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Table 3 Life course analysis—contribution of fetal and postnatal influences (FDR threshold < 0.05). For the prenatal analysis, results are expressed as the change in log(IgE) concentration per 1% increase in cord blood methylation value. While for the postnatal analysis, results are expressed as the change in log(IgE) concentration per 1% increase in Δ-DNAm methylation value

From: Epigenome-wide association study of total serum immunoglobulin E in children: a life course approach

     Prenatal influences Postnatal influences (Δ-DNAm)
CpG CHR MAPINFO Gene Estimate P value FDR Estimate P value FDR
Life course analysis—prenatal influences
 cg25854298 10 73,936,754 ASCC1 − 0.36 8.02E−09 0.003 − 0.40 1.80E−13 6.28E−09
 cg16416603 20 57,593,014 TUBB1 0.58 5.17E−08 0.008 0.28 1.32E−04 8.24E−02
 cg11848324 14 20,403,845 OR4K1 0.57 1.48E−07 0.016 0.44 3.35E−06 5.26E−03
 cg19549714 18 3,447,713 TGIF1 − 2.00 2.40E−07 0.017 − 0.10 4.45E−01 9.71E−01
 cg23933289 1 178,998,656 FAM20B − 0.18 2.66E−07 0.017 − 0.17 8.01E-08 2.54E−04
 cg24576940 7 150,648,283 KCNH2 − 1.54 3.31E−07 0.017 − 1.66 2.95E−08 1.10E−04
 cg13443997 9 139,743,586 PHPT1 − 3.39 7.11E−07 0.028 − 1.83 1.50E−03 3.32E−01
 cg19954205 12 122,211,282 TMEM120B − 1.20 7.20E−07 0.028 − 0.55 1.72E−02 7.37E−01
 cg01782059 1 44,715,942 ERI3 − 0.96 1.25E−06 0.033 − 0.60 4.04E−04 1.69E−01
 cg02133716 8 128,981,622 PVT1 − 0.45 1.25E−06 0.033 − 0.54 2.63E−11 3.31E−07
 cg06226630 4 48,493,420 ZAR1 − 0.39 1.24E−06 0.033 − 0.02 5.24E−01 9.76E−01
 cg20675173 3 43,795,541 − 1.22 1.03E−06 0.033 − 0.72 1.11E−03 2.91E−01
 cg08067346 16 25,011,481 ARHGAP17 − 0.24 1.44E−06 0.035 − 0.30 2.18E−11 2.85E−07
 cg09597192 6 32,141,591 AGPAT1 − 0.31 1.78E−06 0.040 − 0.28 3.70E−06 5.67E−03
 cg16096766 13 52,419,714 FLJ37307 − 0.36 2.30E−06 0.048 − 0.19 2.48E−04 1.23E−01
 cg00026222 1 2,144,244 − 1.02 2.63E−06 0.049 − 0.29 9.59E−02 9.09E−01
 cg24575275 7 1,094,737 C7orf50 − 0.31 2.49E−06 0.049 − 0.02 5.23E−01 9.76E−01
Life course analysis—postnatal influences (top 20 methylation sites)
 cg11699125 1 6,341,327 ACOT7 − 0.10 3.29E−02 5.88E-01 − 0.25 2.81E−23 7.95E−18
 cg02970679 17 56,269,818 EPX − 0.17 9.50E−04 2.86E-01 − 0.25 5.06E−23 7.95E−18
 cg24491618 7 150,649,807 KCNH2 − 0.12 1.23E−03 3.05E-01 − 0.19 2.12E−16 2.22E−11
 cg01614759 10 45,495,435 C10orf25 − 0.17 2.17E−03 3.46E-01 − 0.28 2.97E−16 2.33E−11
 cg13054523 17 81,055,722 − 0.30 9.45E−05 1.53E-01 −0.43 4.23E−15 2.66E−10
 cg21220721 1 6,341,230 ACOT7 0.01 7.03E−01 9.51E-01 − 0.11 1.30E−14 6.81E−10
