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Table 7 Methylation quality control probe evaluation

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

   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
  1. 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).