Epigenome analysis of placental DNA methylation and added sugar intake during pregnancy

Genome wide DNA methylation profiling of placenta at birth. A 1 cm3 sample of the placenta was collected (using scissor, midway between the umbilical cord and the outer edge of the placenta) and genomic DNA was extracted. DNA integrity was assessed by agarose gel electrophoresis with ethidium bromide staining and PicoGreen (Life Technologies, Carlsbad, Calif.). Starting with 500 ng of genomic DNA, bisulfite conversion and methylation profiling was performed according to the manufacturer’s instructions for Illumina Human Methylation 450K BeadChips. All assays were performed at the Roswell Park Cancer Institute Genomics Shared Resource. After background correction and normalization to internal controls, Genome Studio software was used to calculate the fractional methylation (AVG_Beta) at each CpG (N= 453,144 CpG sites). Samples includes XX placenta. Bisulphite converted DNA from the 89 samples were hybridised to Illumina Human Methylation 450K BeadChips with at least one sugar intake variable and non-missing at covariates of interest.