Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing

Hidesato Kumagai, Shinichi Utsunomiya, Shin Nakamura, Rintaro Yamamoto, Akira Harada, Toru Kaji, Makoto Hazzama, Tetsuo Ohashi, Atsushi Inami, Takashi Ikegami, Keisuke Miyamoto, Keisuke Miyamoto, Naoya Endo, Kenichi Yoshimi, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

We have described a new DNA sequencing platform based on the Sanger chemistry, in which the large-scale microfabricated channel plates and electrophoretic system result in higher-throughput DNA sequencing. Three hundred and eighty-four channels are arranged in a fan-like shape on a 25 × 47 cm glass plate, on which 384 oval sample holes are connected to each channel coupled to the opposite anode access holes. Two microfabricated plates are set on the sequencing apparatus, in which sequencing electrophoresis is conducted on one plate and the preparation process is on another plate. Each sample hole is loaded with 2.3 μL volume of sample and injected into separation channels electrokinetically. High-quality sequencing data were acquired using the pUC18 template, achieving an average read-length of 1001 bases with 99% accuracy and a throughput of 5 Mbases per day per instrument. To assess the performance in actual sequencing field, the bacterial artificial chromosome shotgun library of the Pseudorca crassidens genome was sequenced, using 1/80 of the quantity of Sanger reagent (0.1 μL). We believe that this is the first demonstration of the useful performance of DNA sequencing using monolithic microfabricated devices with walk-away operation.

Original languageEnglish
Pages (from-to)4723-4732
Number of pages10
JournalElectrophoresis
Volume29
Issue number23
DOIs
Publication statusPublished - 2008
Externally publishedYes

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DNA Sequence Analysis
Throughput
Dolphins
Bacterial Artificial Chromosomes
High-Throughput Nucleotide Sequencing
DNA
Firearms
Libraries
Glass
Electrophoresis
Electrodes
Genome
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Equipment and Supplies
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Demonstrations
Genes
Data Accuracy

Keywords

  • DNA sequencing
  • Microfabricated device
  • Sanger chemistry

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry

Cite this

Kumagai, H., Utsunomiya, S., Nakamura, S., Yamamoto, R., Harada, A., Kaji, T., ... Sakaki, Y. (2008). Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. Electrophoresis, 29(23), 4723-4732. https://doi.org/10.1002/elps.200800301

Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. / Kumagai, Hidesato; Utsunomiya, Shinichi; Nakamura, Shin; Yamamoto, Rintaro; Harada, Akira; Kaji, Toru; Hazzama, Makoto; Ohashi, Tetsuo; Inami, Atsushi; Ikegami, Takashi; Miyamoto, Keisuke; Miyamoto, Keisuke; Endo, Naoya; Yoshimi, Kenichi; Toyoda, Atsushi; Hattori, Masahira; Sakaki, Yoshiyuki.

In: Electrophoresis, Vol. 29, No. 23, 2008, p. 4723-4732.

Research output: Contribution to journalArticle

Kumagai, H, Utsunomiya, S, Nakamura, S, Yamamoto, R, Harada, A, Kaji, T, Hazzama, M, Ohashi, T, Inami, A, Ikegami, T, Miyamoto, K, Miyamoto, K, Endo, N, Yoshimi, K, Toyoda, A, Hattori, M & Sakaki, Y 2008, 'Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing', Electrophoresis, vol. 29, no. 23, pp. 4723-4732. https://doi.org/10.1002/elps.200800301
Kumagai H, Utsunomiya S, Nakamura S, Yamamoto R, Harada A, Kaji T et al. Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. Electrophoresis. 2008;29(23):4723-4732. https://doi.org/10.1002/elps.200800301
Kumagai, Hidesato ; Utsunomiya, Shinichi ; Nakamura, Shin ; Yamamoto, Rintaro ; Harada, Akira ; Kaji, Toru ; Hazzama, Makoto ; Ohashi, Tetsuo ; Inami, Atsushi ; Ikegami, Takashi ; Miyamoto, Keisuke ; Miyamoto, Keisuke ; Endo, Naoya ; Yoshimi, Kenichi ; Toyoda, Atsushi ; Hattori, Masahira ; Sakaki, Yoshiyuki. / Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. In: Electrophoresis. 2008 ; Vol. 29, No. 23. pp. 4723-4732.
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