Replication and exploratory analysis of 24 candidate risk polymorphisms for neural tube defects

BMC Medical Genetics

Volumn 15, Issue 1, 2014, Pages

  Pangilinan, Faith ^a   Molloy, Anne M ^b   Mills, James L ^c   Troendle, James F ^d   Parle McDermott, Anne ^e   Kay, Denise M ^f   Browne, Marilyn L ^g,h   McGrath, Emily C ^f   Abaan, Hatice O ^a   Sutton, Marie ⁱ   Kirke, Peadar N ⁱ   Caggana, Michele ^f   Shane, Barry ^j   Scott, John M ^b   Brody, Lawrence C ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b TRINITY COLLEGE DUBLIN   (Ireland)

^c EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^d NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^e DUBLIN CITY UNIVERSITY   (Ireland)

^f WADSWORTH CENTER   (United States)

^g NEW YORK STATE DEPARTMENT OF HEALTH   (United States)

^h UNIVERSITY AT ALBANY   (United States)

ⁱ HEALTH RESEARCH BOARD   (Ireland)

^j UNIVERSITY OF CALIFORNIA   (United States)

more..

Author keywords

Folate; Folic acid; Neural tube defects; One carbon metabolism; Replication; Spina bifida

Indexed keywords

ADENOSINE DEAMINASE; ALCOHOL DEHYDROGENASE; CATECHOL METHYLTRANSFERASE; DNA METHYLTRANSFERASE 3B; FOLIC ACID; GENOMIC DNA; METHYLENETETRAHYDROFOLATE DEHYDROGENASE; TRANSCRIPTION FACTOR AP 2; 5 METHYLTETRAHYDROFOLATE HOMOCYSTEINE METHYLTRANSFERASE; ADA PROTEIN, HUMAN; ALDH1A2 PROTEIN, HUMAN; ARID1A PROTEIN, HUMAN; MTR PROTEIN, HUMAN; NUCLEAR PROTEIN; RETINAL DEHYDROGENASE; TRANSCRIPTION FACTOR;

AFRICAN AMERICAN; ALLELE; ANENCEPHALUS; ARTICLE; CARBON METABOLISM; CONGENITAL MALFORMATION; ENCEPHALOCELE; GENE LINKAGE DISEQUILIBRIUM; GENETIC MODEL; GENETIC RISK; GENOTYPE; HEREDITY; HISPANIC; HUMAN; HYDROCEPHALUS; MAJOR CLINICAL STUDY; METABOLISM; NATIONAL HEALTH ORGANIZATION; NEURAL TUBE; NEURAL TUBE DEFECT; NEWBORN SCREENING; OCCULT SPINAL DYSRAPHISM; RANDOM SAMPLE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM; SPINAL DYSRAPHISM; UNITED KINGDOM; UNITED STATES; ASIAN CONTINENTAL ANCESTRY GROUP; CAUCASIAN; ETHNOLOGY; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS;

5-METHYLTETRAHYDROFOLATE-HOMOCYSTEINE S-METHYLTRANSFERASE; ADENOSINE DEAMINASE; AFRICAN AMERICANS; ASIAN CONTINENTAL ANCESTRY GROUP; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GREAT BRITAIN; HUMANS; NEURAL TUBE DEFECTS; NEW YORK; NUCLEAR PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; RETINAL DEHYDROGENASE; TRANSCRIPTION FACTORS;

EID: 84908075516     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/s12881-014-0102-9     Document Type: Article

References (62)

