Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples

Brando Poggiali, Mikkel Eriksen Dupont, Marie‐Louise Kampmann, Athina Vidaki, Vânia Pereira, Claus Børsting, Jacob Tfelt‐Hansen, Jeppe Dyrberg Andersen

Both DNA fragment size and DNA input amounts affect DNAm analysis on the EPIC v2.0, with the investigated DNA fragment size having a greater impact than the investigated DNA input amount. DNAm measurements were achieved with the EPIC v2.0 microarray down to an average DNA fragment size of 165 bp and a 20 ng DNA input. Highly fragmented DNA (95 bp) did not result in usable DNAm analysis as all samples failed QC. Overall, our study demonstrates the potential and limitations of EPIC v2.0 microarray with low quality and quantity DNA samples.