Epigenetic Associations with Ancestry and Nutrition

Statistical analyses were done on the R platform (http://www.r-project.org) and JMP Statistics (JMP Pro 10.0.0). We applied linear regression to test association between methylation M-values and ancestry (self-reported race). Since maternal age and cellular heterogeneity are known to influence methylation values [17 (link)–19 (link)], both maternal age and estimated proportions of lymphocytes and granulocytes were used as covariates in the regression model. Birth weight only has limited influence on DNA methylation and this was not added as a factor in the regression model [38 (link)]. For association with maternal nutritional factors, the M-values were regressed on maternal plasma vitamin D or folate with race, maternal age, and estimated blood cell counts as covariates. P-values were adjusted for false discovery using the Benjamini and Hochberg method [48 (link)]. Enrichment in cis-meQTLS among CpG sites with population difference was evaluated using the hypergeometric test. Gene ontology and pathway enrichment analysis was done using DAVID 6.7 [49 (link)] (http://david.abcc.ncifcrf.gov).