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Table 5 Comparison of stage 2 (n = 367) and replication (n = 464) results

From: DNA methylation loci associated with atopy and high serum IgE: a genome-wide application of recursive Random Forest feature selection

Genetic annotations*

IOW: atopy statusa

IOW: high IgEb

BAMSE: atopy statusc

CpG Site

Chr

Gene name

CpG location

Adj. OR

P-Value

Adj. OR

P-value

Adj. OR

P-value

cg04983687

16

ZFPM1

Body

0.239

6.46E−09

0.158

3.54E−05

0.269

3.17E−06

cg09249800

1

ACOT7

Body

0.239

8.52E−09

0.141

1.13E−05

–

–

cg12819873

11

PRG2

5′UTR

0.065

1.38E−08

0.045

7.37E−05

0.140

2.36E−05

cg07908654

13

–

–

0.145

1.14E−07

0.103

8.44E−05

0.206

2.21E−04

cg06824199

1

KIAA0494

Body

0.107

6.28E−07

0.073

1.93E−04

0.118

2.96E−06

cg27469152

17

EPX

3′UTR

0.091

1.34E−06

0.025

6.06E−05

0.099

1.00E−05

cg27468224

4

–

–

0.123

1.62E−06

0.073

5.01E−04

0.262

1.89E−02

cg13233042

11

ATL3

Body

0.192

5.06E−06

0.105

1.82E−04

0.194

9.75E−05

cg13197551

20

LSM14B

3′UTR

0.160

5.67E−06

0.094

5.64E−04

0.312

1.04E−02

cg07765167

17

MRPL45

TSS1500

0.087

6.50E−06

0.043

5.96E−04

–

–

cg09332506

1

COPA

Body

0.123

7.77E−06

0.126

3.62E−03

0.196

8.72E−05

cg17041511

17

–

–

0.143

1.27E−05

0.075

8.14E−04

0.133

4.31E−05

cg24836822

7

KCNH2

Body

0.311

1.36E−05

0.225

7.13E−04

–

–

cg07970948

7

ZNF862

Body

0.243

1.38E−05

0.109

2.55E−04

0.313

1.61E−05

cg25854298

10

ASCC1

Body

0.221

3.69E−05

0.144

1.24E−03

0.149

1.21E−06

cg09635874

13

FARP1

Body

8.084

4.89E−05

2.591

2.44E−01

1.149

8.59E−01

cg04085542

5

FAM172A

Body; 5′UTR

2.663

7.99E−05

1.250

5.48E−01

0.936

7.93E−01

cg03553407

4

ARHGAP10

Body

4.330

1.63E−04

2.411

1.92E−01

2.010

2.16E−01

cg12819826

19

PPAN; PPAN-P2RY11

TSS1500

0.213

2.45E−04

0.229

4.02E−02

1.788

2.87E−01

cg00854799

1

PEX10; RER1

3′UTR

4.209

2.48E−04

2.930

8.27E−02

1.464

5.18E−01

cg05652668

7

LUC7L2

1st exon; 5′UTR

0.280

3.07E−04

0.517

2.39E−01

0.820

7.35E−01

cg17971837

22

PVALB

TSS1500

0.122

7.90E−04

0.102

4.11E−02

0.188

2.60E−02

  1. Associations for methylation M-values with atopy and high IgE from the IOW epigenetic sample, as well as with atopy in the BAMSE replication sample. IOW analyses were adjusted for predicted cell proportions of CD8+ T cells, CD4+ T cells, natural killer cells, B cells, monocytes, granulocytes, and sex. BAMSE replication analyses were adjusted for the same predicted cell proportions, sex, batch (bisulfite treatment date), and asthma treatment
  2. Abbreviations: Adj. OR adjusted odds ratio, BAMSE Children, Allergy, Milieu, Stockholm, Epidemiology cohort, Chr Chromosome number, CpG cytosine–phosphate–guanine, IgE Immunoglobulin E, IOW Isle of Wight cohort, TSS Transcription Start Site, UTR untranslated region
  3. *CpGs and their annotations highlighted in bold were the sites replicated in the BAMSE cohort
  4. aAtopy defined as at least one positive skin prick test; significant sites determined via α = 8.06E−4 (0.05/62 tests)
  5. bHigh IgE defined as serum IgE ≥ 200 kU/L; significant sites determined via α = 8.06E−4 (0.05/62 tests)
  6. cAtopy defined as serum IgE antibody ≥ 0.35 kUA/L, to any allergen; significant sites determined via α = 0.05
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Genome Medicine

ISSN: 1756-994X

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