma Genitalium
  • MESH: Polymerase Chain Reaction
  • MESH: Reproducibility Of Results
  • MESH: Sensitivity And Specificity
  • MESH: Sequence Analysis, Dna
  • MESH: Time Factors

    • Author Affiliations

  • Roche (United States)
  • University of California, Berkeley
  • Rockefeller University
  • Rothberg Institute For Childhood Diseases

    • From Grant

  • 454 Life Sciences Massively Parallel System For Dna Sequencing Technology

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  • Detection Of Nucleic Acid Reactions On Bead Arrays
  • Mapping Of Genomic Interactions
  • Microfluidic Devices And Methods Of Use In The Formation And Control Of Nanoreactors
  • Device For Nucleic Acid Analysis And Nucleic Acid Analyzer
  • High Throughput Screening Of Populations Carrying Naturally Occurring Mutations
  • Device And Method For Producing A Replicate Or Derivative From An Array Of Molecules, And Applications Thereof
  • Compositions And Methods For Molecular Labeling
  • Massively Parallel Single Cell Analysis
  • Use Of Galerina Marginata Genes And Proteins For Peptide Production
  • Methods And Compositions For Incorporating Nucleotides
  • Quantification Of A Minority Nucleic Acid Species
  • One-Transistor Pixel Array
  • Microfluidic Devices And Methods For Gene Synthesis
  • Systems And Methods For Use Of Known Alleles In Read Mapping
  • Chemically-Sensitive Sample And Hold Sensors
  • Methods For Operating Chemically Sensitive Sensors With Sample And Hold Capacitors
  • Preparation Enhancements And Methods Of Use For Maldi Mass Spectrometry
  • Methods And Systems For Aligning Sequences
  • Method For Analyzing Nucleic Acid Derived From Single Cell
  • Methods And Apparatus For Measuring Analytes Using Large Scale Fet Arrays
  • Methods And Apparatus For Measuring Analytes Using Large Scale Fet Arrays
  • Electron Beam Sculpting Of Tunneling Junction For Nanopore Dna Sequencing
  • Methods Of Selecting Biologic-Producing Cell Lines By Next Generation Sequencing
  • Digital Analyte Analysis
  • Data Processing System And Methods
  • Novel Macrocyles And Methods For Their Production
  • Method For Identifying The Sequence Of One Or More Variant Nucleotides In A Nucleic Acid Molecule
  • Methods For Accurate Sequence Data And Modified Base Position Determination
  • Paired End Bead Amplification And High Throughput Sequencing
  • Method And System For Delta Double Sampling
  • Integrated Sample Preparation Systems And Stabilized Enzyme Mixtures
  • Methods For Estimating Genome-Wide Copy Number Variations
  • Detecting And Classifying Copy Number Variation
  • High Throughput Genome Sequencing On Dna Arrays
  • Chemical Sensors With Consistent Sensor Surface Areas
  • Methods To Diagnose And Immunize Against The Virus Causing Human Merkel Cell Carcinoma
  • Biological Analysis Arrangement And Approach Therefor
  • System And Method For Producing Functionally Distinct Nucleic Acid Library Ends Through Use Of Deoxyinosine
  • Methods And Apparatus For Measuring Analytes
  • Detection And Quantification Of Biomolecules Using Mass Spectrometry
  • Chemical Sensor With Sidewall Spacer Sensor Surface
  • Method For Determining Fetal Chromosomal Abnormality
  • Methods And Solutions For Inhibiting Undesired Cleaving Of Labels
  • Massive Parallel Method For Decoding Dna And Rna
  • Oligomer Sequences Mapping
  • Four-Color Dna Sequencing By Synthesis Using Cleavable Fluorescent Nucleotide Reversible Terminators
  • Methods And Apparatus For Measuring Analytes Using Large Scale Fet Arrays
  • Composition, Method And Kit For Detecting Bacteria By Means Of Sequencing
  • Chemical Sensor With Protruded Sensor Surface
  • Solid Support For High-Throughput Nucleic Acid Analysis
  • Nanogap Transducers With Selective Surface Immobilization Sites
  • Methods For Forming Mixed Droplets
  • Piscine Reovirus Diagnostic Compositions
  • Nucleic Acid Analysis Using Sequence Tokens
  • Method For Identifying The Sequence Of One Or More Variant Nucleotides In A Nucleic Acid Molecule
  • Methods And Apparatus For Measuring Analytes Using Large Scale Fet Arrays
  • Models For Analyzing Data From Sequencing-By-Synthesis Operations
  • Programmable Oligonucleotide Synthesis
  • Massive Parallel Method For Decoding Dna And Rna
  • Assay Methods Using Nicking Endonucleases
  • One-Transistor Pixel Array
  • Electron Beam Sculpting Of Tunneling Junction For Nanopore Dna Sequencing
  • Active Chemically-Sensitive Sensors With Reset Switch
  • Manufacturable Sub-3 Nanometer Palladium Gap Devices For Fixed Electrode Tunneling Recognition
  • Massively Parallel Single Cell Analysis
  • Method For Sequencing A Polynucleotide Template
  • Methods, Compounds And Systems For Detecting A Microorganism In A Sample
  • Method Of Performing One-Step, Single Cell Rt-Pcr
  • Dna Sequencing Using Multiple Metal Layer Structure With Different Organic Coatings Forming Different Transient Bondings To Dna
  • Amplification Primers And Methods
  • Massive Parallel Method For Decoding Dna And Rna
  • Method For Generating Clonotype Profiles Using Sequence Tags
  • Variant Database
  • Nucleic Acid Interaction Analysis
  • Massively Parallel Single Cell Analysis
  • Analysis Methods
  • Efficient Arrays Of Amplified Polynucleotides
  • Second Harmonic Imaging Nanoprobes And Techniques For Use Thereof
  • Method And System For Delta Double Sampling

    • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature03959

    DOI

    http://dx.doi.org/10.1038/nature03959

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1021574562

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16056220

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