Plastic biochannel hybridization devices: a new concept for microfluidic DNA arrays

Lenigk, Ralf; Liu, Robin H.; Athavale, M. M.; Chen, Zhijian; Ganser, Dale; Yang, Jianing; Rauch, Cory B.; Liu, Yingjie; Chan, Betty; Yu, Haoran; Ray, Melissa; Marrero, R; Grodzinski, Piotr

doi:10.1016/s0003-2697(02)00391-3

Cited by 93 publications

(63 citation statements)

References 21 publications

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“…One system using chemiluminescence has a detection limit of 250 amol, but requires a 3-h hybridization period (49 ), too long for practical use in clinical diagnostics (50 ). Here we report a microfluidic system that allows detection of PCR amplicons generated from the amplification of 10 bacterial genome copies, which is at least 1000 times more sensitive than results obtained by other groups using microarray hybridization on microfluidic devices (15 ). The addition of an amplicon concentration step, as well as the use of a microfluidic device for faster PCR thermocycling, should allow detection of even lower copy numbers.…”

Section: Discussionmentioning

confidence: 97%

“…Fluid propulsion and controlled valves must be designed to allow sequential displacement of liquids into the desired channels and chambers (14 ). Microfluidic systems for nucleic acid hybridization with micropumps (15 ), pneumatic pumps (16 ), and syringe pumps (6 ) have been developed. However, these systems are complex, expensive, and require special procedures for arraying bioprobes and for detecting hybridization signals.…”

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confidence: 99%

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Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization

et al. 2005

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Background: Current hybridization protocols on microarrays are slow and need skilled personnel. Microfluidics is an emerging science that enables the processing of minute volumes of liquids to perform chemical, biochemical, or enzymatic analyzes. The merging of microfluidics and microarray technologies constitutes an elegant solution that will automate and speed up microarray hybridization. Methods: We developed a microfluidic flow cell consisting of a network of chambers and channels molded into a polydimethylsiloxane substrate. The substrate was aligned and reversibly bound to the microarray printed on a standard glass slide to form a functional microfluidic unit. The microfluidic units were placed on an engraved, disc-shaped support fixed on a rotational device. Centrifugal forces drove the sample and buffers directly onto the microarray surface. Results: This microfluidic system increased the hybridization signal by ϳ10fold compared with a passive system that made use of 10 times more sample. By means of a 15-min automated hybridization process, performed at room temperature, we demonstrated the discrimination of 4 clinically relevant Staphylococcus species that differ by as little as a single-nucleotide polymorphism. This process included hybridization, washing, rinsing, and drying steps and did not require any purification of target nucleic acids. This platform

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Section: Discussionmentioning

confidence: 97%

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confidence: 99%

Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization

et al. 2005

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“…The XT-8 instrument then activates a pneumatic pump membrane within each cartridge to propel the mixture of amplified and hybridized sample through a narrow channel across a single-file microarray of preassembled gold-plated electrodes positioned in a serpentine path and coated with single-stranded oligonucleotide capture probes specific for individual viral targets (15,33). Target DNA-signal probe complexes present in the sample hybridize to the capture probes, bringing the ferrocene label in proximity with the gold electrode.…”

Section: Specimensmentioning

confidence: 99%

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Pierce

Hodinka

2012

J Clin Microbiol

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A novel eSensor respiratory viral panel (eSensor RVP) multiplexed nucleic acid amplification test (GenMark Diagnostics, Inc., Carlsbad, CA) was compared to laboratory-developed real-time PCR assays for the detection of various respiratory viruses. A total of 250 frozen archived pediatric respiratory specimens previously characterized as either negative or positive for one or more viruses by real-time PCR were examined using the eSensor RVP. Overall agreement between the eSensor RVP and corresponding real-time PCR assays for shared analytes was 99.2% (kappa ‫؍‬ 0.96 [95% confidence interval {CI}, 0.94 to 0.98]). The combined positive percent agreement was 95.4% (95% CI, 92.5 to 97.3); the negative percent agreement was 99.7% (95% CI, 99.4 to 99.8). The mean real-time PCR threshold cycle (C T ) value for specimens with discordant results was 39.73 (95% CI, 38.03 to 41.43). Detection of coinfections and correct identification of influenza A virus subtypes were comparable between methods. Of note, the eSensor RVP rhinovirus assay was found to be more sensitive and specific than the corresponding rhinovirus real-time PCR. In contrast, the eSensor RVP adenovirus B, C, and E assays demonstrated some cross-reactivity when tested against known adenovirus serotypes representing groups A through F. The eSensor RVP is robust and relatively easy to perform, it involves a unique biosensor technology for target detection, and its multiplexed design allows for efficient and simultaneous interrogation of a single specimen for multiple viruses. Potential drawbacks include a slower turnaround time and the need to manipulate amplified product during the protocol, increasing the possibility of contamination.A cute viral upper and lower respiratory tract infections are responsible for substantial morbidity in both pediatric and adult populations worldwide. These infections can be severe and even fatal, especially in susceptible infants, older adults, patients with compromised immune systems, and individuals with underlying cardiopulmonary diseases. Rapid and accurate laboratory detection of respiratory viruses plays an important role in clinical management, guiding the appropriate prescription of antivirals, reducing the need for additional diagnostic studies and hospital procedures, and limiting the use of unnecessary antibiotics (2,4,5,6,10,19,31,35). In addition, a virologic diagnosis is instrumental to efforts focused on prevention of health care-associated infections (3,9,23,24).PCR has demonstrated superior sensitivity for the detection of respiratory viruses over the more conventional laboratory methods of virus culture and rapid direct antigen detection tests (7,12,20,22,34). Both laboratory-developed and commercial molecular assays are now available, but the overall complexity of most of these tests has made implementation challenging for many clinical laboratories (18). However, significant recent advances in microfluidics, microelectronics, and microfabrication have allowed the development of simplified molecular systems t...

