Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea.
Institute for New Drug Development, College of Life Science and Bioengineering, Incheon National University, Incheon, Republic of Korea.
Sci Rep. 2024 Nov 7;14(1):27026. doi: 10.1038/s41598-024-77914-5.
DNA methylation is a molecular process that mediates gene-environment interactions. Epigenome-wide association studies (EWAS) using the Illumina Human Methylation BeadChip are powerful tools for quantifying the relationship between DNA methylation and phenotypes. Recently, the Illumina Methylation EPICv2 BeadChip (EPICv2) was released, which includes new features, such as duplicated probes and changed probe names. Several published algorithms have been updated to address these features in EPICv2. However, appropriate EPICv2 preprocessing and integration with previous microarray versions remain complex. Therefore, MethylCallR, an open-source R package designed to provide standard procedures for performing EWAS using Illumina methylation microarrays including EPICv2, was developed. MethylCallR can be used to control duplicated probes in EPICv2, by using pre-set data implemented in MethylCallR or new customized data. MethylCallR includes a straightforward conversion function between different types of Illumina Human Methylation BeadChips. Using MethylCallR, potential outlier sample detection and statistical power estimation were conducted and used to select meaningful probes. Publicly available data was analyzed using MethylCallR and the findings were compared to that of a previous study.
DNA 甲基化是一种介导基因-环境相互作用的分子过程。使用 Illumina Human Methylation BeadChip 的全基因组关联研究 (EWAS) 是量化 DNA 甲基化与表型之间关系的有力工具。最近，Illumina Methylation EPICv2 BeadChip (EPICv2) 发布了，它包含了新的特性，如重复探针和改变的探针名称。几个已发布的算法已经更新以解决 EPICv2 中的这些特性。然而，EPICv2 的适当预处理和与以前的微阵列版本的集成仍然很复杂。因此，开发了 MethylCallR，这是一个开源的 R 包，旨在为使用包括 EPICv2 在内的 Illumina 甲基化微阵列进行 EWAS 提供标准程序。MethylCallR 可以通过使用 MethylCallR 中实现的预设数据或新定制的数据来控制 EPICv2 中的重复探针。MethylCallR 包括不同类型的 Illumina Human Methylation BeadChips 之间的直接转换功能。使用 MethylCallR 进行了潜在异常样本检测和统计功效估计，并用于选择有意义的探针。使用 MethylCallR 分析了公开可用的数据，并将结果与之前的一项研究进行了比较。
