Table 1.

Nucleic acid detection technologies and their analytical performance.

Technology	Quantitative	Amplification	Sensitivity (dynamic range)	Single-Nucleotide Specificity	Multiplexing ability	Instrumentation	Reagents
qRT-PCR[13, 27, 30–32]	Yes	Amplification-based	zM to fM	>95%	Limited	Real-time PCR instrument (e.g., ThermoFisher QuantStudio. Bio-Rad CFX96)	Extraction kits, primers, fluorogenic probes, thermostable polymerase, dNTPs
ddPCR [27, 33]	Yes	Amplification-based	zM to fM	99.99%	Limited	Droplet generator + droplet reader (e.g., Bio-Rad QX100), thermal cycler	Extraction kits, droplet generation reagents, primers, fluorogenic probes, thermostable polymerase
Illumina sequencing (TruSeq) [27]	Yes	Amplification-based	zM to fM	>99%	High	Illumina sequencer (e.g., MiSeq, HiSeq, NovaSeq), thermal cycler	Extraction kits, library preparation kits, fluorescent dNTPs, thermostable polymerase, flow cells
Microarray[27, 31]	Yes	Amplification-free	nM to mM	50–80%	High	Microarray plate scanner (e.g., AffyMetrix GeneChip HT)	Extraction and PCR/labeling kits, microarray chips
ADNA [22]	Yes	Amplification-free	aM to fM	Not available	Not available	Dark field microscope (e.g., Zeiss Axiovert 200M)	Probe-conjugated nanoparticles, patterned lipid arrays
NanoString [27]	Yes	Amplification-free	fM to nM	90–95%	High	nCounter system (e.g., nCounter MAX)	Flow cells, capture probes, fluorescently barcoded affinity probes
Simoa [24]	Yes	Amplification-free	fM to pM	>95%	Limited	Simoa analyzer (e.g., HD-1, SR-X)	Probe-conjugated microparticles, droplet generation reagents, primary and secondary detection probes, enzymatic signal developing reagents
Time gated FRET ligation [26]	Yes	Amplification-free	pM to nM	Not available	Limited	Fluorescence plate reader (e.g., ThermoFisher KRYPTOR)	FRET probes, adaptor probes, DNA or RNA ligase
SiMREPS [17]	Yes	Amplification-free	fM to pM	≥99.99999%	Limited	TIRF microscope (e.g., Olympus IX83, Oxford NanoImager)	Flow cells, capture probes, fluorescent probes