1. Canfield MA, Honein MA, Yuskiv N, Xing J, Mai CT, Collins JS, Devine O, Petrini J, Ramadhani TA, Hobbs CA, Kirby RS. National estimates and race/ethnic-specific variation of selected birth defects in the United States, 1999-2001. Birth Defects Res A Clin Mol Teratol 2006, 76:747-756. 10.1002/bdra.20294, 17051527.
2. Botto LD, Lisi A, Bower C, Canfield MA, Dattani N, De Vigan C, De Walle H, Erickson DJ, Halliday J, Irgens LM, Lowry RB, McDonnell R, Metneki J, Poetzsch S, Ritvanen A, Robert-Gnansia E, Siffel C, Stoll C, Mastroiacovo P. Trends of selected malformations in relation to folic acid recommendations and fortification: an international assessment. Birth Defects Res A Clin Mol Teratol 2006, 76:693-705. 10.1002/bdra.20307, 17029289.
3. Berry RJ, Li Z, Erickson JD, Li S, Moore CA, Wang H, Mulinare J, Zhao P, Wong LY, Gindler J, Hong SX, Correa A. Prevention of neural-tube defects with folic acid in China. China-U.S. Collaborative Project for Neural Tube Defect Prevention. N Engl J Med 1999, 341:1485-1490. 10.1056/NEJM199911113412001, 10559448.
4. Blencowe H, Cousens S, Modell B, Lawn J. Folic acid to reduce neonatal mortality from neural tube disorders. Int J Epidemiol 2010, 39(Suppl 1):i110-i121. 10.1093/ije/dyq028, 20348114.
5. A Report from the International Clearinghouse for Birth Defects Monitoring Systems 1991, Elsevier Science Publishers, Amsterdam.
6. Busby A, Abramsky L, Dolk H, Armstrong B. Preventing neural tube defects in Europe: population based study. BMJ 2005, 330:574-575. 10.1136/bmj.330.7491.574, 15760997.
7. Botto LD, Lisi A, Robert-Gnansia E, Erickson JD, Vollset SE, Mastroiacovo P, Botting B, Cocchi G, de Vigan C, de Walle H, Feijoo M, Irgens LM, McDonnell B, Merlob P, Ritvanen A, Scarano G, Siffel C, Metneki J, Stoll C, Smithells R, Goujard J: International retrospective cohort study of neural tube defects in relation to folic acid recommendations: are the recommendations working?BMJ 2005, 330:571..
8. Cherian A, Seena S, Bullock RK, Antony AC. Incidence of neural tube defects in the least-developed area of India: a population-based study. Lancet 2005, 366:930-931. 10.1016/S0140-6736(05)67319-9, 16154020.
9. Rosenthal J, Casas J, Taren D, Alverson CJ, Flores A, Frias J. Neural tube defects in Latin America and the impact of fortification: a literature review. Public Health Nutr 2014, 17(3):537-550. 10.1017/S1368980013000256, 23464652.
10. Kirke PN, Molloy AM, Daly LE, Burke H, Weir DG, Scott JM. Maternal plasma folate and vitamin B12 are independent risk factors for neural tube defects. Q J Med 1993, 86:703-708. 8265769.
11. Prevention of neural tube defects: results of the Medical Research Council Vitamin Study. Lancet 1991, 338:131-137. 10.1016/0140-6736(91)90133-A.
12. Czeizel AE, Dudas I. Prevention of the first occurrence of neural-tube defects by periconceptional vitamin supplementation. N Engl J Med 1992, 327:1832-1835. 10.1056/NEJM199212243272602, 1307234.
13. 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, 10:111-113. 10.1038/ng0595-111, 7647779.
14. Botto LD, Yang Q. 5,10-Methylenetetrahydrofolate reductase gene variants and congenital anomalies: a HuGE review. Am J Epidemiol 2000, 151:862-877. 10.1093/oxfordjournals.aje.a010290, 10791559.