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“…[30][31][32][33][34][35][36] For oligonucleotides it is found that D AB ͑oligo/water͒ Х 10 −10 m 2 / s. The diffusion coefficient of small noninteracting spherical particles in a fluid ͑dilute solution͒ is given by the Stokes-Einstein formula 9…”

Section: Diffusion Time Constants For the Single Droplet Casementioning

confidence: 99%

Fluid dynamical analysis of the distribution of ink jet printed biomolecules in microarray substrates for genotyping applications

Dijksman

Pierik

2008

Biomicrofluidics

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Oligonucleotide microarrays are tools used to analyze samples for the presence of specific DNA sequences. In the system as presented here, specific DNA sequences are first amplified by a polymerase chain reaction ͑PCR͒ during which process they are labeled with fluorophores. The amplicons are subsequently hybridized onto an oligonucleotide microarray, which in our case is a porous nylon membrane with microscopic spots. Each spot on the membrane contains oligonucleotides with a sequence complementary to part of one specific target sequence. The solution containing the amplicons flows by external agitation many times up and down through the porous substrate, thereby reducing the time delaying effect of diffusion. By excitation of the fluorophores the emitted pattern of fluorophores can be detected by a charge-coupled device camera. The recorded pattern is a characteristic of the composition of the sample. The oligonucleotide capture probes have been deposited on the substrate by using noncontact piezo ink jet printing, which is the focus of our study. The objective of this study is to understand the mechanisms that determine the distribution of the ink jet printed capture probes inside the membrane. The membrane is a porous medium: the droplets placed on the membrane penetrate in the microstructure of it. The three-dimensional ͑3D͒ distribution of the capture probes inside the membrane determines the distribution of the hybridized fluorescent PCR products inside the membrane and thus the emission of light when exposed to the light source. As the 3D distribution of the capture probes inside the membrane eventually determines the detection efficiency, this parameter can be controlled for optimization of the sensitivity of the assay. The main issues addressed here are how are the capture probes distributed inside the membrane and how does this distribution depend on the printing parameters. We will use two model systems to study the influences of different parameters: a single nozzle print head jetting large droplets at a low frequency and a multinozzle print head emitting small droplets at a high frequency. In particular, we have investigated the effects when we change from usage of the first system to the second system. Furthermore, we will go into detail how we can obtain smaller spot sizes in order to increase the spot density without having overlapping spots, leading eventually to lower manufacturing costs of microarrays. By controlling the main print parameters influencing the 3D distribution inside the porous medium, the overall batch-to-batch variations can possibly be reduced.

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Plastic biochannel hybridization devices: a new concept for microfluidic DNA arrays

Cited by 93 publications

References 21 publications

Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization

Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Fluid dynamical analysis of the distribution of ink jet printed biomolecules in microarray substrates for genotyping applications

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Plastic biochannel hybridization devices: a new concept for microfluidic DNA arrays

Cited by 93 publications

References 21 publications

Microfluidic Device for Rapid (&lt;15 min) Automated Microarray Hybridization

Microfluidic Device for Rapid (&lt;15 min) Automated Microarray Hybridization

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Fluid dynamical analysis of the distribution of ink jet printed biomolecules in microarray substrates for genotyping applications

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Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization

Microfluidic Device for Rapid (<15 min) Automated Microarray Hybridization