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Table 2 Comparison of DNA methylation levels assessed using Illumina HM450K array and pyrosequencing assays (PyroAssays)

From: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin

CpG name in HM450K array PyroAssay name Illumina infinium human methylation 450BEAD chip array Pyrosequencing technical validation
beta_mean_CEU beta_mean_CHB CEU.beta_mean -CHB.beta_mean q- value CEU.mean CHB.mean CEU.mean -CHB.mean p-value_beta
(n = 18) (n = 18) (n = 10) (n = 10)
cg24861686 1_CpG1a 0.841 0.697 0.143 0.0000 0.813 0.591 0.222 0.0000
cg03140118 2_CpG1a 0.176 0.503 −0.327 0.0010 0.131 0.518 −0.387 0.0003
3_CpG1 0.410 0.150 0.259 0.0056
3_CpG2 0.289 0.087 0.202 0.0048
cg00862290 3_CpG3a 0.466 0.161 0.305 0.0080
cg07904028 4_CpG1a 0.515 0.714 −0.199 0.0145
cg08979191 5_CpG1a 0.779 0.520 0.258 0.0185 0.782 0.544 0.238 0.0117
5_CpG2 0.609 0.400 0.209 0.1174
5_CpG3 0.599 0.418 0.181 0.1942
6_CpG1 0.067 0.186 −0.119 0.0106
cg04036182 6_CpG2a 0.271 0.486 −0.215 0.0201 0.112 0.470 −0.358 0.0000
cg26367031 7_CpG1a 0.539 0.170 0.369 0.0215
cg18136963 8_CpG1 0.520 0.179 0.341 0.0019
8_CpG2a 0.514 0.162 0.352 0.0355 0.498 0.174 0.324 0.0097
8_CpG3 0.423 0.179 0.243 0.0180
cg07207043 9_CpG1a 0.625 0.820 −0.195 0.0345 0.529 0.813 −0.283 0.0023
9_CpG2 0.422 0.726 −0.304 0.0007
9_CpG3 0.480 0.814 −0.335 0.0004
10_CpG1 0.258 0.531 −0.272 0.0000
cg23669876 10_CpG2a 0.368 0.728 −0.360   0.290 0.590 −0.299 0.0000
  1. HM450K array results are available only for HM450K-based candidate pop-CpGs (marked with a). For cg00862290, which corresponds to the third CpG locus in PyroAssay 3, no reliable pyrosequencing data was obtained. Assays 4 (cg07904028) and 7 (cg26367031) did not pass technical evaluation step