15. Zhang T, Lou J, Zhong R, Wu J, Zou L, Sun Y, Lu X, Liu L, Miao X, Xiong G: Genetic variants in the folate pathway and the risk of neural tube defects: a meta-analysis of the published literature.PLoS One 2013, 8:e59570..
16. Doudney K, Grinham J, Whittaker J, Lynch SA, Thompson D, Moore GE, Copp AJ, Greene ND, Stanier P. Evaluation of folate metabolism gene polymorphisms as risk factors for open and closed neural tube defects. Am J Med Genet A 2009, 149A:1585-1589. 10.1002/ajmg.a.32937, 19533788.
17. Brody LC, Conley M, Cox C, Kirke PN, McKeever MP, Mills JL, Molloy AM, O'Leary VB, Parle-McDermott A, Scott JM, Swanson DA. A polymorphism, R653Q, in the trifunctional enzyme methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase/formyltetrahydrofolate synthetase is a maternal genetic risk factor for neural tube defects: report of the Birth Defects Research Group. Am J Hum Genet 2002, 71:1207-1215. 10.1086/344213, 12384833.
18. De Marco P, Merello E, Calevo MG, Mascelli S, Raso A, Cama A, Capra V. Evaluation of a methylenetetrahydrofolate-dehydrogenase 1958G > A polymorphism for neural tube defect risk. J Hum Genet 2006, 51:98-103. 10.1007/s10038-005-0329-6, 16315005.
19. Parle-McDermott A, Kirke PN, Mills JL, Molloy AM, Cox C, O'Leary VB, Pangilinan F, Conley M, Cleary L, Brody LC, Scott JM. Confirmation of the R653Q polymorphism of the trifunctional C1-synthase enzyme as a maternal risk for neural tube defects in the Irish population. Eur J Hum Genet 2006, 14:768-772. 10.1038/sj.ejhg.5201603, 16552426.
20. van der Linden IJ, Heil SG, Kouwenberg IC, den Heijer M, Blom HJ. The methylenetetrahydrofolate dehydrogenase (MTHFD1) 1958G > A variant is not associated with spina bifida risk in the Dutch population. Clin Genet 2007, 72:599-600. 10.1111/j.1399-0004.2007.00904.x, 17894836.
21. Franke B, Vermeulen SH, Steegers-Theunissen RP, Coenen MJ, Schijvenaars MM, Scheffer H, den Heijer M, Blom HJ. An association study of 45 folate-related genes in spina bifida: Involvement of cubilin (CUBN) and tRNA aspartic acid methyltransferase 1 (TRDMT1). Birth Defects Res A Clin Mol Teratol 2009, 85:216-226. 10.1002/bdra.20556, 19161160.
22. Yang M, Yang L, Qi L, Guo Y, Lin X, Zhang Y, Du Y. Association between the methionine synthase A2756G polymorphism and neural tube defect risk: a meta-analysis. Gene 2013, 520:7-13. 10.1016/j.gene.2013.02.005, 23438943.
23. Morrison K, Papapetrou C, Hol FA, Mariman EC, Lynch SA, Burn J, Edwards YH. Susceptibility to spina bifida; an association study of five candidate genes. Ann Hum Genet 1998, 62:379-396. 10.1046/j.1469-1809.1998.6250379.x, 10088035.
24. Christensen B, Arbour L, Tran P, Leclerc D, Sabbaghian N, Platt R, Gilfix BM, Rosenblatt DS, Gravel RA, Forbes P, Rozen R. Genetic polymorphisms in methylenetetrahydrofolate reductase and methionine synthase, folate levels in red blood cells, and risk of neural tube defects. Am J Med Genet 1999, 84:151-157. 10.1002/(SICI)1096-8628(19990521)84:2<151::AID-AJMG12>3.0.CO;2-T, 10323741.
25. Akar N, Akar E, Deda G, Arsan S. Spina bifida and common mutations at the homocysteine metabolism pathway. Clin Genet 2000, 57:230-231. 10.1034/j.1399-0004.2000.570310.x, 10782931.
26. Johanning GL, Tamura T, Johnston KE, Wenstrom KD. Comorbidity of 5,10-methylenetetrahydrofolate reductase and methionine synthase gene polymorphisms and risk for neural tube defects. J Med Genet 2000, 37:949-951. 10.1136/jmg.37.12.949, 11186937.
