Additional file 3: of Identifying and correcting epigenetics measurements for systematic sources of variation

Figure S3. Quantile-quantile (QQ) plots for CpG site-specific analysis with respect to smoking using standard adjustment (a), residuals (b), ComBat (c) and SVA (d) correcting methods for the M values. The inflation factor λ is defined as the ratio of the median of the observed log10 transformed p values from the CpG site-specific analysis and the median of the expected log10 transformed p values. (PDF 110 kb

Additional file 2: of Identifying and correcting epigenetics measurements for systematic sources of variation

Figure S2. Quantile-quantile (QQ) plots for CpG site-specific analysis with respect to smoking using standard adjustment (a), residuals (b), ComBat (c) and SVA (d) correcting methods for the β values. The inflation factor λ is defined as the ratio of the median of the observed log10 transformed p values from the CpG site-specific analysis and the median of the expected log10 transformed p values. (PDF 110 kb

Additional file 1: of Identifying and correcting epigenetics measurements for systematic sources of variation

Figure S1. Box plots of global methylation (M values) according to laboratory factors: batch (a), chip position within batches (b), sample position within chips (c). (PDF 99 kb

Additional file 1: of Gene-specific DNA methylation profiles and LINE-1 hypomethylation are associated with myocardial infarction risk

Supplementary methods. A document with supplementary materials, including the following: (1) subjects: cohort details; lifestyle, anthropometrics, and biochemical measurements; and outcome definition; (2) laboratory methods: EPICOR sample preparation; discovery phase: Illumina Human450K Methylation Assay; replication phase on EPIC-NL sample: Sequenom MassARRAY; and (3) supplementary statistical methods: case-control differential methylation; removal of technical biases; DNA methylation and MI risk; DNA methylation and time to disease (TTD); supplementary references. (DOCX 73 kb

Additional file 3: of Gene-specific DNA methylation profiles and LINE-1 hypomethylation are associated with myocardial infarction risk

Supplemental Figures S1, S2, S3, and S4. Figure S1. quantile-quantile plot, EPICOR overall subjects. Figure S2. quantile-quantile plot, EPICOR men. Figure S3. quantile-quantile plot, EPICOR women. Figure S4. locations of ZBTB12 and LINE-1 CpG sites investigated by Sequenom MassARRAY. CpGs (in red) investigated within ZBTB12-DMR, LINE-1, and flanking primers (upper case: complementary to DNA; lower case: T7-promoter sequence and 10mer tag). CpG sites that could not be tested individually due to MassARRAY technology constrains, but had to be tested jointly with neighboring CpGs as a single unit, are underlined: the methylation level is the cumulative value of all the sites within the CpG unit. (ZIP 91 kb

Additional file 2 of A blood DNA methylation biomarker for predicting short-term risk of cardiovascular events

Additional file 2. Supplementary Tables S1, S2, and S3

Six-way Venn diagram showing polymorphic putative functional variants shared by reported ethnicities.

<p>Numbers of shared variants are shown at intersections. The total numbers of polymorphic variants by ethnicity are listed in the upper-left hand corner.</p

Analysis of SMAD6 cg01339004 probe methylation.

<p>Ai: Boxplot of β-value methylation of cg01339004 probe as measured with Illumina 450 k beadchip in Stage 2. Aii: Boxplot of methylation level of cg01339004 probe as measured with bisulphite pyrosequencing in Stage 3. B: Volcano plot: Difference in median methylation between the two menarcheal age groups (>11 (n = 268) vs. ≤11 years, (n = 62), against the –log(P-Value) of a linear regression analysis with methylation as a continuous outcome (M-values) and age at menarche (>11 vs. ≤11 years) as a categorical exposure, adjusting for age, case-control status, and chip position. C. Q-Q plot on P-values from a linear regression analysis with methylation as a continuous outcome (M-values) and age at menarche (>11 vs. ≤11 years) as a categorical exposure, adjusting for age, case-control status, and chip position.</p

Boxplots of median genome-wide methylation between the three menarcheal age categories.

<p>A: Median % global methylation as measured with LUMA in Stage 1. Bi. Genome-wide methylation across all probes (averaged per individual). Bii. Genome-wide methylation across probes on CpG islands (averaged per individual). Biii. Genome-wide methylation across probes on promoter regions (averaged per individual). M^¤ = Median methylation value. p = p value from Wilcoxon rank-sum test comparisons.</p

Anthropometric and lifestyle variables in healthy controls with respect to LUMA genome wide methylation quartiles (Stage 1).

a<p>For continuous variables, P-value was derived from Kruskal-Wallis test. For categorical variables, P-value was derived from a chi square test, with the exclusion of “Unknown” categories due to their small cell counts. Both reflect the association between quartiles of methylation and the investigated variables.</p>*<p>Significant at the Bonferroni-corrected significance cut off (P = 0.003) for multiple comparisons.</p>±<p>BMI: Body Mass Index, FFTP: First Full Term Pregnancy, HRT: Hormone Replacement Therapy, OC: Oral Contraceptive.</p