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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