Analysis of variability and epigenetic age prediction across microarray and methylation sequencing technologies

Using 100 technical replicate samples from two adult buccal cohorts, we compared technical methylation variability and signal strength between the Infinium MethylationEPIC v2.0 array and the Twist Human Methylome Panel across 753,648 shared CpGs. Twist methylation sequencing showed skewed methylation distributions and fewer highly correlated CpGs than MethylationEPIC arrays.

Variance analysis revealed a skew toward higher signal strength in MethylationEPIC datasets with a subset of CpGs showing high signal strength in both methylation sequencing and array datasets. Despite these biases, four principal component (PC) trained epigenetic clocks (pcHorvath1, pcHorvath2, pcHannum, and pcDNAm PhenoAge) were robust across both technologies, even with missing data. While pcHannum and pcDNAm PhenoAge had similar replicate errors across both technologies, pcHorvath1 was more reproducible on arrays while pcHorvath2 was more reproducible on methylation sequencing.