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Background  Folic acid taken in early pregnancy reduces risks for delivering offspring with several congenital anomalies. The mechanism by which folic acid reduces risk is unknown. Investigations into genetic variation that influences transport and metabolism of folate will help fill this data gap. We focused on 118 SNPs involved in folate transport and metabolism.    Methods  Using data from a California population-based registry, we investigated whether risks of spina bifida or conotruncal heart defects were influenced by 118 single nucleotide polymorphisms (SNPs) associated with the complex folate pathway. This case-control study included 259 infants with spina bifida and a random sample of 359 nonmalformed control infants born during 1983–86 or 1994–95. It also included 214 infants with conotruncal heart defects born during 1983–86. Infant genotyping was performed blinded to case or control status using a designed SNPlex assay. We examined single SNP effects for each of the 118 SNPs, as well as haplotypes, for each of the two outcomes.    Results  Few odds ratios (ORs) revealed sizable departures from 1.0. With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0 for the following SNPs (heterozygous or homozygous) relative to the reference genotype:  BHMT  (rs3733890) OR = 1.8 (1.1–3.1),  CBS  (rs2851391) OR = 2.0 (1.2–3.1);  CBS  (rs234713) OR = 2.9 (1.3–6.7);  MTHFD1  (rs2236224) OR = 1.7 (1.1–2.7);  MTHFD1  (hcv11462908) OR = 0.2 (0–0.9);  MTHFD2  (rs702465) OR = 0.6 (0.4–0.9);  MTHFD2  (rs7571842) OR = 0.6 (0.4–0.9);  MTHFR  (rs1801133) OR = 2.0 (1.2–3.1);  MTRR  (rs162036) OR = 3.0 (1.5–5.9);  MTRR  (rs10380) OR = 3.4 (1.6–7.1);  MTRR  (rs1801394) OR = 0.7 (0.5–0.9);  MTRR  (rs9332) OR = 2.7 (1.3–5.3);  TYMS  (rs2847149) OR = 2.2 (1.4–3.5);  TYMS  (rs1001761) OR = 2.4 (1.5–3.8); and  TYMS  (rs502396) OR = 2.1 (1.3–3.3). However, multiple SNPs observed for a given gene showed evidence of linkage disequilibrium indicating that the observed SNPs were not individually contributing to risk. We did not observe any ORs with confidence intervals that did not include 1.0 for any of the studied SNPs with conotruncal heart defects. Haplotype reconstruction showed statistical evidence of nonrandom associations with  TYMS ,  MTHFR ,  BHMT  and  MTR  for spina bifida.    Conclusion  Our observations do not implicate a particular folate transport or metabolism gene to be strongly associated with risks for spina bifida or conotruncal defects.

118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects