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Folate deficiency is implicated in the causation of neural tube defects (NTDs). The preventive effect of periconceptional folic acid supplement use is partially explained by the treatment of a deranged folate-dependent one carbon metabolism, which provides methyl groups for DNA-methylation as an epigenetic mechanism. Here, we hypothesize that variations in DNA-methylation of genes implicated in the development of NTDs and embryonic growth are part of the underlying mechanism. In 48 children with a neural tube defect and 62 controls from a Dutch case-control study and 34 children with a neural tube defect and 78 controls from a Texan case-control study, we measured the DNA-methylation levels of imprinted candidate genes ( IGF2 -DMR,  H19, KCNQ1OT1)  and non-imprinted genes (the  LEKR/CCNL  gene region associated with birth weight, and  MTHFR  and  VANGL1  associated with NTD). We used the MassARRAY EpiTYPER assay from Sequenom for the assessment of DNA-methylation. Linear mixed model analysis was used to estimate associations between DNA-methylation levels of the genes and a neural tube defect. In the Dutch study group, but not in the Texan study group we found a significant association between the risk of having an NTD and DNA methylation levels of  MTHFR  (absolute decrease in methylation of −0.33% in cases, P-value = 0.001), and  LEKR/CCNL  (absolute increase in methylation: 1.36% in cases, P-value = 0.048), and a borderline significant association for  VANGL  (absolute increase in methylation: 0.17% in cases, P-value = 0.063). Only the association between  MTHFR  and NTD-risk remained significant after multiple testing correction. The associations in the Dutch study were not replicated in the Texan study. We conclude that the associations between NTDs and the methylation of the  MTHFR  gene, and maybe  VANGL  and  LEKKR/CNNL , are in line with previous studies showing polymorphisms in the same genes in association with NTDs and embryonic development, respectively.

Epigenetic Profiles in Children with a Neural Tube Defect; A Case-Control Study in Two Populations