Table 1.
Overview of the conventional and nanomaterials-based methods for the detection of circulating tumor DNA (ctDNA).
| Method | Features | Detection limit | Advantages | Limitations |
|---|---|---|---|---|
| NGS | PCR-based sequencing | 0.1–5% [17] | High-throughput analysis, detection of unknown genetic alterations | Time-consuming and expensive detection; low sensitivity |
| ARMS | qRT-PCR based on the 3′-end of the primer targeting the mutant sequence for extension | 0.2% [18] | Ease of use, lower cost | Detection of known mutations, lower sensitivity |
| PNA-PCR | qRT-PCR based on PNA inhibiting the extension of the wild-type sequence | 0.1% [20] | High specificity, ease of use | Detection of known mutations, lower sensitivity |
| ddPCR | DNA templates amplified separately in water-oil droplets and quantified | 0.001% (20/200,000 copies) [22], 0.04% [23] |
High sensitivity, a single molecule analysis, absolute quantitation | Detection of known mutations |
| BEAMing | DNA templates amplified on beads and quantified | 0.01% (1/10,000 copies) [28] | High sensitivity, a single molecule analysis, absolute quantitation | Detection of known mutations, pre-amplification of the target sequence |
| PCR-SERS | PCR products analyzed by SERS detection | 0.1% (10/10,000 copies) [42]; 9.24–59.7 pM [40,41]. |
Multiplexed analysis | Detection of known mutations. |
| PAPL | DNA templates amplified by PNA-aPCR and detected by suspension array | 0.02–0.05% (2/10,000–5/10,000 copies) [47] | Multiplexed analysis, high specificity, high sensitivity | Detection of known mutations, qualitative analysis |
| Fe-Au nanoparticle-coupling strategy | Hybridization-based detection | 0.12% [55] | PCR-independent detection | Lower sensitivity, detection of known mutations |
| Electrochemical DNA biosensor | Detection based on generated electronic signal | 1 aM–1.72 fM (mutations) [60,62]; 2 fM–42 pM (DNA methylation) [59,63,70,71] |
High sensitivity, PCR-independent analysis, detection of methylated DNA without sample pretreatment | Detection of known genetic alterations |
| IC3D ddPCR | ddPCR analysis based on the microfluidic device | 0.00125–0.005% [76] | High sensitivity, a single molecule analysis, miniaturization | Detection of known mutations |
NGS – next-generation sequencing; ARMS – amplification refractory mutation system; qRT-PCR – quantitative real-time polymerase chain reaction; PNA-PCR – peptide nucleic acid clamping polymerase chain reaction; ddPCR – droplet digital polymerase chain reaction; BEAMing – beads, emulsion, amplification, magnetics; SERS – surface-enhanced Raman spectroscopy; PNA – peptide nucleic acid; aPCR – asymmetric polymerase chain reaction; PAPL – peptide nucleic acid clamping asymmetric polymerase chain reaction and liquidchip; IC3D – integrated comprehensive droplet.