Semiconductor design methodologies for epigenetic monitoring

Abstract

Epigenetics governs environmental influences on gene expressions, and plays a crucial role in chronic disease progressions. The binary nature of methylation and microRNAs (miRNA), defined by their “on” and “off” states or “up” and “down” regulations respectively, makes them accessible as potential biomarkers and therapeutics. Integration of such epigenetic modifications as part of future healthcare depends on the development of appropriate technology for monitoring. Therefore the thesis envisions an ISFET (ion-sensitive field effect transistor) based epigenetic microchip, to enable portability in methylation detection and miRNA quantification. Four circuits were designed and implemented to carry out or improve the accuracy of suitable analysis methods that are compatible with ISFETs. For methylation-specific PCR (MSP), a novel configuration of ISFETs as a current mirror was proposed for differential sensing of opposite strand primers. With the circuit operating in weak inversion, drift and temperature sensitivities were reduced while achieving sufficient pH resolution to detect nominal changes expected in MSP reactions. For single-base resolution, a novel ISFET switched current integrator fabricated in unmodified CMOS was proposed to overcome one of the primary limitations in ion-semiconductor sequencing, namely base calling for repeated nucleotides known as homopolymers. The application of integration can potentially increase both accuracy and window for detection of base incorporations. Additionally, the feasibility of a new compressed work flow unique to ISFET-based sequencing for methylation is investigated. For evaluating miRNA expressions in relative quantification analysis, the first implementation of an on-chip back-end using the Derivative method to compute threshold cycles is presented. The process also led to the development of a new algorithm that compares three data points to provide real-time assessment of positive amplifications based on exponential characteristics, enabling detection times to be decreased whilst providing similar estimates of threshold cycles to the established Derivative method. Overall work express potential of implementing epigenetics detection using ISFETs, with CMOS microchips presented as a fast and affordable solution for future monitoring.