BIOMEMS-768 DNA Sequencer

Ehrlich, D. J.; Adourian, Aram; Barr, Charles A.; Breslau, David; Buonocore, Scott; Burger, Robert; Carey, Loucinda; Carson, Steve; Chiou, Jeffrey T.; Dee, R.H.; Desmarais, Samantha M.; El-Difrawy, Sameh; King, Ronald C.; Koutny, Lance; Lam, Roger; Matsudaira, Paul; Mitnik-Gankin, Luba; O’Neil, Tom; Novotny, M. A.; Saber, Gil; Salas‐Solano, Oscar; Schmalzing, Dieter; Srivastava, Alok Kumar; Vázquez, Maribel

doi:10.1007/978-94-010-1015-3_6

Cited by 5 publications

(3 citation statements)

References 3 publications

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“…We refer this assembly as a microfabricated hybrid device. Compared to the large glass plates [9], the microfabricated hybrid devices provide significantly improved fabrication yields at low cost, albeit both devices are used to extend the straight separation channel lengths on chips. There are two main reasons for this improvement: (i) injector arrays are normally fabricated on 10 or 15 cm diameter wafers and the fabrication yield of these chips is normally high (about 90%), and (ii) parallel structures of injector arrays can be made in one chip.…”

Section: Resultsmentioning

confidence: 99%

“…Large plates (53-58 cm by 7.6-13 cm) have been used [5,6] to attack this problem, but fabrication of these plates requires special equipment and facilities. Recently, a 384-channel device with a cross-channel injection scheme was fabricated on a large plate [7][8][9] with effective channel lengths of , 40 cm. One of the main goals of this approach was to replace the separation capillaries in conventional high-throughput sequencing machines with a single multiple-channel chip.…”

Section: Introductionmentioning

confidence: 99%

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Sequencing of real‐world samples using a microfabricated hybrid device having unconstrained straight separation channels

2003

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We describe a microfabricated hybrid device that consists of a microfabricated chip containing multiple twin-T injectors attached to an array of capillaries that serve as the separation channels. A new fabrication process was employed to create two differently sized round channels in a chip. Twin-T injectors were formed by the smaller round channels that match the bore of the separation capillaries and separation capillaries were incorporated to the injectors through the larger round channels that match the outer diameter of the capillaries. This allows for a minimum dead volume and provides a robust chip/capillary interface. This hybrid design takes full advantage, such as sample stacking and purification and uniform signal intensity profile, of the unique chip injection scheme for DNA sequencing while employing long straight capillaries for the separations. In essence, the separation channel length is optimized for both speed and resolution since it is unconstrained by chip size. To demonstrate the reliability and practicality of this hybrid device, we sequenced over 1000 real-world samples from Human Chromosome 5 and Ciona intestinalis, prepared at Joint Genome Institute. We achieved average Phred20 read of 675 bases in about 70 min with a success rate of 91%. For the similar type of samples on MegaBACE 1000, the average Phred20 read is about 550-600 bases in 120 min separation time with a success rate of about 80-90%.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sequencing of real‐world samples using a microfabricated hybrid device having unconstrained straight separation channels

2003

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“…Because no cross nor twin-T injectors were used in these devices, advantages from a twin-T injector could not be realized. Recently, a 384-channel device with cross injectors were fabricated on a large plate [8,9]. Separation distances of these channels were about 40 cm.…”

Section: Introductionmentioning

confidence: 99%

A microfabricated hybrid device for DNA sequencing

Liu

2003

Electrophoresis

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We have created a hybrid device of a microfabricated round-channel twin-T injector incorporated with a separation capillary in order to extend the straight separation distance for high speed and long readlength DNA sequencing. Semicircular grooves on glass wafers are obtained using a photomask with a narrow line-width and a standard isotropic photolithographic etching process. Round channels are made when two etched wafers are face-to-face aligned and bonded. A two-mask fabrication process has been developed to make channels of two different diameters. The twin-T injector is formed by the smaller channels whose diameter matches the bore of the separation capillary, and the "usual" separation channel, now called the connection channel, is formed by the larger ones whose diameter matches the outer diameter of the separation capillary. The separation capillary is inserted through the connection channel all the way to the twin-T injector to allow the capillary bore flush with the twin-T injector channels. The total dead-volume of the connection is estimated to be approximately 5 pL. To demonstrate the efficiency of this hybrid device, we have performed four-color DNA sequencing on it. Using a 200 microm twin-T injector coupled with a separation capillary of 20 cm effective separation distance, we have obtained readlengths of 800 plus bases at an accuracy of 98.5% in 56 min, compared to about 650 bases in 100 min on a conventional 40 cm long capillary sequencing machine under similar conditions. At an increased separation field strength and using a diluted sieving matrix, the separation time has been reduced to 20 min with a readlength of 700 bases at 98.5% base-calling accuracy.

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Applications of capillary electrophoresis on microchip

Dolnı́k¹,

Liu

2005

J of Separation Science

107

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CE on microchip is an emerging separation technique that has attracted wide attention and gained considerable popularity. Because of miniaturization of the separation format, CE on chip typically offers shorter analysis time and lower reagent consumption with potential development of portable analytical instrumentation. This review with 143 references is focused on proteins and peptides analysis, DNA separation including fragment sizing, genotyping, mutation detection and sequencing, and also the analysis of low-molecular-weight compounds, namely explosive residues and warfare agents, pharmaceuticals and drugs of abuse, and various small molecules in body fluids.

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BIOMEMS-768 DNA Sequencer

Cited by 5 publications

References 3 publications

Sequencing of real‐world samples using a microfabricated hybrid device having unconstrained straight separation channels

Sequencing of real‐world samples using a microfabricated hybrid device having unconstrained straight separation channels

A microfabricated hybrid device for DNA sequencing

Applications of capillary electrophoresis on microchip

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