Next-generation DNA sequencing

Shendure, Jay; Ji, Hanlee P.

doi:10.1038/nbt1486

Cited by 3,730 publications

(2,615 citation statements)

References 96 publications

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“…After digestion, the digestion solution was pushed out for matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS analysis. Note: the bioreactor was rinsed with 25 mM DHC− NH 4 OH buffer after each enzyme digestion.…”

Section: ■ Experimental Sectionmentioning

confidence: 99%

“…Meanwhile, the buffer of 25 mM DHC− NH 4 OH, pH 9.4 was chosen for the followed enzyme digestion. By keeping the immobilizing buffer at pH 6.9, the buffer of 25 mM DHC−NH 4 OH can effectively reduce the signal of the K + adducts ( Figure 4C), but the two buffers of 25 mM Tris−HCl and 25 mM phosphate increase the signal of K + adducts ( Figure 4, parts A and B). Moreover, by adjusting the buffer of DHC− NH 4 OH from pH 6.9 to pH 9.4, the K + adducts almost disappeared ( Figure 4D).…”

Section: Maldi-tof Ms Analysismentioning

confidence: 99%

“…By keeping the immobilizing buffer at pH 6.9, the buffer of 25 mM DHC−NH 4 OH can effectively reduce the signal of the K + adducts ( Figure 4C), but the two buffers of 25 mM Tris−HCl and 25 mM phosphate increase the signal of K + adducts ( Figure 4, parts A and B). Moreover, by adjusting the buffer of DHC− NH 4 OH from pH 6.9 to pH 9.4, the K + adducts almost disappeared ( Figure 4D). These results consistently suggest the effective repression of K + adducts by DHC in combination of the SVP immobilization.…”

Section: Maldi-tof Ms Analysismentioning

confidence: 99%

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Capillary Monolithic Bioreactor of Immobilized Snake Venom Phosphodiesterase for Mass Spectrometry Based Oligodeoxynucleotide Sequencing

Zhao

Yin

et al. 2011

Anal. Chem.

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A capillary monolithic bioreactor of snake venom phosphodiesterase (SVP) was constructed to generate different single-nucleotide mass ladders of oligodeoxynucleotides for mass spectrometry (MS)-based sequencing by immobilization. The immobilization of SVP in the porous silica monolith significantly enhances its stability for prolonged and repeated applications. The constructed capillary bioreactor has the advantages of handling (sub)microliter DNA samples and having good permeability. Benefiting from its good permeability, DNA solutions can be directly injected into the sequential digestion bioreactor simply by hand pushing or a low-pressure microinjection pump. Moreover, the immobilization of SVP facilitates the elimination or repression of the metal adducts of oligodeoxynucleotides, improving the analytical performance of MS sequencing. By the application of capillary bioreactor of immobilized SVP, the sequence-specific modification of singlestranded oligodeoxynucleotide induced by a ubiquitous pollutant acrolein (Acr) was identified, demonstrating its promising applications in identification of sequence-specific damage, which may further our understanding of DNA damage caused mutagenesis.T he rapid development in DNA sequencing has greatly stimulated the research in life sciences. 1−8 Modern mass spectrometry (MS) technologies can provide an accurate mass measurement and possess an extraordinary capacity of structural elucidation; therefore, these technologies are attractive in complement to high-throughput sequencing technologies. 9−13 In addition to the uncoding of normal sequence information, sequence-specific DNA damages can also be explicitly located and characterized by employing MS sequencing. In general, the mutations, which are largely caused by DNA damage, can be mapped and the mutational hot spots in genes can be identified using a variety of DNA sequencing, but the DNA damages in the sequence context and their chemical structures are only obtained by MS-based sequencing. By identification of the sequence-specific damages, the links between the damages and the mutations can be established, which are very helpful to the understanding of the selective formation and repair of DNA damages and consequent mutagenesis and carcinogenesis. 14−19 In this work, we made an effort to construct a capillary monolithic bioreactor to generate mass ladders of oligodeoxynucleotides for MS-based sequencing and identification of sequence-specific damage through the immobilization of an exonuclease in a porous silica monolith. Previously, no attempt had been made to develop nuclease bioreactors for DNA sequencing. Snake venom phosphodiesterase (SVP) is chosen because of its unique ability as an exonuclease to sequentially cleave one nucleotide from single-stranded DNA. By taking advantage of this unique ability of SVP, the mass ladders of oligodeoxynucleotides with a single nucleotide difference can be produced, allowing for MS-based sequencing. 20−24 However, it is hard to control the sequence cleavage reac...

