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Updated: Jul 27, 2026

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
Published on: July 12, 2012
Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation
Kristen M Kocher1,2, Julius Ngwa1, Kushal J Kapse1
1Developing Brain Institute, Center for Prenatal, Neonatal and Maternal Health Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
Abstract:
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 that 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 post-processing techniques must be considered in the evaluation and interpretation of epigenetic studies.

