Quality control of next‐generation sequencing library through an integrative digital microfluidic platform

Thaitrong, Numrin; Kim, Hanyoup; Renzi, Ronald F.; Bartsch, Michael; Meagher, Robert J.; Patel, Kamlesh D.

doi:10.1002/elps.201200441

Cited by 26 publications

(19 citation statements)

References 29 publications

(31 reference statements)

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“…Thaitrong et al . developed an automated platform for NGS quality control to improve upon these commercially available instruments 203 . The system integrates a droplet-based digital microfluidic system, capillary-based reagent delivery unit, and quantitative capillary electrophoresis module.…”

Section: Library Construction For Ngsmentioning

confidence: 99%

Microfluidics for genome-wide studies involving next generation sequencing

Murphy

2017

Biomicrofluidics

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Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.

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Section: Library Construction For Ngsmentioning

confidence: 99%

Microfluidics for genome-wide studies involving next generation sequencing

Murphy

2017

Biomicrofluidics

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“…As described previously 14,29 , pattern the bottom plate of the DMF device with forty-six indium tin oxide (ITO) electrodes (drivers of droplet actuation) by photolithography and etching, and coat with 5 μm of Parylene-C and 50 nm of Teflon-AF. Form the top plate of the DMF device by coating an unpatterned ITO glass substrate with Teflon-AF, as above.…”

Section: Fabricate the Dmf Device And Assemble The Hub Architecturementioning

confidence: 99%

A Versatile Automated Platform for Micro-scale Cell Stimulation Experiments

Sinha

Jebrail

Kim

et al. 2013

JoVE

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Study of cells in culture (in vitro analysis) has provided important insight into complex biological systems. Conventional methods and equipment for in vitro analysis are well suited to study of large numbers of cells (≥10 5 ) in milliliter-scale volumes (≥0.1 ml). However, there are many instances in which it is necessary or desirable to scale down culture size to reduce consumption of the cells of interest and/or reagents required for their culture, stimulation, or processing. Unfortunately, conventional approaches do not support precise and reproducible manipulation of micro-scale cultures, and the microfluidics-based automated systems currently available are too complex and specialized for routine use by most laboratories. To address this problem, we have developed a simple and versatile technology platform for automated culture, stimulation, and recovery of small populations of cells (100 -2,000 cells) in micro-scale volumes (1 -20 μl). The platform consists of a set of fibronectincoated microcapillaries ("cell perfusion chambers"), within which micro-scale cultures are established, maintained, and stimulated; a digital microfluidics (DMF) device outfitted with "transfer" microcapillaries ("central hub"), which routes cells and reagents to and from the perfusion chambers; a high-precision syringe pump, which powers transport of materials between the perfusion chambers and the central hub; and an electronic interface that provides control over transport of materials, which is coordinated and automated via pre-determined scripts. As an example, we used the platform to facilitate study of transcriptional responses elicited in immune cells upon challenge with bacteria. Use of the platform enabled us to reduce consumption of cells and reagents, minimize experiment-to-experiment variability, and re-direct hands-on labor. Given the advantages that it confers, as well as its accessibility and versatility, our platform should find use in a wide variety of laboratories and applications, and prove especially useful in facilitating analysis of cells and stimuli that are available in only limited quantities. Video LinkThe video component of this article can be found at

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“…However, as those methods do not include a separation step, it is difficult to quantify the target DNA in a mixture of several DNAs. On the other hand, agarose gel electrophoresis, microchip electrophoresis, CE, and microcapillary hydrodynamic chromatography are used to analyze specific DNA [5,6]. Because of their ability to separate DNA by length (molecular weight), those techniques are used to confirm DNA of a particular length.…”

mentioning

confidence: 99%

“…Microchip electrophoresis and CE offer many benefits, including high resolution with a very small amount of sample, short analysis time, low cost, and low risk of contamination, but the peak area varies from 20 to 30 % [5]. Therefore, the development of a highly quantitative method for DNA analysis is required.…”

mentioning

confidence: 99%