Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis

To assess the impact of postnatal processing on placental DNA methylation, array data from flash frozen placental tissue was compared to perfluorocarbon-immersed and formalin fixed paraffin embedded placental tissue. We observed tissue exposed to perfluorocarbon showed no significant DNA methylation differences when compared to unprocessed tissue, while formalin processing altered the quality and reliability of the data produced on the DNA methylation array platform. Placental DNA methylation allows for the study of gene-environment interactions that influence the fetal environment and development. Our study highlights that placental postprocessing techniques must be considered in the evaluation and interpretation of epigenetic studies. Matched samples exposed to various processing methods (flash frozen, exposure to perfluorocarbon MRI media, FFPE processing, and FFPE processing restored chemically using the Illumina Restore Protocol) from 6 term placentas were used to assess DNA methylation data quality