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

BMC Biotechnology

Table 7 Methylation quality control probe evaluation

		Probe		Beta-value
	Sample	Number of CpGs detected with p < 0.01	Percentage of CpGs detected with p < 0.01	Average	Minimum	Maximum
Neonatal Blood DNA	NB 1672	485405	99.96	0.4886	0.0012	0.9929
	NB 1597	485392	99.96	0.4729	0.0006	0.9947
	NB 1842	485358	99.95	0.4911	0.0009	0.9940
	NB 1645	485119	99.91	0.4704	0.0011	0.9914
DBS DNA	NCS 37a	484990	99.88	0.4712	0.0038	0.9953
	NCS 37b	484946	99.87	0.4719	0.0045	0.9916
	NCS 38a	483897	99.65	0.4226	0.0005	0.9942
	NCS 38b	482519	99.37	0.4240	0.0001	0.9935
Cell Line DNA	Cell Line 1	485124	99.91	0.4748	0.0022	0.9926
	Cell Line 2	485175	99.92	0.4813	0.0032	0.9920
	Cell Line 3	485342	99.95	0.4738	0.0006	0.9926
	Cell Line 4	485272	99.94	0.4743	0.0021	0.9934

Three sources of DNA are used in HM450 array: neonatal blood (NB), DBS and cell lines. NB and cell line DNA is of good genomic quality and serves as technical reference. NB provides DNA from the same tissue origin as DBS, being blood. The cell line DNA is of hepatic origin. The technical pairs are represented by two punches from each of two blood spots and are labeled as ‘NCS 37a and 37b’ and ‘NCS 38a and 38b’, respectively. Probe p-value was set to 0.01. The percentage of detected probes (p < 0.01) represents the proportion out of the total of 485,577 probes on the HM450 array. The average, minimum and maximum beta-values with detection p < 0.01 are shown (background was not subtracted, so minimum beta-values are not exactly zeros).

ISSN: 1472-6750