Table 3.

Ability to Detect Low Concentrations of Short DNA

Urine cfDNA extraction method	Samples with ≥1 positive PCR well, % (number/total)	Positive PCR wells, % (number/total)	Detected copies/well, mean ± SD	Expected copies/well if theoretical 100% recovery∗
Hybridization capture	100 (6/6)	100 (6/6)	7.8 ± 5.1	10
Wizard/GuSCN	83 (5/6)	44 (8/18)	1.6 ± 0.87	2.5
Q Sepharose	100 (6/6)	89 (16/18)	5.0 ± 1.5	4.7
Norgen Urine Cell-Free Circulating DNA Purification Kit	100 (6/6)	89 (16/18)	1.42 ± 0.67	2
Qiagen QIAamp Circulating Nucleic Acid Kit	17 (1/6)	6 (1/18)	0.05 ± 0.12	4
Thermo Fisher Scientific MagMAX Cell-Free DNA Isolation Kit	33 (2/6)	11 (2/18)	0.77 ± 0.31	2.5

Hybridization, Q Sepharose, and Norgen methods can detect low concentrations of short cfDNA fragments; Wizard/GuSCN, QIAamp, and MagMAX methods are not expected to perform well under these conditions. The ability of each urine cfDNA extraction method to detect low-concentration samples was tested using the experiment design shown in Figure 2. Full results, including no template controls (n = 6), are given in Supplemental Table S2.

Wizard/GuSCN, Wizard resin/guanidinium thiocyanate.

^∗Calculated on the basis of the initial 10 copies/mL target concentration and adjusted for the urine input and elution volume of each method.