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Section: ■ Experimental Sectionmentioning

confidence: 99%

Section: Maldi-tof Ms Analysismentioning

confidence: 99%

Section: Maldi-tof Ms Analysismentioning

confidence: 99%

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Capillary Monolithic Bioreactor of Immobilized Snake Venom Phosphodiesterase for Mass Spectrometry Based Oligodeoxynucleotide Sequencing

Zhao

Yin

et al. 2011

Anal. Chem.

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“…A number of different platforms are available for NGS, and although they differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner (Voelkerding, et al, 2009). This massively parallel approach has reduced the base-pair cost of sequencing by several orders of magnitude (Shendure and Ji, 2008). Using this technology complete genome sequencing could in theory, be carried out in a single run, although multiple runs are currently required for sufficient coverage due to the small fragment sizes sequenced (Mardis, 2008).…”

Section: Genomicsmentioning

confidence: 99%

The integration of ‘omic’ disciplines and systems biology in cattle breeding

Berry

Meade

Mullen

et al. 2011

Animal

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Enormous progress has been made in the selection of animals, including cattle, for specific traits using traditional quantitative genetics approaches. Nevertheless, considerable variation in phenotypes remains unexplained, and therefore represents potential additional gain for animal production. In addition, the paradigm shift in new disciplines now being applied to animal breeding represents a powerful opportunity to prise open the 'black box' underlying the response to selection and fully understand the genetic architecture controlling the traits of interest. A move away from traditional approaches of animal breeding toward systems approaches using integrative analysis of data from the 'omic' disciplines represents a multitude of exciting opportunities for animal breeding going forward as well as providing alternatives for overcoming some of the limitations of traditional approaches such as the expressed phenotype being an imperfect predictor of the individual's true genetic merit, or the phenotype being only expressed in one gender or late in the lifetime of an animal. This review aims to discuss these opportunities from the perspective of their potential application and contribution to cattle breeding. Harnessing the potential of this paradigm shift also poses some new challenges for animal scientists -and they will also be discussed.

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“…The last decade has witnessed a rapid development in DNA sequencing by the introduction of next generation high-throughput DNA sequencing [1] technologies. The equipment based on that new technology produces billions of reads in a single day per machine [2].…”

Section: Introductionmentioning

confidence: 99%

Ψ-RA: a parallel sparse index for genomic read alignment

Külekçi¹,

Hon

Shah

et al. 2011

BMC Genomics

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BackgroundGenomic read alignment involves mapping (exactly or approximately) short reads from a particular individual onto a pre-sequenced reference genome of the same species. Because all individuals of the same species share the majority of their genomes, short reads alignment provides an alternative and much more efficient way to sequence the genome of a particular individual than does direct sequencing. Among many strategies proposed for this alignment process, indexing the reference genome and short read searching over the index is a dominant technique. Our goal is to design a space-efficient indexing structure with fast searching capability to catch the massive short reads produced by the next generation high-throughput DNA sequencing technology.ResultsWe concentrate on indexing DNA sequences via sparse suffix arrays (SSAs) and propose a new short read aligner named Ψ-RA (PSI-RA: parallel sparse index read aligner). The motivation in using SSAs is the ability to trade memory against time. It is possible to fine tune the space consumption of the index based on the available memory of the machine and the minimum length of the arriving pattern queries. Although SSAs have been studied before for exact matching of short reads, an elegant way of approximate matching capability was missing. We provide this by defining the rightmost mismatch criteria that prioritize the errors towards the end of the reads, where errors are more probable. Ψ-RA supports any number of mismatches in aligning reads. We give comparisons with some of the well-known short read aligners, and show that indexing a genome with SSA is a good alternative to the Burrows-Wheeler transform or seed-based solutions.ConclusionsΨ-RA is expected to serve as a valuable tool in the alignment of short reads generated by the next generation high-throughput sequencing technology. Ψ-RA is very fast in exact matching and also supports rightmost approximate matching. The SSA structure that Ψ-RA is built on naturally incorporates the modern multicore architecture and thus further speed-up can be gained. All the information, including the source code of Ψ-RA, can be downloaded at: http://www.busillis.com/o_kulekci/PSIRA.zip.

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Next-generation DNA sequencing

Cited by 3,730 publications

References 96 publications

Capillary Monolithic Bioreactor of Immobilized Snake Venom Phosphodiesterase for Mass Spectrometry Based Oligodeoxynucleotide Sequencing

Capillary Monolithic Bioreactor of Immobilized Snake Venom Phosphodiesterase for Mass Spectrometry Based Oligodeoxynucleotide Sequencing

The integration of ‘omic’ disciplines and systems biology in cattle breeding

Ψ-RA: a parallel sparse index for genomic read alignment

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