Progress toward the application of molecular force spectroscopy to <scp>DNA</scp> sequencing

Cheng, Perry; Oliver, Piercen M.; Barrett, Michael J.; Vezenov, Dmitri V.

doi:10.1002/elps.201200351

Cited by 6 publications

(4 citation statements)

References 46 publications

(79 reference statements)

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“…In these approaches, the error-prone amplification step is eliminated during sample preparation. This category consists of a series of techniques, including nanopore sequencing (Branton et al, 2008 ), stepwise single-molecule sequencing by synthesis (SBS) (Harris et al, 2008 ), single-molecule real-time SBS (Eid et al, 2009 ), single-molecule motion sequencing (Greenleaf and Block, 2006 ; Ding et al, 2012 ), electron microscopy (Bell et al, 2012 ), molecular force spectrometry (Cheng et al, 2012 ), sequencing by tip-enhanced Raman scattering (Bailo and Deckert, 2008 ; Treffer et al, 2011 ), etc.…”

Section: Introductionmentioning

confidence: 99%

The evolution of nanopore sequencing

2015

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The “$1000 Genome” project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the “$1000 Genome” while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

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Section: Introductionmentioning

confidence: 99%

The evolution of nanopore sequencing

2015

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“…Currently, the most commonly applied base calling method is Phred base-calling, which provides high sensitivity and a low error rate when compared to other methods. 30 Both CMOS and SMRT have the potential to become essential parts of the third-generation sequencing technology, which includes nanopore sequencing, 31 molecular force spectrometry, 32 single-molecule motion sequencing, 33 electron microscopy, 34 sequencing by tip-enhanced Raman scattering, 35 and others.…”

Section: Primary Stage: Template Preparation Sequencing and Imagingmentioning

confidence: 99%

An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

Batcha

Grüning

et al. 2015

Cancer Inform

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Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGSbased software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.

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“…The mechanism to manipulate micro-objects can generally be categorized as electrophoresis (DEP) [3], dielectrophoresis [4], optical force [5], magnetic force [6], and hydrodynamic force [7]. Cheng et al [8] employed DEP to pattern molecules and DNAs for force spectroscopy. Messner et al [9] applied a stencil to pattern cancerous cells in an array for analysis.…”

Section: Introductionmentioning

confidence: 99%

Microchip System for Patterning Cells on Different Substrates via Negative Dielectrophoresis

Huang

Lai

et al. 2019

IEEE Trans. Biomed. Circuits Syst.

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Seeding cells on a planar substrate is the first step to construct artificial tissues in vitro. Cells should be organized into a pattern similar to native tissues and cultured on a favorable substrate to facilitate desirable tissue ingrowth. In this study, a microchip system is designed and fabricated to form cells into a specific pattern on different substrates. The system consists of a microchip with a dot-electrode array for cell trapping and patterning and two motorized platforms for providing relative motions between the microchip and the substrate. AC voltage is supplied to the selected electrodes by using a programmable micro control unit to control relays connected to the dot-electrodes. Nonuniform electric fields for cell manipulation are formed via negative dielectrophoresis (n-DEP). Experiments were conducted to create different patterns by using yeast cells. The effects of different experimental parameters and material properties on the patterning efficiency were evaluated and analyzed. Mechanisms to remove abundant cells surrounding the constructed patterns were also examined. Results show that the microchip system could successfully create cell patterns on different substrates. The use of calcium chloride (CaCl2) enhanced the cell adhesiveness on the substrate. The proposed n-DEP patterning technique offers a new method for constructing artificial tissues with high flexibility on cell patterning and selecting substrate to suit application needs.

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Progress toward the application of molecular force spectroscopy to DNA sequencing

Cited by 6 publications

References 46 publications

The evolution of nanopore sequencing

The evolution of nanopore sequencing

An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

Microchip System for Patterning Cells on Different Substrates via Negative Dielectrophoresis

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