Optimized DNA extraction from neonatal dried blood spots: application in methylome profiling

BMC Biotechnology

Table 3 Combinations of GenSolve, Qiagen and NucleoSpin protocols for DNA extraction from DBS: GQ versus GN-XS and Gn-XS methods

						65°C, 65 min
	Sample code	DNA (ng/μl)	DNA (ng)	260/280	260/230	260/280	260/230	Protocol
	NCS 28a	20.3	873	1.84	0.95	1.82	0.97	GQ
	NCS 28b	37	1813	1.87	0.11	1.78	0.13	GN-XS
	NCS 27a	19.4	834	1.85	0.85	1.80	0.90	GQ
	NCS 27b	27.9	1339	2.19	0.61	2.26	0.61	GN-XS
	NCS 26a	19.7	847	1.83	0.97	1.74	0.93	GQ
	NCS 26b	23.7	1161	1.66	0.79	1.77	0.80	GN-XS
	NCS 25a	16.3	701	1.9	1.07	1.79	1.07	GQ
	NCS 25b	21.7	1042	1.83	0.34	1.96	0.28	GN-XS
	NCS 24a	11.3	486	1.82	0.78	1.79	0.82	GQ
	NCS 24b	21.6	1037	1.53	0.08	1.48	0.07	GN-XS
	NCS 23a	11.9	512	1.18	0.49	1.27	0.54	GQ
	NCS 23b	11.4	547	1.44	0.50	1.52	0.42	GN-XS
Precipitation buffer in GN-XS changed to ethanol, leading to protocol Gn-XS	NCS 19a	30.1	1174	1.53	0.71	1.57	0.81	GQ
	NCS 19b	15.1	725	1.49	0.65	1.50	0.70	Gn-XS
	NCS 18a	12.2	488	1.81	0.62	1.78	0.64	GQ
	NCS 18b	20.4	979	1.30	0.64	1.44	0.72	Gn-XS
	NCS 17a	59	2360	1.80	1.37	1.91	1.56	GQ
	NCS 17b	42.6	2130	1.65	0.53	1.75	0.57	Gn-XS
Washing volume and frequency in GN-XS increased	NCS 16a	16.8	823	1.71	0.76	1.80	0.78	GQ
	NCS 16b	13.1	707	1.43	0.21	1.55	0.22	GN-XS
	NCS 15a	27.1	1382	1.76	1.04	1.79	0.97	GQ
	NCS 15b	12.6	668	7.83	0.39	Error *	0.45	GN-XS
	NCS 14a	30.3	1545	1.77	1.01	1.83	1.07	GQ
	NCS 14b	22.8	1208	2.37	0.60	2.60	0.61	GN-XS

Two punches, each having 9 mm diameter, were analyzed per DBS. Punches labeled “a” were tested with GQ while their matched pairs, labeled “b”, were tested with GN-XS. When the DNA precipitation buffer in GN-XS was changed to ethanol, the resultant protocol was termed Gn-XS. For NCS 16b, 15a and 14b, the washing volume was increased from 100 to 500 μl, and washing was performed twice instead of once. Average eluate volumes by GQ and GN-XS/Gn-XS were 42 μl and 48 μl, respectively. Data represent averages of 2–4 readings per sample. ^* The error represents values out of range.

ISSN: 1472-6750