The causal effect of red blood cell folate on genome-wide methylation in cord blood: A Mendelian randomization approach

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Binder, Alexandra M ^a   Michels, Karin B ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

DNA methylation; Epigenomic epidemiology; Folate; Mendelian randomization

Indexed keywords

BIOLOGICAL MECHANISMS; DNA METHYLATION; EPIGENETIC MODIFICATION; FOLATE; MENDELIAN RANDOMIZATION; METABOLIC PROCESSING; METHYLENETETRAHYDROFOLATE REDUCTASE; ORDINARY LEAST SQUARES REGRESSIONS;

ALKYLATION; BIOASSAY; BIOCHIPS; BLOOD; DNA SEQUENCES; FUNCTIONAL GROUPS; GENES; METABOLISM; METHYLATION; NUCLEIC ACIDS; REGRESSION ANALYSIS; RISK MANAGEMENT;

RANDOM PROCESSES;

FOLIC ACID;

ADULT; ARTICLE; BLOOD; CHILD; COMPARATIVE STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; ERYTHROCYTE; FEMALE; FETUS BLOOD; GENETICS; GENOTYPE; HUMAN; INFANT; MENDELIAN RANDOMIZATION ANALYSIS; METABOLISM; METHODOLOGY; PHYSIOLOGY; RANDOMIZATION; PROCEDURES;

ADULT; CHILD; CPG ISLANDS; DNA METHYLATION; EPIGENOMICS; ERYTHROCYTES; FEMALE; FETAL BLOOD; FOLIC ACID; GENOTYPE; HUMANS; INFANT; MENDELIAN RANDOMIZATION ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RANDOM ALLOCATION;

EID: 84888788432     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-353     Document Type: Article

References (54)

