Table 3.

Comparison of methods for ctDNA detection

Method	Description	Detection limit (% ctDNA)	Strengths	Limitations	Refs.
Allele-specific PCR	Preferentially amplifying rare mutant DNA molecules	0.10–1.00	Ease to use; lowest cost	Lower sensitivity; only able to test small number of genomic positions in a sample	[141]
Digital PCR	Counting mutant molecules via partitioning of DNA molecules	0.01	High sensitivity	Only able to test small number of genomic positions in a sample	[142]
NGS amplicon based	Deep sequencing of PCR amplicons	0.01–2.00	High sensitivity (some methods); less expensive than other NGS methods	Less comprehensive than other NGS methods; unable to detect SCNAs; unable to detect rearrangements without assay customization	[55]
WGS	Deep sequencing of entire genome	1.00	Interrogating entire genome; broadly applicable without personalization	Expensive; low sensitivity; mostly limited to SCNA detection	[41]
WES	Deep sequencing of exome	5.00	Interrogating entire exome; broadly applicable without personalization	Expensive; low sensitivity	[41]
CAPP-Seq	Targeted hybrid capture	0.01	High sensitivity for SNVs, indels, rearrangement, and SCNAs detection; broadly applicable without personalization	Less comprehensive than WGS or WES	[143], [144]
iDES-enhanced CAPP-Seq	Targeted hybrid capture and integrated digital error suppression	0.01	High scalability, flexibility, and coverage uniformity; able to reliably evaluate all mutation classes in a single assay	Less comprehensive than WGS or WES	[145]

Note: Table was adapted from Chaudhuri et al. [4] with permission. ctDNA, circulating tumor DNA; SCNA, somatic copy number alteration; SNV, single nucleotide variation; WES, whole-exome sequencing; WGS, whole-genome sequencing; CAPP-Seq, CAncer personalized profiling by deep sequencing; iDES, integrated digital error suppression.