 cg10065736 12 117,440,120 FBXW8 − 0.10 2.28E−02 5.53E-01 − 0.18 2.73E−14 1.23E−09
 cg06558622 7 149,543,177 ZNF862 − 0.29 3.37E−05 1.02E-01 − 0.41 8.05E−14 3.16E−09
 cg25854298 10 73,936,754 ASCC1 − 0.36 8.02E−09 2.52E-03 − 0.40 1.80E−13 6.28E−09
 cg05300717 11 65,546,210 DKFZp761E198 0.0002 9.93E−01 9.99E-01 − 0.33 2.11E−13 6.63E−09
 cg09596645 3 181,897,670 − 0.15 2.74E−03 3.67E-01 − 0.25 5.56E−13 1.59E−08
 cg19928703 13 30,143,971 SLC7A1 − 0.19 3.05E−03 3.75E-01 − 0.31 1.06E−12 2.78E−08
 cg18368116 14 21,436,271 − 0.13 2.02E−02 5.40E-01 − 0.27 1.91E−12 4.62E−08
 cg20885063 17 17,939,419 ATPAF2 − 0.16 1.85E−04 1.90E-01 − 0.23 4.05E−12 9.09E−08
 cg08077807 14 62,001,072 PRKCH − 0.53 7.33E−04 2.63E-01 − 0.76 4.45E−12 9.11E−08
 cg07908654 13 41,631,052 − 0.20 3.94E−06 5.14E-02 − 0.26 4.64E−12 9.11E−08
 cg08940169 16 88,540,241 ZFPM1 − 0.05 1.56E−01 7.57E-01 − 0.18 6.34E−12 1.17E−07
 cg18879389 21 43,771,120 TFF2 − 0.16 6.64E−04 2.58E-01 − 0.28 6.73E−12 1.17E−07
 cg20263733 3 130,616,293 ATP2C1 − 0.25 4.25E−03 3.99E-01 − 0.50 7.45E−12 1.23E−07
 cg02985445 7 97,908,505 − 0.08 3.50E−02 5.94E-01 − 0.18 8.09E−12 1.27E−07
Life course analysis—prenatal and postnatal influences
 cg25854298 10 73,936,754 ASCC1 − 0.36 8.02E−09 0.003 − 0.40 1.80E−13 6.28E−09
 cg11848324 14 20,403,845 OR4K1 0.57 1.48E−07 0.016 0.44 3.35E−06 0.005
 cg23933289 1 178,998,656 FAM20B − 0.18 2.66E−07 0.017 − 0.17 8.01E−08 2.54E−04
 cg24576940 7 150,648,283 KCNH2 − 1.54 3.31E−07 0.017 − 1.66 2.95E−08 1.10 E−04
 cg02133716 8 128,981,622 PVT1 − 0.45 1.25E−06 0.033 − 0.54 2.63E−11 3.31E−07
 cg08067346 16 25,011,481 ARHGAP17 − 0.24 1.44E−06 0.035 − 0.30 2.18E−11 2.85E−07
 cg09597192 6 32,141,591 AGPAT1 − 0.31 1.78E−06 0.040 − 0.28 3.70E−06 0.006
  1. Model adjusted for maternal [age at enrollment (continuous), smoking status (smoking during pregnancy/former/never), college graduate (yes/no), maternal atopy history (yes/no)], children [child’s sex (female/male), race (white/black/other), gestational age (continuous), age at blood drawn (continuous)], and the cell-type proxys using the first five ReFACTor components estimated from cord blood
  2. Corresponding model: log(IgE) = β0 + β1CpG_cbi + β2ΔCpGi + β3X3 + … + βpXp + η
  3. Life course analysis—prenatal influence: association between cord blood methylation and mid-childhood IgE independent of postnatal changes in DNA methylation, which correspond to β1CpG_cbi
  4. Life course analysis—postnatal influence: association between changes in postnatal DNA methylation from birth and mid-childhood IgE independent of baseline/cord blood DNA methylation, which correspond to ΔCpGi