Cell-free circulating tumor DNA in cancer

Cancer Communications

Table 1 Technologies for circulating tumor DNA (ctDNA) detection

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™				[66, 68]
	CAPP-Seq				[68]
	OnTarget				[121]
Whole-genome sequencing	Digital karyotyping	Genome-wide SNVs, CNVs, and rearrangements	Broad application	Expensive	[73]
Whole-genome sequencing	PARE	Genome-wide SNVs, CNVs, and rearrangements	Broad application	Expensive	[70, 72, 74]

PCR polymerase chain reaction, ARMS amplified refractory mutation system, SSCP single-strand conformation polymorphism, Bi-PAP-A amplification bidirectional pyrophosphorolysis-activated polymerization allele-specific amplification, BEAMing beads, emulsion, amplification, and magnetics, SafeSeq safe sequencing system, TamSeq tagged amplicon deep sequencing, CAPP-Seq cancer personalized profiling by deep sequencing, PARE personalized analysis of rearranged ends, KRAS Kirsten rat sarcoma viral oncogene homolog, EGFR epidermal growth factor receptor, PIK3CA phosphatidylinositol-4,5-biphosphate 3-kinase, catalytic subunit alpha, SNV single-nucleotide variants, CNVs copy number variations, WES whole-exome sequencing