Principle of detection | Method | Type of alteration | Advantage(s) | Limitation(s) | Selected reference(s) |
---|---|---|---|---|---|
PCR-based | Nested real-time PCR | Known point mutations such as KRAS, EGFR, and PIK3CA hotspot alterations | Ease of use, lowest cost | Lower sensitivity, only detect limited genomic loci | [70] |
ARMS/Scorpion PCR | [116] | ||||
PCR-SSCP | [117] | ||||
Mutant allele-specific PCR | [118] | ||||
Mass spectrometry | [119] | ||||
Bi-PAP-A amplification | [120] | ||||
Digital PCR | BEAMing | Known point mutations, genomic rearrangements | High sensitivity | Only detect limited genomic loci | [59] |
Droplet-based digital PCR | [56] | ||||
Microfluidic digital PCR | [10] | ||||
Targeted deep sequencing | SafeSeq | Selected SNVs, CNVs, and rearrangements across targeted regions | High sensitivity, relatively inexpensive | Less comprehensive than WES methods | [64] |
TamSeq | [57] | ||||
Ion-AmpliSeq™ | |||||
CAPP-Seq | [68] | ||||
OnTarget | [121] | ||||
Whole-genome sequencing | Digital karyotyping | Genome-wide SNVs, CNVs, and rearrangements | Broad application | Expensive | [73] |
PARE |