Table 2. Clinical sample evaluation of crude DNA lysis combined LAMP-GE and LAMP-AuNP, compared with a commercial DNA extraction kit and PCR-GE.

For specificity, the values in parentheses represent the number of true negatives divided by the number of true negatives and false positives. For sensitivity, the values in parentheses represent the number of true positives divided by the number of true positives and false negatives.

Clinical Groups (number of samples)	Test Statistics	PCR-GE	LAMP-GE	LAMP-AuNP
Symptomatic STD (96)	Specificity	0.97 (70/72)	0.96 (69/72)	0.99 (72/73)
	Sensitivity	1.00 (24/24)	0.92 (22/24)	0.96 (22/23)
	False positive	0.03	0.04	0.01
	False negative	0.00	0.08	0.04
Healthy (34)	Specificity	1.00 (33/33)	1.00 (33/33)	1.00 (33/33)
	Sensitivity	1.00 (1/1)	1.00 (1/1)	1.00 (1/1)
	False positive	0.00	0.00	0.00
	False negative	0.00	0.00	0.00
Total (130)	Specificity	0.98 (103/105)	0.97 (102/105)	0.99 (105/106)
	Sensitivity	1.00 (25/25)	0.92 (23/25)	0.96 (23/24)
	False positive	0.02	0.03	0.01
	False negative	0.00	0.08	0.04
Detection limit (copies)		22.5	11.25–45	11.25–45*
Diagnosis time (h)		4:46	1:02–1:17	0:32–0:47*
USD Price/reaction†		30	3	3

* The detection limit of LAMP reduced from 45 to 11.25 copies when the LAMP reaction was incubated at 61°C for 35 minutes (45 copies when the reaction was incubated at 61°C for 20 minutes). Therefore, diagnosis time and detection limit of LAMP have two numbers, depending on the reaction time.

†The differences in the nucleic acid preparation step between PCR (using High Pure Template Preparation Kit, Roche Diagnostics, Indianapolis, IN) and LAMP (heat-treated) were excluded in price per reaction. The price per reaction of the High Pure Template Preparation Kit is approximately 3 USD.

Abbreviations: AuNP, gold nanoparticle probe; GE, gel-electrophoresis; LAMP, loop-mediated isothermal amplification; LOD, limit of detection; PCR, polymerase chain reaction; USD, United States dollars.