Fig. 4. Epigenome-wide association study (EWAS) identified significant signals associated with lowered neurodevelopment in Group 2.
a EWAS Manhattan plot in the IMAGEN population. Group 2 (n = 463) (relative to Group 1, n = 446) status was used as the phenotype, adjusting for potential confounders. One hypermethylated site cg06064461 achieved genome-wide significant effect (one sample two-sided t-test: P < 5 × 10−8, BH-FDR corrected Padj < 0.05) and was mapped to ATF2 and MIR933 on chromosome 2. Validation of EWAS results in IMAGEN (n = 909). cg06064461 methylation was positively correlated with total GMV trajectory (b; r = 0.14, P = 6.85 × 10−6) and negatively correlated with peak gray matter volume (GMV) (c; r = −0.07, P = 0.020), adjusting for potential confounders. The error bands in (b, c) represent the pointwise 95% confidence intervals of the corresponding estimated correlations. One sample t-test was used. d Proportion of the mediation effects through cg06064461 methylation in the environmental exposure - peak GMV pathway, adjusting for potential confounders (n = 750 independent samples; the estimates and standard deviation of mediation proportion were estimated using the 1000-iteration bootstrap approach). The bar, also the central of the error bars, represents the point-wise estimated mediation proportion, while error bars indicate 95% confidence intervals of the estimated mediation proportion. Thus, the left/right whiskers represent the lower bound and upper bound of the confidence interval, respectively. Environmental factors were sorted by P values of the corresponding mediation effects. No mediation effects of cg06064461 methylation showed statistical significance (one sample two-sided t-test) after correcting for multiple testing using BH-FDR method, although uncorrected significance was observed between family affirmation and peak GMV. Childexp, child’s experience of family life; FamStress, family stressors; CTQ, Childhood Trauma Questionnaire. e Mediation model was conducted to analyse the direct and indirect effect of family affirmation on peak GMV, with cg06064461 methylation as the mediator. Results showed that cg06064461 methylation mediated the relationship between family affirmation and peak GMV with an unadjusted p value of 0.048 (one sample two-sided t-test: β = 0.005, mediation proportion = 9.26%, Punadj = 0.048, Padj = 0.191). Relevant source data were provided in the Source Data file.