A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data

Background: Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical power Results: We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content. Conclusions: Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.</p

Power curves for RITSS1, RITSS2, GESAT, and GAMsv over increasing signal density <i>p</i>_<i>XE</i>.

Significance level α = 0.005, μXE = 0.05, and results based on 1,000 replicates. Power was simulated for pXE = 0.05, 0.1, 0.2, 0.3, 0.4, 0.5.</p

Power curves for RITSS1, RITSS2, GESAT, and GAMsv over increasing signal density <i>p</i>_<i>XE</i>.

Significance level α = 0.005, μXE = 0.1, and results based on 1,000 replicates. Power was simulated for pXE = 0.05, 0.1, 0.2, 0.3, 0.4, 0.5.</p

Analysis configurations and number of genetic variants incorporated.

Analysis configurations and number of genetic variants incorporated.</p

Type 1 error: Quantile-quantile-plots for RITSS1, RITSS2, GESAT, and GAMsv for scenarios 1–5 with SELECT:yes.

All results based on 10,000 replicates. P-values with p−10 were set to p = 10−10. SELECT:yes refers to the scenario where the simulated genetic variants are selected into the analysis based on marginal association p-values.</p

Additional information regarding genetic variants tested in the UK Biobank analysis.

These tables contain all genetic variants as well as the m4/m3 information for the sex-interaction analysis in the UK Biobank. (XLSX)</p

Density plots for standardized residuals for all four traits in the analysis.

FEV1: forced expiratory volume in 1 second, FVC: forced vital capacity. (TIF)</p

Type 1 error: Quantile-quantile-plots for RITSS1, RITSS2, GESAT, and GAMsv for scenarios 1–5 with SELECT:no.

All results based on 10,000 replicates. P-values with p−10 were set to p = 10−10. SELECT:no refers to the scenario where all simulated genetic variants are included in the analysis.</p

Results of the interaction testing using the two approaches RITSS1 and RITSS2 in the UK Biobank.

The environmental factor tested for interaction is denoted by Eit. |m| is the number of total SNPs in the analysis, |m4| and |m3| are the number of SNPs that are shared by all four and exactly three interaction scores, respectively. P-Y-S: pack-years of smoking, E-S: ever-smoking.</p

Visualization of the RITSS algorithm.

Visualization of the RITSS algorithm.</p