Clinical Epigenetics

Table 3 Variance explained by genome-wide DNA methylation using independent CpG sites/methylation correlated blocks

From: Epigenome-wide contributions to individual differences in childhood phenotypes: a GREML approach

		ALSPAC						Generation R						Pooled
		Baseline		Methylation		Delta		Baseline		Methylation		Delta		Baseline		Methylation		Delta
Outcome	Covariates	R²	SD_CV	R²	SD_CV	R²	SD_CV	R²	SD_CV	R²	SD_CV	ΔR²	SD_CV	R²	SD_CV	R²	SD_CV	ΔR²	SD_CV
Gestational age	Basic	0.016	0.019	0.411	0.099	0.395	0.098	0.007	0.009	0.648	0.132	0.641	0.134	0.009	0.008	0.497	0.079	0.480	0.079
	Full	0.091	0.054	0.357	0.096	0.266	0.075	0.110	0.065	0.640	0.125	0.530	0.103	0.099	0.042	0.463	0.076	0.359	0.061
Birth weight	Basic	0.028	0.027	0.136	0.064	0.108	0.063	0.024	0.022	0.262	0.084	0.237	0.085	0.026	0.017	0.182	0.051	0.154	0.051
	Full	0.072	0.049	0.117	0.064	0.045	0.029	0.073	0.042	0.251	0.075	0.178	0.057	0.073	0.032	0.174	0.049	0.073	0.026
BMI	Basic	0.008	0.011	0.008	0.011	0.000	0.007	0.008	0.010	0.007	0.010	0.000	0.014	0.008	0.007	0.008	0.007	0.000	0.007
	Full	0.032	0.033	0.030	0.033	− 0.002	0.007	0.069	0.037	0.069	0.037	0.000	0.009	0.048	0.025	0.048	0.025	− 0.001	0.005
ADHD	Basic	0.043	0.033	0.041	0.034	− 0.002	0.018	0.018	0.019	0.021	0.022	0.003	0.011	0.024	0.016	0.027	0.018	0.002	0.009
	Full	0.038	0.035	0.034	0.030	− 0.004	0.014	0.040	0.031	0.039	0.031	− 0.001	0.003	0.039	0.023	0.037	0.022	− 0.001	0.003
IQ	Basic	0.016	0.020	0.015	0.021	− 0.001	0.012	0.006	0.009	0.006	0.009	0.000	0.005	0.008	0.008	0.008	0.008	0.000	0.005
	Full	0.029	0.036	0.028	0.036	− 0.001	0.005	0.070	0.042	0.070	0.042	0.000	0.002	0.047	0.027	0.046	0.027	0.000	0.002

Basic sex and batch
Full sex, maternal age, maternal smoking, maternal education, cell type proportions, batch, gestational age*, birth weight* (* not when outcome is gestational age or birth weight)
Baseline Model with either basic or full covariates
Methylation Model with methylation matrix plus either basic or full covariates
Delta The difference between model with methylation matrix minus baseline only model
R² Variance explained
SD_CV Standard-deviation of cross-validation estimates, adjusted for between imputation variance

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ISSN: 1868-7083

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