Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome

  title={Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome},
  author={Jay A. Shendure and Gregory Porreca and Nikos Basil Reppas and Xiaoxia Nina Lin and John P. McCutcheon and Abraham M. Rosenbaum and Michael D. Wang and Kun Zhang and Robi David Mitra and George M. Church},
  pages={1728 - 1732}
We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized… 

Polony DNA Sequencing

Polony DNA sequencing provides an inexpensive, accurate, high‐throughput way to resequence genomes of interest by comparison to a reference genome by identifying differences between sequences.

Single-Molecule DNA Sequencing of a Viral Genome

An amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously is reported, which demonstrates a strategy for high-throughput low-cost resequencing.

Oral bacterial genome sequencing using the high-throughput Roche Genome Sequencer FLX System.

This work provides laboratory and bioinformatic protocols that will allow the average research group to undertake high-throughput sequencing of oral bacterial genomes using the Roche Genome Sequencer FLX System which employs 454 pyrosequencing technology.

Rapid genome sequencing with short universal tiling probes

A DNA sequencing method based on hybridization of a universal panel of tiling probes that consumes only dilute solutions of the probes, resulting in reduced sequencing cost and substantially increased speed is described.

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

A genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs is described.

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A method for genomic library construction on microbeads using emulsion PCR, which has various applications such as next-generation sequencing (NGS) and the directed evolution of various functional biomolecules, is described.

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A flexible method for selective capture of sequence fragments from complex, eukaryotic genome libraries for next-generation sequencing based on hybridization to DNA microarrays is reported, which represents a flexible and cost-effective approach for large-scale resequencing of complex genomes.

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A procedure for the PFGE of intact long DNA genomes from bacteriophage particles in unfractionated, infected cell lysates of either liquid or gelled cultures is developed.

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Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.

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This chapter describes the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference.



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A method to clone and amplify DNA by performing the polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide, and techniques to make replicas of these polony slides, and high throughput sequencing protocols for this technology are described.

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    Proceedings of the National Academy of Sciences of the United States of America
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A novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 μm diameter microbeads provides an unprecedented depth of analysis permitting application of powerful statistical techniques for discovery of functional relationships among genes.

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Various novel sequencing technologies are being developed, each aspiring to reduce costs to the point at which the genomes of individual humans could be sequenced as part of routine health care.

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An approach for real-time DNA sequencing without the need for electrophoresis has been developed that relies on the detection of DNA polymerase activity by an enzymatic luminometric inorganic pyrophosphate (PPi) detection assay (ELIDA) and the possibility for parallel processing of many samples in an automated manner is discussed.

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