Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray

摘要: DNA methylation, an important type of epigenetic modification in humans, participates crucial cellular processes, such as embryonic development, X-inactivation, genomic imprinting and chromosome stability. Several platforms have been developed to study genome-wide methylation. Many investigators the field chosen Illumina Infinium HumanMethylation microarray for its ability reliably assess methylation following sodium bisulfite conversion. Here, we analyzed profiles 489 adult males 357 females generated by HumanMethylation450 microarray. Among autosomal CpG sites that displayed significant differences between two sexes, observed a enrichment cross-reactive probes co-hybridizing sex chromosomes with more than 94% sequence identity. This could lead mistakenly infer existence sex-associated Using identity cutoffs derived from analysis, concluded 6% array can potentially generate spurious signals because co-hybridization alternate sequences highly homologous intended targets. Additionally, discovered targeting polymorphic CpGs overlapped SNPs. The levels detected these are simply reflection underlying genetic polymorphisms but be misinterpreted true signals. or target microarrays confound data obtained microarrays. Therefore, should exercise caution when biological associations found using platforms. A list all identified us annotated this paper.