Our data for the total study population show associations between omphalocele and variants in two genes: the transcobalamin receptor gene (TCblR
) and the methylenetetrahydrofolate reductase gene (MTHFR
). Variants in TCblR
have recently been shown to be a risk factor for neural tube defects (Pangilinan et al. 2010
) and the SNP that we found to be associated with omphalocele, (rs2232775) p.Q8R is in linkage disequilibrium with the SNP that was associated with neural tube defects in that study. Despite very conservative correction for multiple testing, this finding remained statistically significant. The MTHFR
gene has been studied extensively because of its importance in converting the methylene form of tetrahydrofolate to the methyl form. This function is critical to the conversion of homocysteine to methionine, the major source of methyl groups for methylation reactions.
This finding is noteworthy because of the associations we identified in the race/ethnic group specific analysis. Despite modest numbers, we found a number of variants in genes related to homocysteine metabolism in the African-American and Asian groups. MTHFR and betaine-homocysteine S-methyltransferase (BHMT) SNPs were associated with omphalocele in both groups. The latter gene plays an important role in the generation of methyl groups via the choline pathway. The other associations we identified in African-Americans all related to vitamin B12 transport and receptor functions. Transcobalamin 2 (TCN2) and the transcobalamin receptor (TCblR) play a critical role in delivery of vitamin B12 into the cell. Vitamin B12 is necessary for the function of the methionine synthase reaction that transports a methyl group from folate to homocysteine to form methionine.
It is interesting that an association between low maternal circulating vitamin B12 levels and neural tube defects independent of maternal folate has been reported (Kirke et al. 1993
). Omphalocele has been linked to folate via the finding that women who use folic acid-containing vitamins are at reduced risk (Botto et al. 2002
). Our data suggest that vitamin B12, another constituent of multivitamins, could be contributing to this protective effect. Our finding that variants in multiple genes involved in homocysteine metabolism are associated with increased risk for omphalocele is noteworthy because women carrying a fetus with a neural tube defect have significantly higher homocysteine levels during pregnancy than women who have unaffected fetuses (Mills et al. 1995
). The relationship between homocysteine and omphalocele has not, to our knowledge, been investigated previously except for a study of complex defects of various types in which the mothers whose fetuses had defects, only 7 (9%) of which were omphaloceles, had 25% higher amniotic fluid homocysteine levels than controls (Brouns et al. 2008
). Higher homocysteine levels could be associated with disturbances in one carbon metabolism. This pathway is the source of methyl groups used during DNA methylation.
Because non-syndromic omphalocele cases are rare, little has been published regarding genetic risk factors. Our pilot study (Mills et al. 2005
) showed an association between omphalocele and another MTHFR
variant, 677C>T, in 25 cases and called for additional investigation. The current, much larger study, does not confirm this finding.
Some strengths and limitations of this study should be noted. This study is, to our knowledge, the largest to date; it is population-based; and birth defects have been shown to be well ascertained in the New York system. Samples were available for study on a very large percentage of cases. Thus, neither selection bias, nor or lack of participation, are a concern. Controls are also a representative sample; they were selected from the entire underlying population of births. Limitations include the limited information available on covariates such as diabetes, alcohol and exposure to teratogenic drugs, although these would not be expected to account for many cases. Furthermore, information on family history and details on possible syndromes were limited. Details on syndromes and other clinical information come from hospital reports and the amount of detail varies from case to case. Checks of medical records showed that reporting of omphalocele was accurate. Although many of the associations we found were no longer significant after correction for multiple comparisons, it could be argued that this is overcorrecting because several of the positive findings occurred in genes that were tested as a priori hypotheses because of their association with neural tube defects. In any case, these positive findings occurred in race/ethnic group specific analyses where the number of subjects was very small even in this large study. Therefore, they deserve careful follow up.
In summary this study found that numerous SNPs related to homocysteine metabolism via folate, vitamin B12 or choline were associated with omphalocele. These findings suggest that the previously reported protective effect of multivitamin use might have been due to production of methyl groups by converting homocysteine to methionine, a process which would be assisted by several multivitamin constituents including folate and vitamin B12. Our results suggest that the relationship between omphalocele and methylation, and the roles of vitamin B12, and the transcobalamin receptor in particular, merit investigation. Our findings, if confirmed, suggest that both folic acid and vitamin B12 might be useful in preventing omphaloceles.