Additional file 11: Figure S4. of The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

Boxplots of the methylation values for the CS-CS individuals (current smokers at both baseline and follow-up) and the NS-NS individuals (never smokers at both baseline and follow-up). Figure S4a shows the technically adjusted beta values and Figure S4b shows the methylation beta values after residualization to account for confounding (see Statistical Methods). (PDF 23 kb

Summary of the quality control.

<p>The number of <b>mtSNPs</b> refers to the SNPs that passed QC and were included in the analysis. Several mtSNPs were excluded due to the upper bound cut-off (<b>UB</b>) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126294#pone.0126294.ref077" target="_blank">77</a>] or because the basepair position was not available in Build 38 (<b>no_B38</b>). Sample size is based on the particular chip. Total sample size is 2,803 independent individuals. One person may be present on more than one chip. <i>I</i>_<i>SNP</i> stands for the number of intensity measures per allele. <i>I</i>_<i>tot</i> represents the total number of intensity measures in the sample (I_SNP*2*sample-size*mtSNPs).</p><p>Summary of the quality control.</p

Summary of significant mtSNPs.

<p>Genomic position in base pairs (bp), alleles, rs_number, and point mutation are based on the NCBI dbSNP GRCh38 human genome assembly (rCRS, GeneBank ID J01415.2). Alleles are given in terms of major→minor allele. The population minor allele frequency “maf” is based on 2,704 individuals provided by mitomap (<a href="http://www.mitomap.org" target="_blank">http://www.mitomap.org</a>). Note that these allele frequency estimates do not account for the presence of heteroplasmy. An estimated effect size (β_SNP) < 0 indicates that the risk allele is the minor allele. Nominal p-values and adjusted p-values are provided. mtSNPs mt3336, mt5285 and mt14000 are also included in other chips.</p><p>Summary of significant mtSNPs.</p

Distribution of characteristics of the study population.

<p>Sample size is based on the particular chip. Total sample size is 2,815 independent individuals. One person may be present on more than one chip. Distributions are presented as means ± standard deviation.</p><p>Distribution of characteristics of the study population.</p

Illustration by phenotype of the 11 significant mtSNPs after correcting for multiple testing.

<p>On the y axis, the p-values transformed into the negative of the base 10 logarithm, −log₁₀(p-value), are shown. The x-axis represents the mitochondrial genome for each phenotype.</p

Maternal Smoking during Pregnancy and DNA-Methylation in Children at Age 5.5 Years: Epigenome-Wide-Analysis in the European Childhood Obesity Project (CHOP)-Study - Fig 1

<p><b>Volcano plot (A) and QQ-plot (B) of 433 313 differentially methylated CpG sites for 366 children at age 5.5 exposed vs. not-exposed to maternal smoking beyond week 12 of gestation.</b> Figures are based on linear regression of M-values on exposure variable and adjustment factors.</p

Top 25 EWAS associations of differentially methylated CpG sites in children at age 5.5 years exposed to maternal smoking beyond week 12 of gestation.

<p>Top 25 EWAS associations of differentially methylated CpG sites in children at age 5.5 years exposed to maternal smoking beyond week 12 of gestation.</p

Characteristics of the analysed population.

<p>Characteristics of the analysed population.</p

Forest plot of meta-analyzed results for the effect per minor allele of rs3748312 on FEV1 in ever-smokers, adjusted for sex, age, height, population stratification factors and the presence of PI S and Z alleles.

<p>Studies based on population isolates with a high degree of cryptic relatedness are presented separately. Effect estimates of meta-analyses are shown with green diamonds. I² is a measure of the heterogeneity between studies. Random effect meta-analyses are included if I²>0.5. Study weights (blue squares) correspond to fixed effect meta-analyses.</p

Manhattan plot of genome-wide -log(10) p-values for association with AAT serum level.

<p>SNPs reaching genome-wide significance are shown in green. They all belong to the <i>SERPINA</i> gene cluster.</p