Circulating DNA as biomarker in breast cancer

Breast Cancer Research

Table 2 Commonly used technologies to analyze cell-free DNA

Technique	Advantages	Limitations
Quantitative PCR	High sensitivity and specificity	Quantification of only annotated sequences
Quantitative PCR	High dynamic range	Quantification of only annotated sequences
BEAMing, PAP, COBRA, etc.	Higher sensitivity and specificity than quantitative PCR	Analyses of only predetermined sequences
BEAMing, PAP, COBRA, etc.	Detection of at least 0.01 % altered alleles	Analyses of only predetermined sequences
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	High signal-to-noise ratio
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
	Ability to distinguish similar sequences	Sequence-specific bias

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

ISSN: 1465-542X