Evaluating the presence of Mycoplasma hyorhinis, Fusobacterium nucleatum, and Helicobacter pylori in biopsies of patients with gastric cancer

Table 2 Evaluation of purity and amount of DNA extracted from fragments of FFPE gastric tissue samples

DNA extraction method	260/230*	260/280*	DNA (ng/µL)
EM1
Xylol dewaxing material	2.12	1.91	2.507
Non-dewaxing material	2.35	1.75	47
EM2
Xylol dewaxing material	2.10	1.92	475
Non-dewaxing material	2.47	1.66	168
EM3
Xylol dewaxing material	1.82	1.59	99
Non-dewaxing material	1.59	1.56	53
EM4
Xylol dewaxing material	0.38	1.19	800
Non-dewaxing material	0.38	1.27	431
EM5
Xylol dewaxing material	1.38	1.81	243
Mineral oil dewaxing material	1.24	1.94	112
Non-dewaxing material	1.69	2.06	183
EM6
Xylol dewaxing material	2.50	2.60	21
Mineral oil dewaxing material	2.09	1.98	82
Non-dewaxing material	2.96	2.78	16

*The wavelengths of 260/230 nm (ratio: 2.0–2.2) and 260/280 nm (ratio: 1.7–2.0) were considered acceptable for evaluation
In the 260/230 nm wavelength, EM1 and EM2 extraction methods and EM6 dewaxed with mineral oil show good DNA extraction. EM3, EM4, and EM5 extractions show low absorbance values, indicating contamination of salts (e.g. EDTA). At 260/280 nm, EM1, EM2 (dewaxed), EM5, and EM6 (dewaxed with mineral oil) present sufficient DNA purity. EM2 (Non-dewaxing material), EM3, EM4, and EM6 (xylol dewaxing material and non-dewaxing material) present insufficient DNA purity, indicating protein contamination and other organic compounds

ISSN: 1750-9378