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

<b>Background:</b> 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 <b>Results:</b> 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. <b>Conclusions:</b> 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.

<b>背景：</b> 近期研究已鉴定出数千个DNA甲基化CpG位点（CpG）与复杂疾病/性状之间的关联，凸显了表观遗传学在解析疾病病因学与筛选生物标志物中的核心作用。然而，基于甲基化芯片数据的关联分析易受批次/玻片效应影响，可能导致假阳性率升高或统计效力降低。
<b>结果：</b> 本研究依托主流的Illumina Infinium MethylationEPIC BeadChip芯片，整合多组DNA甲基化数据集，刻画了跨CpG位点的玻片效应的一致模式与联合分布，验证并拓展了既往研究结论。易受此类效应影响的CpG位点与Illumina Infinium HumanMethylation450 BeadChip芯片的检测内容存在重叠。
<b>结论：</b> 本研究揭示了玻片效应的系统性模式。上述发现进一步阐明了该效应的特征，可为现有校正方法的优化提供支撑。