DNA methylation array

Overview

DNA methylation arrays measure genome-wide CpG methylation levels using hybridization-based platforms (e.g., Illumina 450K, EPIC 850K). They quantify beta-values (proportion of methylated alleles) at hundreds of thousands of CpG sites simultaneously, enabling identification of differentially methylated regions, CpG island methylator phenotype (CIMP), and epigenomic subtypes.

Used by

• Illumina 450K methylation array profiling of 333 cutaneous melanoma samples contributed to iCluster integrative analysis; DNA methylation data identified a CIMP phenotype strongly associated with IDH1 (OR = 4.05, p = 0.005) and ARID2 (OR = 3.5, p = 0.0003) mutations. PMID:26091043
• DNA methylation arrays applied to 173 PCPG tumors in the TCGA PCPG study; MAML3 fusion-positive tumors showed a unique expansive hypomethylation signature (4,229 significant probes); pseudohypoxia subtype associated with hypermethylated and intermediate-methylated clusters PMID:28162975.

Notes

• In TCGA SKCM, Illumina 450K arrays (same platform as 450k-methylation-array) were applied; this page covers the generic method category.
• CIMP methylation cluster was associated with higher NRAS hot-spot frequency and lower BRAF hot-spot frequency in melanoma.

Sources

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