Rapid Diagnostics for Colorectal Cancer using Lab-on-Chip Technology with Machine Learning

• Published in: IEEE International Symposium on Circuits and Systems proceedings pp. 1 - 5
• Main Authors: Yapeter, Calista Adele, Gulli, Costanza, Mantikas, Katerina-Theresa, Lali, Francis, Moser, Nicolas, Simillis, Constantinos, Kalofonou, Melpomeni, Georgiou, Pantelis
• Format: Conference Proceeding
• Language: English
• Published: IEEE 19.05.2024
• Subjects: Accuracy; Biomarkers; BRAF; Brain modeling; colorectal cancer; DNA; ISFET; Lab-on-a-chip; Lab-on-Chip; LAMP; machine learning; point-of-care; Signal processing algorithms; Training
• ISSN: 2158-1525
• DOI: 10.1109/ISCAS58744.2024.10558018

BRAF p.V600E mutations are key biomarkers for colorectal cancer (CRC) which are associated with poor patient prognosis and response to EGFR treatment. This paper demonstrates a proof-of-concept study for a portable Lab-on-Chip (LoC) device integrated with Ion-Sensitive Field-Effect Transistor (ISFET) sensors in detecting BRAF p.V600E biomarkers with high accuracy and speed, for Point-of-Care (PoC) testing of CRC. Wild-type and mutant-type copies of the BRAF gene were successfully distinguished using chip-compatible loop-mediated isothermal amplification (LAMP) reactions. Optimisation of the LAMP assay targeting BRAF p.V600E was performed and tested using qPCR instrumentation as a gold standard and benchmark for the LoC, exhibiting improved limits of detection (LODs) at 10 2 copies/µL in under 15 minutes. A bespoke signal processing methodology was also developed using the Convolutional Neural Network EEGNet to classify nucleic acid amplification experiments on ISFET arrays, achieving an accuracy of over 95% and designed to be easily transferable to novel DNA/RNA targets. The findings show evidence of the potential to employ ISFET sensing in PoC diagnostics for CRC, ultimately bridging the gap in accessibility in limited resource settings.