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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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