Table 3.

Results of the methylation score prediction of birth weight, BMI, prenatal maternal smoking and current and former smoking.

Trait	Group—DNA methylation tissue	CpGs included in MS	N CpGs	βMS	SEMS	PMS	MS R2 (%)
Birth weight	Adults—Whole blood (N = 2,040)	p < 10−1	72,570	0.044	0.029	0.127	0.192
		p < 10−5	2,274	0.055	0.029	0.057	0.304
		p < 10−7	963	0.049	0.027	0.074	0.238
		p < 10−1 pruned**	934	0.062	0.022	0.004	0.386
		p < 10−5 pruned	30	0.015	0.023	0.513	0.023
		p < 10−7 pruned	18	0.025	0.023	0.277	0.064
	Children—Buccal cells (N = 1,070)	p < 10−1	72,205	−0.013	0.031	0.679	0.016
		p < 10−5	2,249	0.031	0.032	0.344	0.094
		p < 10−7**	958	0.038	0.032	0.237	0.141
		p < 10−1 pruned	184	0.015	0.029	0.613	0.022
		p < 10−5 pruned	13	0.016	0.032	0.613	0.025
		p < 10−7 pruned	9	−0.005	0.033	0.882	0.002
BMI	Adults—Whole blood (N = 2,410)	p < 10−1	55,653	0.134	0.025	6.98 × 10−08*	1.786
		p < 10−5	1,067	0.261	0.026	5.07 × 10−24*	6.822
		p < 10−7**	412	0.277	0.026	9.79 × 10−27*	7.673
		p < 10−1 pruned	671	0.124	0.021	3.14 × 10−09*	1.538
		p < 10−5 pruned	13	0.220	0.023	1.70 × 10−22*	4.827
		p < 10−7 pruned	6	0.206	0.023	7.50 × 10−20*	4.258
	Children—Buccal cells (N = 1,072)	p < 10−1	55,279	0.003	0.017	0.878	0.001
		p < 10−5	1,079	−0.006	0.017	0.733	0.003
		p < 10−7	422	−0.008	0.018	0.676	0.006
		p < 10−1 pruned**	183	0.021	0.019	0.276	0.042
		p < 10−5 pruned	13	0.005	0.019	0.772	0.003
		p < 10−7 pruned	6	0.007	0.018	0.720	0.004
Prenatal maternal smoking	Adults—Whole blood (N = 720)	p < 10−1	76,531	0.761	0.168	5.83 × 10−06*	8.512
		p < 10−5	1,581	0.946	0.140	1.51 × 10−11*	15.115
		p < 10−7**	607	1.009	0.136	1.28 × 10−13*	17.277
		p < 10−1 pruned	962	0.580	0.136	2.01 × 10−05*	7.076
		p < 10−5 pruned	33	0.661	0.123	7.12 × 10−08*	6.820
		p < 10−7 pruned	16	0.620	0.119	1.94 × 10−07*	5.963
	Children—Buccal cells (N = 547)	p < 10−1	76,146	−0.256	0.158	0.105	0.930
		p < 10−5	1,571	−0.285	0.187	0.127	1.683
		p < 10−7**	606	−0.304	0.183	0.096	2.223
		p < 10−1 pruned	187	−0.125	0.153	0.416	0.386
		p < 10−5 pruned	16	−0.096	0.164	0.559	0.149
		p < 10−7 pruned	9	−0.120	0.161	0.456	0.274
Smoking current vs. never	Adults—Whole blood (N = 1,914)	p < 10−1	98,972	1.420	0.095	4.65 × 10−43*	20.974
		p < 10−5	11,433	1.923	0.104	1.93 × 10−66*	40.086
		p < 10−7	6,938	1.999	0.105	6.89 × 10−69*	44.449
		p < 10−1 pruned	913	1.170	0.070	2.70 × 10−47*	27.626
		p < 10−5 pruned	37	2.194	0.108	5.21 × 10−75*	56.237
		p < 10−7 pruned**	24	2.245	0.111	1.25 × 10−73*	57.461
Smoking former vs. never	Adults—Whole blood (N = 1,938)	p < 10−1 from current vs. never smoking EWAS	98,972	0.429	0.085	6.63 × 10−07*	2.004
		p < 10−5 from current vs. never smoking EWAS	11,433	0.689	0.086	2.73 × 10−15*	5.127
		p < 10−7 from current vs. never smoking EWAS	6,938	0.758	0.086	3.37 × 10−18*	6.217
		FDR significant from Former vs. Never Smoking EWAS	2,568	0.935	0.088	3.56 × 10−24*	9.340
		p < 10−1 pruned from current vs. never smoking EWAS	913	0.499	0.066	3.38 × 10−13*	4.399
		p < 10−5 pruned from current vs. never smoking EWAS	37	1.186	0.087	6.64 × 10−36*	15.625
		p < 10−7 pruned from current vs. never smoking EWAS**	24	1.226	0.088	5.44 × 10−36*	16.316
		FDR significant from Former vs. Never Smoking EWAS, pruned	2,330	0.692	0.071	1.96 × 10−18*	7.569

β is the regression coefficient for each methylation score (MS) with standard error (SE) and p-value (P). MS R² is the phenotypic variance explained by the MS.

^*indicates p < 0.0012 in adults and <0.0016 in children.

^**indicate methylation score with lowest p-value for a trait/exposure.