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Table 2 High-dimensional mediation analysis for the association between PM10 (exposure), DNAm (mediator) and neurodevelopment (outcome) using DACT for CpG sites identified via formal causal mediation analysis with a significant indirect effect and total effect

From: DNA methylation as a potential mediator of the association between indoor air pollution and neurodevelopmental delay in a South African birth cohort

 

Chr

Pos

Closest gene

Cognition

Languageb

General Adaptiveb

Raw p-value

FDR

Raw p-value

FDR

Raw p-value

FDR

cg13690126

1

26,502,524

CNKSR1

1.29E−4

3.30E−3

3.50E−4

5.60E−3

–

–

cg07070893

1

44,412,074

RP11-7O11.3

4.20E−4

7.50E−3

–a

–

–

–

cg23560546

2

159,652,019

DAPL1

7.20E−4

0.011

–

–

–

–

cg15007548

2

159,950,276

TANC1

3.70E−3

0.039

–

–

–

–

cg16975959

2

223,184,510

AC010980.2

1.80E−3

0.022

–

–

–

–

cg00694520

2

223,916,687

KCNE4

3.30E−3

0.044

–

–

–

–

cg08967927

5

30,346,164

RP11-136H13.2

4.29E−05

1.40E−3

–

–

–

–

cg22572779

6

10,434,761

RP1-290I10.7

4.5E−4

7.70E−3

–

–

–

–

cg15074838

6

32,406,521

HLA-DRA

2.60E−4

5.50E−3

–

–

–

–

cg26668632

6

137,540,814

IFNGR1

2.90E−4

5.50E−3

–

–

–

–

cg01550799

7

114,561,804

MDFIC

1.80E−3

0.022

–

–

–

–

cg25405984

10

31,074,039

ZNF438

2.90E−3

0.031

–

–

–

–

cg25544551

12

104,531,891

NFYB

1.51E−05

6.40E−4

–

–

–

–

cg19187486

15

74,833,838

ARID3B

3.30E−13

5.87E−11

–

–

–

–

cg05796992

15

101,547,339

LRRK1

4.39E−05

1.40E−3

–

–

–

–

cg06233301

16

1,500,359

CLCN7

2.30E−3

0.027

–

–

–

–

cg01085137

16

48,278,085

ABCC11

1.10E−3

0.015

–

–

–

–

cg23989635

16

68,771,203

CDH1

1.10E−3

0.015

–

–

–

–

cg26756782

16

89,922,218

SPIRE2

5.90E−05

1.60E−3

–

–

–

–

cg26894552

17

5,323,715

RPAIN

2.60E−3

0.029

–

–

–

–

cg13465852

17

27,942,115

CORO6

2.36E−10

2.10E−08

–

–

–

–

cg10159032

17

30,347,989

LRRC37B

2.20E−4

5.30E−3

–

–

–

–

cg14714923

17

43,238,186

HEXIM2

2.34E−07

1.66E−05

–

–

–

–

cg15000966

17

73,128,123

NT5C

1.62E−05

6.4E−4

–

–

–

–

cg14243899

17

74,580,397

ST6GALNAC2

9.00E−4

0.013

–

–

–

–

cg23054321

19

2,289,682

LINGO3

3.36E−07

1.99E−05

–

–

6.97E−09

6.76E−07

cg05023582

19

50,093,541

PRRG2

2.42E−11

2.87E−09

–

–

–

–

cg03234186

19

58,220,657

ZNF551

8.94E−16

3.18E−13

3.05E−26

1.26E−23

–

–

cg00660655

21

46,368,151

FAM207A

7.20E−4

0.011

–

–

–

–

  1. This table includes raw and corrected p-values from the DACT method for CpG sites identified across domains restricted to those for which we found with nominally significant indirect effects and total effects (domain-dependent) via causal mediation analysis following high-dimensional mediation analysis (BH FDR <  = 0.05)
  2. aMissingness in this table is resultant of our DACT filtering process which is described in more detail in the methods section
  3. 35 CpG sites were considered for multiple testing correction in the cognition domain, 45 in the language domain,
  4. 39 in the general adaptive behavior domain, and 13 in the motor function domain
  5. bNo CpG sites with both a significant indirect effect and significant total effect were identified in the language, motor, or general adaptive behavior domains. Two significant CpG sites identified in the cognitive domain overlap with two in the language domain and one in the general adaptive domain and therefore, information for two CpG sites identified with DACT are depicted for the language domain and one for the general adaptive domain alongside the cognition domain
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Clinical Epigenetics

ISSN: 1868-7083

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