Optimization of polymerase chain reaction on a cyberphysical digital microfluidic biochip

Abstract

The amount of DNA strands available in a biological sample is a major limitation for many genomic bioanalyses. To amplify the traces of DNA strands, polymerase chain reaction (PCR) is widely used for conducting subsequent experiments. Compared to conventional instruments and analyzers, the execution of PCR on a digital microfluidic biochip (DMFB) can achieve short time-to-results, low reagent consumption, rapid heating/cooling rates, and high integration of multiple processing modules. However, the PCR biochip design methods in the literature are oblivious to the inherent randomness and complexity of bioanalyses, and they do not consider the interference among on-chip devices and the cost of droplet transportation. We present, for the first time, an integrated design method to optimize the complete PCR procedure, including (i) DNA amplification and termination control, (ii) resource placement that satisfies physical constraints needed to avoid interference, and (iii) droplet transportation needed for mixing and detection. We propose a statistical model for sensor feedback-driven (cyberphysical) on-line decision making in order to optimize and control the execution sequence for DNA amplification. Next, we present a geometric algorithm for layout design to avoid device interference and reduce the cost of droplet routing. Simulation results on three laboratory protocols demonstrate that the proposed design method results in a compact layout and produces an execution sequence for efficient control of PCR operations on a cyberphysical DMFB.

An efficient module-less synthesis approach for Digital Microfluidic Biochip

“…2b. Similarly, mixing, storage (incubation) and detection of the microdroplets are also inevitable operations for accomplishing any real-life assay on the cyberphysical chip [15]. Apart from that, external devices such as heaters, photo-detectors [12,32] capacitance sensors, impedance sensors [20] are used to offer additional functionality.…”

“…In all of the above discussed cases as well as in other cases also module-based synthesis techniques are used predominantly on DMFB platform [15,17,18,28] till date. This, in turn, increases the completion time of the bioassays, because a limited number of 'mixing-modules' are available at any point of time on the chip [4].…”

An open-source compiler and PCB synthesis tool for digital microfluidic biochips

“…2 shows the basic instruction set of a DMFB, which consists of five operations: droplet transport, splitting, merging, mixing, and storage. Additional operations can be realized by adding external devices to the device such as heaters [45], optical detectors [47,87], integrated sensors [13,57,68], etc. Fig.…”

Design and Optimization of a Cyberphysical Digital-Microfluidic Biochip for the Polymerase Chain Reaction

“…T HE AMOUNT of 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 [1].…”