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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