Comparison of Six Commercial DNA Extraction Kits for Recovery of Cytomegalovirus DNA from Spiked Human Specimens

Gary A. Fahle; Steven H. Fischer

doi:10.1128/JCM.38.10.3860-3863.2000

DOI: 10.1128/JCM.38.10.3860-3863.2000

Article Figures & Data

Tables

Table 1.

Comparison of DNA extraction kit sensitivity from spiked specimens as determined by mean time-resolved fluorescence values^a

Specimen (concn [PFU/ml])	NS		PG		QIA		MP		IQ		GCC
Specimen (concn [PFU/ml])	Mean value	No. pos^b	Mean value	No. pos^b	Mean value	No. pos^b	Mean value	No. pos^b	Mean value	No. pos^b	Mean value	No. pos^b
BAL (4)	293,768	6/6	242,640	6/6	123,226	6/6	375,405	5/6	97,325	4/6	14,300	2/6
BLD (4)	292,375	6/6	79,808	5/6	587,679	6/6	42,176	4/6	63,402	4/6	220,722	6/6
Plasma (4)	359,998	6/6	296,304	6/6	123,173	6/6	303,136	6/6	47,882	2/6	8,894	1/6
CSF
4	662,433	6/6	527,460	5/6	65,469	3/6	97,573	2/6	31,787	2/6	1,486	0/6
2	72,042	5/6	64,069	4/6
0.8	35,542	5/6	25,847	3/6
0.4	28,943	3/6	8,193	1/6

↵a Six replicates from each sample. pos, positive.
↵b Number of replicates out of six with a DELFIA fluorescence value of >15,000.

Table 2.

Comparison of the NucliSens isolation kit sensitivity to other extraction methods from spiked specimens as determined by mean time-resolved fluorescence values^a

Specimen (concn [PFU/ml])	Mean time-resolved fluorescence values (P value) for paired tests:
Specimen (concn [PFU/ml])	NS/PG	NS/QIA	NS/MP	NS/IQ	NS/GCC
BAL (4)	293,768/242,640 (0.3807^b)	293,768/123,226 (0.0255)	293,768/375,405 (0.3637^b)	293,768/97,325 (0.0654^b)	293,768/14,300 (0.0009)
BLD (4)	292,375/79,808 (0.0265)	292,375/587,679 (0.5139^b)	292,375/42,176 (0.0235)	292,375/63,402 (0.0087)	292,375/220,722 (0.4887^b)
Plasma (4)	359,998/296,304 (0.6317^b)	359,998/123,173 (0.0105)	359,998/303,136 (0.3558^b)	359,998/47,882 (0.0022)	359,998/8,894 (0.0027)
CSF
4	662,433/527,460 (0.4165^b)	662,433/65,469 (0.0121)	662,433/97,573 (0.0416)	662,433/31,787 (0.0085)	662,433/1,486 (0.0076)
2	72,042/64,069 (0.7741^b)
0.8	35,542/25,847 (0.4816^b)
0.4	28,943/8,193 (0.1353^b)

↵a Six replicates were performed from each sample. Results are presented as pairwise comparisons and Pvalues (by paired t test; calculated with StatView).
↵b Not significant (P > 0.05).

Table 3.

Comparison of cost, processing time, and other miscellaneous aspects between the evaluated DNA extraction kits

Extraction method	Cost/test^a	Processing time^b (h:min)		Maximum sample vol (μl)	Recovered extraction vol (μl)	Required reagents not included in kit	Special equipment^e
Extraction method	Cost/test^a	Hands-on^c	Total^d	Maximum sample vol (μl)	Recovered extraction vol (μl)	Required reagents not included in kit	Special equipment^e
NS^f	$4.00	02:28	03:08	200^g	50	70% ethanol	Vacuum aspirator
						Acetone
PG	0.23	01:49	04:39	100	20	Proteinase K
						100% isopropanol
						70% ethanol
						Glycogen
QIA	1.10	01:35	01:55	200	200	100% ethanol
MP	0.69	01:04	01:59	150 (BAL, CSF)	35	100% isopropanol	Refrigerated centrifuge
				50 (PLM)		75% ethanol
				12.5 (BLD)
IQ	0.84	01:53	02:38	100	100	100% isopropanol
						70% ethanol
GCC	1.08	00:45	00:55	200	200		Fitted heat block^h

↵a Based on pricing quote (early 1999) from each manufacturer for large-volume orders.
↵b Determined for an 18-sample run. Timing began with aliquoting of first reagent or sample and concluded with recovery of extracted DNA.
↵c Time required to perform manual manipulation of tubes, reagents, and samples.
↵d Time required to obtain extracted DNA, including hands-on time and incubation periods.
↵e Excluding standard laboratory equipment.
↵f An automated extractor is available for laboratories with high sample volumes.
↵g Kit available for larger-sample-volume processing.
↵h Bore size must be large enough to completely contain capture column. Manufacturer recommends specific models.