Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada.
Epigenetics. 2013 Feb;8(2):203-9. doi: 10.4161/epi.23470. Epub 2013 Jan 11.
DNA methylation, an important type of epigenetic modification in humans, participates in crucial cellular processes, such as embryonic development, X-inactivation, genomic imprinting and chromosome stability. Several platforms have been developed to study genome-wide DNA methylation. Many investigators in the field have chosen the Illumina Infinium HumanMethylation microarray for its ability to reliably assess DNA methylation following sodium bisulfite conversion. Here, we analyzed methylation profiles of 489 adult males and 357 adult females generated by the Infinium HumanMethylation450 microarray. Among the autosomal CpG sites that displayed significant methylation differences between the two sexes, we observed a significant enrichment of cross-reactive probes co-hybridizing to the sex chromosomes with more than 94% sequence identity. This could lead investigators to mistakenly infer the existence of significant autosomal sex-associated methylation. Using sequence identity cutoffs derived from the sex methylation analysis, we concluded that 6% of the array probes can potentially generate spurious signals because of co-hybridization to alternate genomic sequences highly homologous to the intended targets. Additionally, we discovered probes targeting polymorphic CpGs that overlapped SNPs. The methylation levels detected by these probes are simply the reflection of underlying genetic polymorphisms but could be misinterpreted as true signals. The existence of probes that are cross-reactive or of target polymorphic CpGs in the Illumina HumanMethylation microarrays can confound data obtained from such microarrays. Therefore, investigators should exercise caution when significant biological associations are found using these array platforms. A list of all cross-reactive probes and polymorphic CpGs identified by us are annotated in this paper.
DNA 甲基化是人类中一种重要的表观遗传修饰类型，参与了许多重要的细胞过程，如胚胎发育、X 染色体失活、基因组印迹和染色体稳定性。已经开发了几种平台来研究全基因组 DNA 甲基化。该领域的许多研究人员选择 Illumina Infinium HumanMethylation 微阵列，因为它能够可靠地评估亚硫酸氢盐转化后的 DNA 甲基化。在这里，我们分析了 489 名成年男性和 357 名成年女性的甲基化谱，这些样本是由 Infinium HumanMethylation450 微阵列生成的。在两性之间显示出显著甲基化差异的常染色体 CpG 位点中，我们观察到交叉反应探针与性染色体的共杂交显著富集，这些探针与性染色体的序列同一性超过 94%。这可能导致研究人员错误地推断出存在显著的常染色体性别相关甲基化。使用从性别甲基化分析中得出的序列同一性截止值，我们得出结论，由于与目的靶标高度同源的替代基因组序列的共杂交，6%的阵列探针可能会产生虚假信号。此外，我们还发现了针对多态性 CpG 并与 SNPs 重叠的探针。这些探针检测到的甲基化水平仅仅是潜在遗传多态性的反映，但可能被误解为真实信号。Illumina HumanMethylation 微阵列中存在交叉反应探针或目标多态性 CpG 会混淆从这些微阵列获得的数据。因此，研究人员在使用这些阵列平台时应谨慎，因为可能会发现具有显著生物学相关性的探针。本文列出了我们鉴定的所有交叉反应探针和多态性 CpG。
