The emergence of pathogens resistant to existing antimicrobial drugs is a growing worldwide health crisis that threatens a return to the pre-antibiotic era. To decrease the overuse of antibiotics, molecular diagnostics systems are needed that can rapidly identify pathogens in a clinical sample and determine the presence of mutations that confer drug resistance at the point of care. We developed a fully integrated, miniaturized semiconductor biochip and closed-tube detection chemistry that performs multiplex nucleic acid amplification and sequence analysis. The approach had a high dynamic range of quantification of microbial load and was able to perform comprehensive mutation analysis on up to 1,000 sequences or strands simultaneously in <2 h. We detected and quantified multiple DNA and RNA respiratory viruses in clinical samples with complete concordance to a commercially available test. We also identified 54 drug-resistance-associated mutations that were present in six genes of Mycobacterium tuberculosis, all of which were confirmed by next-generation sequencing.
Design and successful implementation of a fully-integrated CMOS
fluorescence biochip for DNA/RNA testing in molecular diagnostics (MDx) is
presented. The biochip includes a 32×32 array of continuous wave
fluorescence detection biosensing elements. Each biosensing element is capable
of having unique DNA probe sequences, wavelength-selective multi-dielectric
emission filter (OD of 3.6), resistive heater for thermal cycling, and a high
performance and programmable photodetector. The dimension of each biosensor is
100µm×100µm with a
50µm×50µm
Nwell-Psub photodiode acting as the optical
transducer, and a ΣΔ modulator based photocurrent sensor. The
measured photodetector performance shows ~116 dB detection dynamic range (10fA
– 10nA) over the 25°C – 100°C temperature range,
while being ~1 dB away from the fundamental shot-noise limit. To empirically
demonstrate the compatibility of this biochip with MDx applications, we have
successfully utilized the array and its thermal cycling capability to adopt a
7-plex panel for detection of 6 human upper respiratory viruses.
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