A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

Kim, Hanyoup; Jebrail, Mais J.; Sinha, Anupama; Bent, Zachary; Solberg, Owen D.; Williams, Kelly P.; Langevin, Stanley A.; Renzi, Ronald F.; Vreugde, James L. Van De; Meagher, Robert J.; Schoeniger, Joseph S.; Lane, Todd W.; Branda, Steven S.; Bartsch, Michael; Patel, Kamlesh D.

doi:10.1371/journal.pone.0068988

Cited by 72 publications

(64 citation statements)

References 36 publications

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“…Moreover, the assembled device does not require external peripherals such as high voltage amplifiers, external power source, microscopic camera, image analysis and post processing stations. The modular system reported here enhances the previous designs [15][16][17]21] as it is monitored and controlled by smartphones, and it is more compact, cost effective and can be easily reproduced.…”

Section: Introductionmentioning

confidence: 83%

Ultra-Portable Smartphone Controlled Integrated Digital Microfluidic System in a 3D-Printed Modular Assembly

et al. 2015

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Portable sensors and biomedical devices are influenced by the recent advances in microfluidics technologies, compact fabrication techniques, improved detection limits and enhanced analysis capabilities. This paper reports the development of an integrated ultraportable, low-cost, and modular digital microfluidic (DMF) system and its successful integration with a smartphone used as a high-level controller and post processing station. Low power and cost effective electronic circuits are designed to generate the high voltages required for DMF operations in both open and closed configurations (from 100 to 800 V). The smartphone in turn commands a microcontroller that manipulate the voltage signals required for droplet actuation in the DMF chip and communicates wirelessly with the microcontroller via Bluetooth module. Moreover, the smartphone acts as a detection and image analysis station with an attached microscopic lens. The holder assembly is fabricated using three-dimensional (3D) printing technology to facilitate rapid prototyping. The holder features a modular design that enables convenient attachment/detachment of a variety of DMF chips to/from an electrical busbar. The electrical circuits, controller and communication system are designed to minimize the power consumption in order to run the device on small lithium ion batteries. Successful controlled DMF operations and a basic colorimetric assay using the smartphone are demonstrated.

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Section: Introductionmentioning

confidence: 83%

Ultra-Portable Smartphone Controlled Integrated Digital Microfluidic System in a 3D-Printed Modular Assembly

et al. 2015

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“…An automated solution for preparing sequencer-ready libraries from genomic DNA was demonstrated by Kim et al 7 through a microfluidic platform. By generating discrete fluid droplets containing DNA, this 'sample-in library-out' device integrates all the steps for library preparation, including dispensing of genomic DNA, fragmentation, ligation, amplification and separation 7 . NGS libraries were prepared from minute quantities of human and bacterial genomic DNA (as low as 5 ng).…”

Section: Genomicsmentioning

confidence: 99%

Microfluidics:A Boon for Biological Research

Mahesh

Vaidya²

2017

Current Science

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Microfluidics is an emerging new interdisciplinary field that deals with the manipulation of fluids at the microscale and nanoscale. Having its origins in other areas of science and technology, microfluidics is slowly beginning to make radical changes in various fields of biological sciences. The exclusivity of fluid behaviour at the microscale offers a large number of advantages in biological research such as miniaturization of assays, faster sample processing and rapid detection. This article provides a concise overview of the applications of microfluidics technology in some of the major disciplines of biological research. Furthermore, it also mentions the hurdles that microfluidics is facing and the solutions that are envisaged for the future to make it a widely available, reliable and costeffective technology.

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“…However, to facilitate high-throughput profiling, it would be important to increase the number of parallel samples to be profiled, as currently these platforms contain a maximum of assaying four samples in parallel [147, 148]. Furthermore, integration with the labor-intensive DNA library preparation procedure would be desirable; stand-alone library preparation platforms on microfluidic devices have been reported [149, 150]. For DNA methylation profiling, various commercial low-input bisulfite conversion kits have been shown to be compatible with automation.…”

Section: Main Textmentioning

confidence: 99%

Genome-wide epigenomic profiling for biomarker discovery

2016

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A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.

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A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

Cited by 72 publications

References 36 publications

Ultra-Portable Smartphone Controlled Integrated Digital Microfluidic System in a 3D-Printed Modular Assembly

Ultra-Portable Smartphone Controlled Integrated Digital Microfluidic System in a 3D-Printed Modular Assembly

Microfluidics:A Boon for Biological Research

Genome-wide epigenomic profiling for biomarker discovery

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