Quantitative and rapid Plasmodium falciparum malaria diagnosis and artemisinin-resistance detection using a CMOS Lab-on-Chip platform

Early and accurate diagnosis of malaria and drug-resistance is essential to effective disease management. Available rapid malaria diagnostic tests present limitations in analytical sensitivity, drug-resistance testing and/or quantification. Conversely, diagnostic methods based on nucleic acid amplification stepped forwards owing to their high sensitivity, specificity and robustness. Nevertheless, these methods commonly rely on optical measurements and complex instrumentation which limit their applicability in resource-poor, point-of-care settings. This paper reports the specific, quantitative and fully-electronic detection of Plasmodium falciparum, the predominant malaria-causing parasite worldwide, using a Lab-on-Chip platform developed in-house. Furthermore, we demonstrate on-chip detection of C580Y, the most prevalent single-nucleotide polymorphism associated to artemisinin-resistant malaria. Real-time non-optical DNA sensing is facilitated using Ion-Sensitive Field-Effect Transistors, fabricated in unmodified complementary metal-oxide-semiconductor (CMOS) technology, coupled with loop-mediated isothermal amplification. This work holds significant potential for the development of a fully portable and quantitative malaria diagnostic that can be used as a rapid point-of-care test

Linear ISFET arrays and optimisation methods for DNA detection

In the early 1970s, at a time when Moore's law was getting up to speed, Piet Bergveld initially described and subsequently pioneered the use of silicon technology in an unconventional way. By combining the field effect present in insulated gate devices and the interfacial double layer formed at the membrane of a glass electrode, he showed that the operation of a MOSFET can be modulated by the ion activity in an aqueous solution. Such a device, aptly called an Ion-Sensitive Field-Effect Transistor, is able to provide chemical inputs to electronic circuits; a concept which has experienced vast developments and a wide range of application to-date. In this context, this thesis largely revolves around the utilization of ISFETs in a practical setting. This begins by exploring readout methods to facilitate linear pH-to-output transduction, achieved by operation in current-mode and biasing the device in the velocity saturation regime. Subsequently, the first ISFET array biased in velocity saturation is shown which leverages on current-mode to demonstrate ion imaging in a scalable, simple and area-efficient topology. This implementation, benefits from short-channel effects in a 0.35um CMOS process, to demonstrate a large linear range of operation that increases the robustness against offsets across the array. In addition, to further reduce mismatch across pixels, a programmable gate has been implemented in-pixel in a scalable way. The capacitor facilitating this operation is obtained as the parasitic capacitance across two interleaved metal structures located inside the pixel stack and can be used to fine tune mismatch. This approach has been adopted in a second array shown here for ion imaging which employs current-mode operation and demonstrates integrated compensation. Thirdly, a linear voltage-mode array has been designed which is loosely based on the widely-used source follower topology. Apart from being used to compare against the performance of the current-mode implementations, the combination of these designs has facilitated the derivation of algorithms and methods used to obtained standard metrics that can be used for the benchmarking of ISFET arrays. The second part of this thesis, focuses on techniques to improve the performance at both a sensor and array level. An investigation into the electrolyte-insulator interface revealed that the two major non-idealities, namely trapped charge and drift, are correlated therefore charge modulation techniques were shown to reduce drift. Additionally, a calibration algorithm is proposed, based on iterative gradient descent, that reduces mismatch due to trapped charge in one iteration step. Lastly, ISFET arrays are demonstrated for the detection of DNA amplification and the diagnosis of infectious diseases. The protocol and methods for improving the robustness of such as platform for monitoring DNA reactions are shown with significant potential towards Point-of-Care diagnostics.Open Acces

A 128 × 128 current-mode ultra-high frame rate ISFET array with in-pixel calibration for real-time ion imaging.

An ultra-high frame rate and high resolution ion-sensing Lab-on-Chip platform using a 128x128 CMOS ISFETarray is presented. Current mode operation is employed to facilitate high-speed operation, with the ISFET sensors biased in the triode region to provide a linear response. Sensing pixels include a reset switch to allow in pixel-calibration for nonidealities such as offset, trapped charge and drift by periodically resetting the floating gate of the ISFET sensor. Current mode row-parallel signal processing is applied throughout the readout pipeline including auto-zeroing circuits for the removal of fixed pattern noise. The 128 readout signals are multiplexed to eight high-sample-rate on-chip current mode ADCs followed by an off-chip PCIe-based digital readout system on a FPGA with a latency of 0.15s. Designed in a 0.35 um CMOS process, the complete system-on-chip occupies an area of 2.6mm x 2.2mm and the whole system achieves a frame rate of 3000fps which is the highest reported in the literature. The platform is demonstrated for real-time ion-imaging through the high-speed visualisation of sodium hydroxide (NaOH) diffusion in water. Furthermore, the proposed platform is able to achieve real-time visualisation of ion dynamics on a screen at 60fps in addition to slow-motion replay in 3000fps

Discrimination of bacterial and viral infection using host-RNA signatures integrated in a lab-on-a-chip technology

ABSTRACT The unmet clinical need for accurate point-of-care (POC) diagnostic tests able to discriminate bacterial from viral infection demands a solution that can be used both within healthcare settings and in the field and that can also stem the tide of antimicrobial resistance. Our approach to solve this problem is to combine the use of Host-gene signatures with our Lab-on-a-chip (LoC) technology enabling low-cost LoC expression analysis to detect Infectious Disease.Host-gene expression signatures have been extensively study as a potential tool to be implemented in the diagnosis of infectious disease. On the other hand LoC technologies using Ion-sensitive field-effect transistor (ISFET) arrays, in conjunction with isothermal chemistries, are offering a promising alternative to conventional lab-based nucleic acid amplification instruments, owing to their portable and affordable nature. Currently, the data analysis of ISFET arrays are restricted to established methods by averaging the output of every sensor to give a single time-series. This simple approach makes unrealistic assumptions, leading to insufficient performance for applications that require accurate quantification such as RNA host transcriptomics. In order to reliably quantify host-gene expression on our LoC platform enabling the classification of bacterial and viral infection on chip, we propose a novel data-driven algorithm for extracting time-to-positive values from ISFET arrays. The algorithm proposed is based on modelling sensor drift with adaptive signal processing and clustering sensors based on their behaviour with unsupervised learning methods. Results show that the approach correctly outputs a time-to-positive for all the reactions, with a high correlation to RT-qLAMP (0.85, R2 = 0.98, p < 0.01), resulting in a classification accuracy of 100 % (CI, 95 - 100). By leveraging more advanced data processing methods for ISFET arrays, this work aims to bridge the gap between translating assays from microarray analysis (expensive lab-based discovery method) to ISFET arrays (cheap point-of-care diagnostics) providing benefits on tackling infectious disease outbreak and diagnostic testing in hard-to-reach areas of the world