Table 2.

Commonly used technologies to analyze cell-free DNA

Technique	Advantages	Limitations
Quantitative PCR	High sensitivity and specificity	Quantification of only annotated sequences
	High dynamic range
BEAMing, PAP, COBRA, etc.	Higher sensitivity and specificity than quantitative PCR	Analyses of only predetermined sequences
	Detection of at least 0.01 % altered alleles
Microarray	High throughput	Not suitable for accurate quantification
	Relatively low cost	Low dynamic range
	Detection of only annotated DNA	High signal-to-noise ratio
	Cross-hybridization between similar sequences
Next-generation sequencing	High sensitivity and specificity	High cost
	Detection of novel and rare alterations	Need for special equipment and bioinformatics
	Ability to distinguish similar sequences	Relatively high amounts of starting material
		Sequence-specific bias

PCR polymerase chain reaction, BEAMing beads, emulsion, amplification and magnetics, PAP pyrophosphorolysis-activated polymerization, COBRA combined bisulfite restriction analysis