Table 1.

Comparison of methods for detecting circulating tumor DNA.

	Allele- specific PCR	Digital PCR	NGS amplicon based	WGS	WES	CAPP-Seq
Method	Preferentially amplifies rare mutant DNA molecules	Counts mutant molecules via partitioning of DNA molecules	Deep sequencing of PCR amplicons	Deep sequencing of entire genome	Deep sequencing of exome	Targeted hybrid-capture
Detection limit (as % ctDNA)	~0.1–1%	~0.01%	~0.01–2.0%	~1%	~5%	~0.01%
Advantages	-Ease of use -Lowest cost	-High sensitivity	-High sensitivity(some methods) -Less expensive than other NGS methods	-Entire genome is interrogated -Broadly applicable w/o personalization	-Entire exome is interrogated -Broadly applicable w/o personalization	-High sensitivity -Detects SNVs, indels, rearrangement & SCNAs -Broadly applicable w/o personalization
Limitations	-Lower sensitivity -Can only test small # of genomic positions in one sample	-Can only test small # of genomic positions in one sample	-Less comprehensive than other NGS methods -Inability to detect SCNAs -Inability to detect rearrangements without assay personalization	-Expensive -Low sensitivity -Mostly limited to SCNA detection	-Expensive -Low sensitivity	-Less comprehensive than WGS or WES

Abbreviations: ctDNA, circulating tumor DNA; SCNA, somatic copy number alteration; NGS, next generation sequencing; WGS, whole genome sequencing; WES, whole exome sequencing; CAPP-Seq, Cancer Personalized Profiling by Deep Sequencing.