1. Rieder MJ. Prevention of neural tube defects with periconceptional folic acid. Clin Perinatol 1994, 21(3):483-503.
2. Pitkin RM. Folate and neural tube defects. Am J Clin Nutr 2007, 85(1):285S-288S.
3. De Wals P, Tairou F, Van Allen MI, Uh SH, Lowry RB, Sibbald B, Evans JA, Van den Hof MC, Zimmer P, Crowley M, Fernandez B, Lee NS, Niyonsenga T. Reduction in neural-tube defects after folic acid fortification in Canada. N Engl J Med 2007, 357(2):135-142. 10.1056/NEJMoa067103, 17625125.
4. Anonymous Prevention of neural tube defects: results of the Medical Research Council Vitamin Study. MRC Vitamin Study Research Group. Lancet 1991, 338(8760):131-137. Anonymous.
5. Wilcox AJ, Lie RT, Solvoll K, Taylor J, McConnaughey DR, Abyholm F, Vindenes H, Vollset SE, Drevon CA. Folic acid supplements and risk of facial clefts: National population based case-control study. BMJ 2007 Mar 3, 334(7591):464.
6. Bailey LB, Berry RJ. Folic acid supplementation and the occurrence of congenital heart defects, orofacial clefts, multiple births, and miscarriage. Am J Clin Nutr 2005, 81(5):1213S-1217S.
7. Czeizel AE. Periconceptional folic acid and multivitamin supplementation for the prevention of neural tube defects and other congenital abnormalities. Birth Defects Res A Clin Mol Teratol 2009, 85(4):260-268. 10.1002/bdra.20563, 19161162.
8. Goh YI, Bollano E, Einarson TR, Koren G. Prenatal multivitamin supplementation and rates of congenital anomalies: a meta-analysis. J Obstet Gynaecol Can 2006, 28(8):680-689.
9. Hollingsworth JW, Maruoka S, Boon K, Garantziotis S, Li Z, Tomfohr J, Bailey N, Potts EN, Whitehead G, Brass DM, Schwartz DA. In utero supplementation with methyl donors enhances allergic airway disease in mice. J Clin Invest 2008, 118(10):3462-3469. 2542847, 18802477.
10. Miller RL. Prenatal maternal diet affects asthma risk in offspring. J Clin Invest 2008, 118(10):3265-3268. 2542856, 18802486.
11. Magdelijns FJ, Mommers M, Penders J, Smits L, Thijs C. Folic acid Use in pregnancy and the development of atopy, asthma, and lung function in childhood. Pediatrics 2011, 128(1):e135-e144. 10.1542/peds.2010-1690, 21690114.
12. Whitrow MJ, Moore VM, Rumbold AR, Davies MJ. Effect of supplemental folic acid in pregnancy on childhood asthma: a prospective birth cohort study. Am J Epidemiol 2009, 170(12):1486-1493. 10.1093/aje/kwp315, 19880541.
13. Haberg SE, London SJ, Nafstad P, Nilsen RM, Ueland PM, Vollset SE, Nystad W. Maternal folate levels in pregnancy and asthma in children at age 3 years. J Allergy Clin Immunol 2011, 127(1):262-264.e1.
14. Martinussen MP, Risnes KR, Jacobsen GW, Bracken MB. Folic acid supplementation in early pregnancy and asthma in children aged 6 years. Am J Obstet Gynecol 2011, 206(1):72.e1-72.e7.
15. Hoyo C, Murtha AP, Schildkraut JM, Jirtle RL, Demark-Wahnefried W, Forman MR, Iversen ES, Kurtzberg J, Overcash F, Huang Z, Murphy SK. Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy. Epigenetics 2011, 6(7):928-936. 10.4161/epi.6.7.16263, 3154433, 21636975.
16. Steegers-Theunissen RP, Obermann-Borst SA, Kremer D, Lindemans J, Siebel C, Steegers EA, Slagboom PE, Heijmans BT. Periconceptional maternal folic acid use of 400 microg per day is related to increased methylation of the IGF2 gene in the very young child. PLoS One 2009, 4(11):e7845. 10.1371/journal.pone.0007845, 2773848, 19924280.
17. Ba Y, Yu H, Liu F, Geng X, Zhu C, Zhu Q, Zheng T, Ma S, Wang G, Li Z, Zhang Y. Relationship of folate, vitamin B12 and methylation of insulin-like growth factor-II in maternal and cord blood. Eur J Clin Nutr 2011, 65(4):480-485. 10.1038/ejcn.2010.294, 3071883, 21245875.
18. Greenland S. An introduction to instrumental variables for epidemiologists. Int J Epidemiol 2000, 29(6):1102. 10.1093/oxfordjournals.ije.a019909, 11101554.
19. Martens EP, Pestman WR, de Boer A, Belitser SV, Klungel OH. Instrumental variables: application and limitations. Epidemiology 2006, 17(3):260-267. 10.1097/01.ede.0000215160.88317.cb, 16617274.
20. Hernan MA, Robins JM. Instruments for causal inference: an epidemiologist's dream?. Epidemiology 2006, 17(4):360-372. 10.1097/01.ede.0000222409.00878.37, 16755261.
21. Smith GD, Ebrahim S. Mendelian randomization: prospects, potentials, and limitations. Int J Epidemiol 2004, 33(1):30-42. 10.1093/ije/dyh132, 15075143.
22. Davey Smith G, Ebrahim S. What can mendelian randomisation tell us about modifiable behavioural and environmental exposures?. BMJ 2005, 330(7499):1076-1079. 10.1136/bmj.330.7499.1076, 557238, 15879400.
23. Didelez V, Sheehan N. Mendelian randomization as an instrumental variable approach to causal inference. Stat Methods Med Res 2007, 16(4):309-330. 10.1177/0962280206077743, 17715159.
24. Bound J, Jaeger DA, Baker RM. Problems with instrumental variables estimation when the correlation between the instruments and the endogeneous explanatory variable is weak. J Am Statistic Assoc 1995, 90(430):443.
25. Burgess S, Thompson SG. CRP CHD genetics collaboration: avoiding bias from weak instruments in Mendelian randomization studies. Int J Epidemiol 2011, 40(3):755-764. 10.1093/ije/dyr036, 21414999.
26. Frosst P, Blom HJ, Milos R, Goyette P, Sheppard CA, Matthews RG, Boers GJ, den Heijer M, Kluijtmans LA, van den Heuvel LP. A candidate genetic risk factor for vascular disease: a common mutation in methylenetetrahydrofolate reductase. Nat Genet 1995, 10(1):111-113. 10.1038/ng0595-111, 7647779.
27. van der Put NM, Gabreels F, Stevens EM, Smeitink JA, Trijbels FJ, Eskes TK, van den Heuvel LP, Blom HJ. A second common mutation in the methylenetetrahydrofolate reductase gene: an additional risk factor for neural-tube defects?. Am J Hum Genet 1998, 62(5):1044-1051. 10.1086/301825, 1377082, 9545395.
