Additional file 3 of Cord blood epigenome-wide meta-analysis in six European-based child cohorts identifies signatures linked to rapid weight growth
Creators: name: Alfano, Rossella
name: Zugna, Daniela
name: Barros, Henrique
name: Bustamante, Mariona
name: Chatzi, Leda
name: Ghantous, Akram
name: Herceg, Zdenko
name: Keski-Rahkonen, Pekka
name: de Kok, Theo M.
name: Nawrot, Tim S
name: Relton, Caroline L
name: Robinson, Oliver
name: Roumeliotaki, Theano
name: Scalbert, Augustin
name: Vrijheid, Martine
name: Vineis, Paolo
name: Richiardi, Lorenzo
name: Plusquin, Michelle
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Figures S1-S12 [60]. Fig. S1. QQ-plot of I2p-values of the meta-analysis of EWASs of rapid weight growth. Fig. S2. Forrest plots and plots from leave out one cohort at time meta-analysis from EWASs of rapid weight growth for the CpGs with PSuggestive &lt; 1e-05. Fig. S3. Quality control of cohort specific EWAS of rapid weight growth. Coefficients, standard errors and p-values distributions visualized via box plots and QQ-plot. Fig. S4. Cohort specific correlation plots between chronological and DNA methylation gestational age. Fig. S5. Forrest plot of the meta-analysis of gestational age acceleration and rapid weight growth in sensitivity analyses adding (A) delivery mode, (B) removing cell types from confounders, excluding mothers with (C) gestational diabetes and (D) non-white European children. Fig. S6. Calibration plots of Random Forest models of rapid weight growth including (A) conventional risk factors, (B) CpGs related to rapid weight growth and (C) both. Fig. S7. Calibration plots of Random Forest models of rapid weight growth including (A) conventional risk factors, (B) CpGs belonging to DMRs related to rapid weight growth and (C) both. Fig. S8. Heatmap shows Pearson’s correlation between methylation levels of the 44 CpGs associated with PSuggestive &lt;1e-05 in the meta-analysis of EWAS of rapid weight growth. Red boxes indicate the three CpGs identified in mediation analyses. Fig. S9. Volcano plots of the association between the 44 CpGs associated with rapid weight growth at PSuggestive &lt; 1e-05/the 96 CpGs belonging to the 16 DMRs associated with rapid weight growth at FDR-adjusted p-value in DMRcate and Siddak p-values in ENmix-comb-p &lt;0.01 and the entire transcriptome (A/C) and restricted to cis transcripts (B/D). Red lines represent Bonferroni-significant threshold, and black lines suggestive threshold (p-value=10-e05). For analyses restricted to cis transcripts only Bonferroni-significant threshold is represented. Fig. S10. Volcano plots of the association between the 44 CpGs associated with rapid weight growth at PSuggestive &lt; 1e-05/the 96 CpGs belonging to the 16 DMRs associated with rapid weight growth at FDR-adjusted p-value in DMRcate and Siddak p-values in ENmix-comb-p &lt;0.01 and the entire metabolome (A/B). Red lines represent Bonferroni-significant threshold, and black lines suggestive threshold (p-value=10-e05). Fig. S11. Forrest plot of the meta-analysis of the analysis of gestational age acceleration and childhood overweight. Fig. S12. Volcano plot from the look-up in the study population of the CpG sites associated with child anthropometrics in a previous systematic review by Alfano et al. [60].