Metabolomic sensing system for personalised medicine using an integrated CMOS sensor array technology

Cheah, Boon Chong (2017) Metabolomic sensing system for personalised medicine using an integrated CMOS sensor array technology. PhD thesis, University of Glasgow.

Abstract

Precision healthcare, also known as personalised medicine, is based on our understanding of the fundamental building blocks of biological systems, with the ultimate aim to clinically identify the best therapeutic strategy for each individual. Genomics and sequencing technologies have brought this to the foreground by enabling an individual’s entire genome to be mapped for less than a thousand dollar in just one day. Recently, metabolomics, the quantitative measurement of small molecules, has emerged as a field to understand an individual’s molecular profile in terms of both genetics and environmental factors. This is crucial because a genome could only indicate an individual’s susceptibility to a particular disease, whereas a metabolome provides an immediate measurement of body function, enabling a means of diagnosis. However, the current approach of measurements depends on large-scale and expensive equipment such as mass spectroscopy and NMR instrumentation, which does not offer a single analytical platform to detect the entire metabolome.
This thesis describes the development of an integrated CMOS sensor array technology as a single platform to quantify different metabolites using specific enzymes. The key stages in the work were: to construct instrumentation systems to perform enzyme assays on the CMOS sensor array; to establish techniques to package the CMOS sensor array for an aqueous environment; to implement and develop a room temperature Ta2O5 sputtering process on CMOS sensor array for hydrogen ion detection; to collaborate with a chemist and investigate an inorganic layer on top of the CMOS ISFET sensor to show an improvement of sensitivity towards potassium ion; to test several different enzyme assays electrochemically and optically and show the functionalities of the sensors; to devise microfluidic channels for segregation of the sensor array into different compartments and perform enzyme immobilisation techniques on CMOS chips; and integrate the packaged chip with microfluidic channels and enzyme immobilisation using 2D inkjet printer into a complete system that has the potential to be used as a multi-enzyme platform for detection of different metabolites.
Two CMOS sensor array chips (1) a 256×256-pixel ISFET array chip and (2) a 16×16-pixel Multi-Corder chip were fully understood. Therefore, a high-speed instrumentation system was constructed for the ISFET array chip with a maximum readout speed of 500 frames per second, with 2D and 3D imaging capability, as well as single pixel analysis. Follow by that, a miniaturised measurement platform was implemented for the Multi-Corder chip that has three different sensor arrays, which are ISFET, PD and SPAD. All the sensor arrays can be operated independently or together (ionic sensor and one of the optical sensors).
Several post-processing steps were investigated to allow suitable fabrication process on small 4×4 mm2 CMOS chips. Post-processing of the CMOS chips was first established using room temperature sputtering process for Ta2O5 layer, achieving Ta:O ratio of 1:1.77 and a surface roughness of 0.42 nm. This Ta2O5 layer was then fabricated on top of CMOS ISFETs, which improves the ISFET pH sensitivity to 45 mV/pH, with an average drift of 6.5 ± 8.6 mV/hour from chip to chip and a working pH range of 2 to 12. Furthermore, a layer of POMs was drop casted on top of Ta2O5 ISFET to make ISFET sensitive to potassium ions. This was investigated in terms of potassium ions sensitivity, hydrogen ions sensitivity and sodium ions as interfering background ions. The POMs Ta2O5 ISFET was found to have a net potassium sensitivity of 75 mV/pK, with a linear range between pH 1.5 to 3. Moreover, the POMs ISFET has -5 mV/pH in pH sensitivity, showing that it is selectivity towards potassium ions and not hydrogen ions. However, sodium ions were found to produce a large interference towards the pK sensitivity of POMs ISFET and reduced the pK sensitivity of POMs ISFET. Hence, further work is still required to modify POMs layer for better selectivity and sensitivity. Besides that, microfluidic channels were fabricated on top of the CMOS chips that could provide segregation for multiple enzyme assays on a single chip. In addition, a PDMS and a manual dam and fill method were developed to encapsulate the CMOS chips for wet biochemistry measurements.
The CMOS sensor array was found to have the ensemble averaging capability to reduce noise as a function of √N , where N is the number of sensors used for averaging. Several enzyme assays that include: hexokinase, lactate dehydrogenase, urease and lipase were tested on the ISFET sensor array. Moreover, using an optical sensor array, namely a PD on the Multi-Corder chip and using LED illumination, quantification of cholesterol levels in human blood serum was demonstrated. Enzyme kinetics calculations were performed for hexokinase and cholesterol oxidase assays and the results were comparable to that obtained from a bench top spectrophotometer. This shows the CMOS sensor array can be used as a low cost portable diagnostic device.
Several enzyme immobilisation techniques were explored but were unsuccessful. Alginate enzyme gel immobilisation with a 2D inkjet printer was found to be the best candidate to bio-functionalise the CMOS sensor array. The packaged chip was integrated with microfluidic channels and alginate enzyme gel immobilisation into a complete system, in order to perform an enzyme assay with its control experiments simultaneously on a single chip. As a proof-of-concept, this complete system has the potential to be used as a multiple metabolite quantification platform.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Keywords: CMOS, biosensor, enzymes, ISFET, metabolomics, microarray, precision healthcare, photodiode.
• Subjects: Q Science > QH Natural history > QH345 Biochemistry; T Technology > TK Electrical engineering. Electronics Nuclear engineering
• Colleges/Schools: College of Science and Engineering > School of Engineering > Electronics and Nanoscale Engineering
• Funder's Name: Engineering & Physical Sciences Research Council (EPSRC)
• Supervisor's Name: Cumming, Professor David
• Date of Award: 2017
• Depositing User: Boon Chong Cheah
• Unique ID: glathesis:2017-8115
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 18 Apr 2017 15:09
• Last Modified: 17 Apr 2018 07:49
• URI: https://theses.gla.ac.uk/id/eprint/8115