28. Davis SR, Quinlivan EP, Shelnutt KP, Maneval DR, Ghandour H, Capdevila A, Coats BS, Wagner C, Selhub J, Bailey LB, Shuster JJ, Stacpoole PW, Gregory JF, Davis SR, Quinlivan EP, Shelnutt KP, Maneval DR, Ghandour H, Capdevila A, Coats BS, Wagner C, Selhub J, Bailey LB, Shuster JJ, Stacpoole PW, Gregory JF. The methylenetetrahydrofolate reductase 677C- > T polymorphism and dietary folate restriction affect plasma one-carbon metabolites and red blood cell folate concentrations and distribution in women. J Nutr 2005, 135(5):1040-1044.
29. Guinotte CL, Burns MG, Axume JA, Hata H, Urrutia TF, Alamilla A, McCabe D, Singgih A, Cogger EA, Caudill MA. Methylenetetrahydrofolate reductase 677C- > T variant modulates folate status response to controlled folate intakes in young women. J Nutr 2003, 133(5):1272-1280.
30. Perry CA, Renna SA, Khitun E, Ortiz M, Moriarty DJ, Caudill MA. Ethnicity and race influence the folate status response to controlled folate intakes in young women. J Nutr 2004, 134(7):1786-1792.
31. Hung J, Yang TL, Urrutia TF, Li R, Perry CA, Hata H, Cogger EA, Moriarty DJ, Caudill MA. Additional food folate derived exclusively from natural sources improves folate status in young women with the MTHFR 677 CC or TT genotype. J Nutr Biochem 2006, 17(11):728-734. 10.1016/j.jnutbio.2005.11.009, 16524711.
32. Hay G, Clausen T, Whitelaw A, Trygg K, Johnston C, Henriksen T, Refsum H. Maternal folate and cobalamin status predicts vitamin status in newborns and 6-month-old infants. J Nutr 2010, 140(3):557-564. 10.3945/jn.109.117424, 20071650.
33. Ogbuanu IU, Zhang H, Karmaus W. Can we apply the Mendelian randomization methodology without considering epigenetic effects?. Emerg Themes Epidemiol 2009, 6:3. 10.1186/1742-7622-6-3, 2698894, 19432981.
34. Relton CL, Davey Smith G. Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease. Int J Epidemiol 2012, 41(1):161-176. 10.1093/ije/dyr233, 3304531, 22422451.
35. Kirkbride JB, Susser E, Kundakovic M, Kresovich JK, Davey Smith G, Relton CL. Prenatal nutrition, epigenetics and schizophrenia risk: can we test causal effects?. Epigenomics 2012, 4(3):303-315. 10.2217/epi.12.20, 22690666.
36. Relton CL, Davey Smith G. Epigenetic epidemiology of common complex disease: prospects for prediction, prevention, and treatment. PLoS Med 2010, 7(10):e1000356. 10.1371/journal.pmed.1000356, 2964338, 21048988.
37. Michels KB, Harris HR, Barault L. Birthweight, maternal weight trajectories and global DNA methylation of LINE-1 repetitive elements. PLoS One 2011, 6(9):e25254. 10.1371/journal.pone.0025254, 3182185, 21980406.
38. Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL. Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics 2009, 1(1):177-200. 10.2217/epi.09.14, 22122642.
39. Chen YA, Choufani S, Ferreira JC, Grafodatskaya D, Butcher DT, Weksberg R. Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray. Genom 2011, 97(4):214-222.
40. Jacques PF, Sulsky SI, Sadowski JA, Phillips JC, Rush D, Willett WC. Comparison of micronutrient intake measured by a dietary questionnaire and biochemical indicators of micronutrient status. Am J Clin Nutr 1993, 57(2):182-189.
41. Selhub J, Jacques PF, Wilson PW, Rush D, Rosenberg IH. Vitamin status and intake as primary determinants of homocysteinemia in an elderly population. JAMA 1993, 270(22):2693-2698. 10.1001/jama.1993.03510220049033, 8133587.
42. Herbert V. Recommended dietary intakes (RDI) of folate in humans. Am J Clin Nutr 1987, 45(4):661-670.
43. Kleiber C, Zeileis A. Applied Econometrics with R 2008, New York: Springer-Verlag.
44. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC genome browser database: update 2011. Nucleic Acids Res 2011, 39:D876-D882. Database issue, 10.1093/nar/gkq963, 3242726, 20959295.
45. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23(2):257-258. 10.1093/bioinformatics/btl567, 17098774.
46. Ogino S, Wilson RB. Genotype and haplotype distributions of MTHFR677C > T and 1298A > C single nucleotide polymorphisms: a meta-analysis. J Hum Genet 2003, 48(1):1-7. 10.1007/s100380300000, 12560871.
47. Relton CL, Wilding CS, Laffling AJ, Jonas PA, Burgess T, Binks K, Tawn EJ, Burn J. Low erythrocyte folate status and polymorphic variation in folate-related genes are associated with risk of neural tube defect pregnancy. Mol Genet Metab 2004, 81(4):273-281. 10.1016/j.ymgme.2003.12.010, 15059614.
48. Castro R, Rivera I, Ravasco P, Jakobs C, Blom HJ, Camilo ME, de Almeida IT. 5,10-Methylenetetrahydrofolate reductase 677C- > T and 1298A- > C mutations are genetic determinants of elevated homocysteine. QJM 2003, 96(4):297-303. 10.1093/qjmed/hcg039, 12651974.
49. Bailey LB, Gregory JF. Polymorphisms of methylenetetrahydrofolate reductase and other enzymes: metabolic significance, risks and impact on folate requirement. J Nutr 1999, 129(5):919-922.
50. Relton CL, Pearce MS, Burn J, Parker L. An investigation of folate-related genetic factors in the determination of birthweight. Epidemiol 2005, 19(5):360-367.
51. Burgess S, Thompson SG. Bias in causal estimates from Mendelian randomization studies with weak instruments. Stat Med 2011, 30(11):1312-1323. 10.1002/sim.4197, 21432888.
52. Chen LS, Emmert-Streib F, Storey JD. Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol 2007, 8(10):R219. 10.1186/gb-2007-8-10-r219, 2246293, 17931418.
53. Millstein J, Zhang B, Zhu J, Schadt EE. Disentangling molecular relationships with a causal inference test. BMC Genet 2009, 10(1):23. 10.1186/1471-2156-10-23, 3224661, 19473544.
54. Houseman EA, Accomando W, Koestler D, Christensen B, Marsit C, Nelson H, Wiencke J, Kelsey K. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinforma 2012, 13:86.