DNAMikroarrays

DNAmikroarrays are a class of DNA microarrays designed to profile DNA methylation at predefined CpG dinucleotides across the genome. They detect methylation status by hybridizing bisulfite-converted genomic DNA to probes anchored on a solid surface, with signals interpreted to yield a methylation level for each locus. The term covers array-based methylation profiling platforms, including both older CpG methylation chips and bead-based systems that report methylation as a value between 0 and 1, often referred to as beta values.

The typical workflow starts with genomic DNA, which is treated with bisulfite to convert unmethylated cytosines to uracil while leaving methylated cytosines intact. The resulting DNA is then applied to the array, where the binding or extension of labeled probes reflects the methylation state at each targeted CpG site. After scanning, raw intensities are processed to correct background noise and normalize across samples. Quality control steps assess hybridization efficiency, detection p-values, and probe performance.

Data analysis for DNAmikroarrays involves converting signal intensities into methylation measures, commonly beta values or M values, followed by statistical testing to identify differential methylation between groups. Popular analysis tools include Bioconductor packages that perform normalization, batch effect correction, and differential methylation analysis, as well as methods for identifying differentially methylated regions.

Applications of DNAmikroarrays include epigenetic research, cancer methylation profiling, imprinting studies, and biomarker discovery. They offer a cost-effective alternative to sequencing-based approaches for large cohorts but provide fixed coverage limited to predefined CpG sites. Limitations include probe design biases, potential cross-hybridization, and restricted genomic coverage compared with whole-genome sequencing methods.