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Optimization of On-Chip Polymerase Chain Reaction

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Hardware/Software Co-Design and Optimization for Cyberphysical Integration in Digital Microfluidic Biochips

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Abstract

The amount of Deoxyribonucleic acid (DNA) strands available in the biological sample is a major limitation for many genomic bioanalyses [1–4]. For example, in the study of gene dosage in tumor DNA by comparative genomic hybridization, the analysis procedure requires several hundred nanograms of DNA strands for fluorescent labeling [2]. It is difficult to obtain such a large amount of DNA strands directly from biological samples. To overcome this problem, the polymerase chain reaction (PCR) technique is used as the first step for these bioanalyses to amplify (replicate) the initial DNA strands [2, 3, 5]. Based on the categories of operations involved, the procedure of genomic analysis can be divided into three separate stages [6]. The first stage is sample preparation for PCR; the second stage is amplification of the DNA strands; after DNA amplification, the third stage includes the subsequent operations, such as mixing the droplet that contains DNA strands with other reagent droplets, detecting the concentration of intermediate product droplets, and the hybridization of the amplified DNA sequences [4].

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Author information

Authors and Affiliations

  1. Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA

    Yan Luo

  2. ECE, Duke University, Durham, NC, USA

    Krishnendu Chakrabarty

  3. CS & Info Engineering, National Cheng Kung University, Tainan City, Taiwan

    Tsung-Yi Ho

Authors
  1. Yan Luo
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  2. Krishnendu Chakrabarty
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  3. Tsung-Yi Ho
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Luo, Y., Chakrabarty, K., Ho, TY. (2015). Optimization of On-Chip Polymerase Chain Reaction. In: Hardware/Software Co-Design and Optimization for Cyberphysical Integration in Digital Microfluidic Biochips. Springer, Cham. https://doi.org/10.1007/978-3-319-09006-1_5

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  • DOI: https://doi.org/10.1007/978-3-319-09006-1_5

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