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. 2019 Apr 30;127(4):047009. doi: 10.1289/EHP3398

Table 6.

Look-up results for 26 CpGs identified as differentially methylated by maternal tobacco smoke exposure by Joubert et al. (2012) in MACHS and the SMKE study.

CpG Position Gene Joubert et al. 2012 MACHS WakeMed SMKE
MoBa (450K) NEST (450K) WGBS EPIC
Percent meth. diff. p-Value Percent meth. diff. p-Value Percent meth. diff. p-Value pFDRa Ave. coverage Percent meth. diff. p-Value
cg10399789 Chr1:92945668 GFI1 −3.7 1.1×10−10 −3.4 0.02 −2.6 0.44 0.44 5.9 −0.5 0.44
cg09662411 Chr1:92946132 GFI1 −6.6 3.0×10−17 −6.8 2.3×10−3 6.8 0.26 0.78 3.3 −1.6 0.61
cg06338710 Chr1:92946187 GFI1 −5.8 5.0×10−14 −5.2 2.6×10−3 −4.3 0.57 0.66 4.0 −0.7 0.39
cg18146737 Chr1:92946700 GFI1 −12.3 3.3×10−25 −15.1 3.7×10−3 0.8 0.66 0.64 4.3 −1.5 0.03
cg12876356 Chr1:92946825 GFI1 −11.9 1.7×10−25 −10.5 1.5×10−3 −0.02 0.15 0.43 5.1 −2.1 0.01
cg18316974 Chr1:92947035 GFI1 −7.1 3.2×10−20 −9.0 2.3×10−3 −4.3 0.50 0.54 3.9 −0.6 0.12
cg09935388b Chr1:92947588 GFI1 −13.7 2.7×10−31 −7.5 1.2×10−3 NA NA NA NA −5.9 5.0×10−4
cg14179389 Chr1:92947961 GFI1 −8.6 2.6×10−25 −8.2 4.3×10−3 −3.4 0.43 0.74 4.1 −10.7 1.9×10−3
cg23067299c Chr5:323907 AHRR 3.2 4.12×10−9 3.7 3.6×10−3 10.3 0.07 0.63 8.1 NA NA
cg03991871c Chr5:368447 AHRR −2.2 2.0×10−10 −2.3 0.07 −6.9 0.52 0.86 8.2 NA NA
cg05575921 Chr5:373378 AHRR −7.5 8.0×10−33 −7.7 3.0×10−4 −1.4 0.79 >0.99 7.3 −4.3 2.1×10−8
cg21161138 Chr5:399360 AHRR −2.3 8.9×10−10 −1.7 3.6×10−3 −0.05 0.99 >0.99 9.3 −3.2 0.01
cg11715943 Chr6:33091841 HLA-DPB2 −1.8 3.6×10−8 −0.3 0.80 1.7 0.69 0.96 7.8 1.2 0.11
cg19089201 Chr7:45002287 MYO1G 1.4 9.1×10−11 2.2 9.2×10−3 0.6 0.71 0.43 3.5 0.4 0.05
cg22132788c Chr7:45002486 MYO1G 2.8 4.8×10−18 2.1 9.6×10−3 4.3 0.81 0.42 2.6 NA NA
cg04180046 Chr7:45002736 MYO1G 5.3 2.9×10−19 4.9 2.7×10−3 −5.1 0.80 0.69 1.9 2.7 0.01
cg12803068 Chr7:45002919 MYO1G 8.3 1.3×10−19 3.8 4.1×10−3 0.0 0.97 0.92 3.5 0.7 0.03
cg04598670 Chr7:68697651 ENSG00000225718 −3.0 1.3×10−9 −5.3 3.6×10−3 −0.3 0.96 >0.99 10.3 −0.5 0.89
cg25949550 Chr7:145814306 CNTNAP2 −1.8 1.0×10−26 −2.5 2.5×10−3 1.1 0.73 0.61 10.6 −1.5 6.7×10−3
cg03346806 Chr8:119157879 EXT1 −1.5 9.3×10−8 −0.1 0.12 5.8 0.21 0.81 6.9 0.6 0.17
cg18655025 Chr14:91008005 TTC7B −1.2 6.8×10−8 −1.1 0.27 6.0 0.21 0.82 9.0 −0.1 0.24
cg05549655 Chr15:75019143 CYP1A1 3.5 2.4×10−10 3.8 6.0×10−4 1.9 >0.99 0.90 7.6 3.9 6.9×10−3
cg22549041 Chr15:75019251 CYP1A1 7.2 8.9×10−9 8.9 4.4×10−3 −8.7 0.07 0.98 7.8 4.9 0.41
cg11924019 Chr15:75019283 CYP1A1 3.2 4.8×10−8 5.3 8.0×10−4 −2.0 0.57 0.98 8.2 1.3 0.68
cg18092474 Chr15:75019302 CYP1A1 5.9 10.0×10−9 5.3 4.4×10−3 −4.5 0.37 0.99 7.9 5.1 0.22
cg12477880 Chr21:36259241 RUNX1 4.6 7.6×10−10 4.0 0.09 3.2 0.21 0.98 8.1 1.6 0.21

Note: Twenty-six CpGs have previously been identified as differentially methylated (after adjusting for multiple testing using the Bonferroni correction) in whole cord blood by maternal tobacco smoke exposure in two study populations (MoBa and NEST), evaluated by Joubert et al. 2012, and have been widely replicated in subsequent studies. Look-up analyses were therefore conducted for these CpGs in both MACHS and the SMKE study. Percent methylation differences and raw p-values are presented for each CpG by study. False discovery rate-adjusted p-values are also presented for MACHS. Chr, chromosome; FDR, false discovery rate; MACHS, Maternal and Child Health Study; MoBa, Norwegian Mother and Child Cohort Study; NEST, Newborn Epigenetics Study; WGBS, whole-genome bisulfite sequencing.

a

Raw p-values from RADmeth beta-binomial regression models were adjusted for correlations with neighboring CpGs, as described previously (Dolzhenko and Smith 2014), and were subsequently adjusted for multiple testing using the Benjamini-Hochberg method to control the false discovery rate.

b

Since all reads in the exposed and unexposed group were methylated in MACHS, RADMeth did not calculate a p-value for this CpG.

c

These CpGs are not represented on the Infinium EPIC array and therefore could not be examined in the SMKE study.