27. De Marco P, Calevo MG, Moroni A, Arata L, Merello E, Finnell RH, Zhu H, Andreussi L, Cama A, Capra V. Study of MTHFR and MS polymorphisms as risk factors for NTD in the Italian population. J Hum Genet 2002, 47:319-324. 10.1007/s100380200043, 12111380.
28. Zhu H, Wicker NJ, Shaw GM, Lammer EJ, Hendricks K, Suarez L, Canfield M, Finnell RH. Homocysteine remethylation enzyme polymorphisms and increased risks for neural tube defects. Mol Genet Metab 2003, 78:216-221. 10.1016/S1096-7192(03)00008-8, 12649067.
29. Brouns R, Ursem N, Lindemans J, Hop W, Pluijm S, Steegers E, Steegers-Theunissen R. Polymorphisms in genes related to folate and cobalamin metabolism and the associations with complex birth defects. Prenat Diagn 2008, 28:485-493. 10.1002/pd.2006, 18435414.
30. De Marco P, Calevo MG, Moroni A, Merello E, Raso A, Finnell RH, Zhu H, Andreussi L, Cama A, Capra V. Reduced folate carrier polymorphism (80A- > G) and neural tube defects. Eur J Hum Genet 2003, 11:245-252. 10.1038/sj.ejhg.5200946, 12673279.
31. Wang HG, Wang JL, Zhang J, Zhao LX, Zhai GX, Xiang YZ, Chang P. Reduced folate carrier A80G polymorphism and susceptibility to neural tube defects: a meta-analysis. Gene 2012, 510:180-184. 10.1016/j.gene.2012.02.020, 22975209.
32. Relton CL, Wilding CS, Pearce MS, Laffling AJ, Jonas PA, Lynch SA, Tawn EJ, Burn J. Gene-gene interaction in folate-related genes and risk of neural tube defects in a UK population. J Med Genet 2004, 41:256-260. 10.1136/jmg.2003.010694, 15060097.
33. Shaw GM, Lammer EJ, Zhu H, Baker MW, Neri E, Finnell RH. Maternal periconceptional vitamin use, genetic variation of infant reduced folate carrier (A80G), and risk of spina bifida. Am J Med Genet 2002, 108:1-6. 10.1002/ajmg.10195, 11857541.
34. Johnson WG, Stenroos ES, Spychala JR, Chatkupt S, Ming SX, Buyske S. New 19 bp deletion polymorphism in intron-1 of dihydrofolate reductase (DHFR): a risk factor for spina bifida acting in mothers during pregnancy?. Am J Med Genet A 2004, 124A:339-345. 10.1002/ajmg.a.20505, 14735580.
35. Parle-McDermott A, Pangilinan F, Mills JL, Kirke PN, Gibney ER, Troendle J, O'Leary VB, Molloy AM, Conley M, Scott JM, Brody LC. The 19-bp deletion polymorphism in intron-1 of dihydrofolate reductase (DHFR) may decrease rather than increase risk for spina bifida in the Irish population. Am J Med Genet A 2007, 143A:1174-1180. 10.1002/ajmg.a.31725, 17486595.
36. van der Linden IJ, Nguyen U, Heil SG, Franke B, Vloet S, Gellekink H, den Heijer M, Blom HJ. Variation and expression of dihydrofolate reductase (DHFR) in relation to spina bifida. Mol Genet Metab 2007, 91:98-103. 10.1016/j.ymgme.2007.01.009, 17336564.
37. Valachis A, Mauri D, Neophytou C, Polyzos NP, Tsali L, Garras A, Papanikolau EG. Translational medicine and reliability of single-nucleotide polymorphism studies: can we believe in SNP reports or not?. Int J Med Sci 2011, 8:492-500. 10.7150/ijms.8.492, 21897762.
38. Munafo MR, Clark TG, Flint J. Assessing publication bias in genetic association studies: evidence from a recent meta-analysis. Psychiatry Res 2004, 129:39-44. 10.1016/j.psychres.2004.06.011, 15572183.
39. Dwan K, Altman DG, Arnaiz JA, Bloom J, Chan AW, Cronin E, Decullier E, Easterbrook PJ, Von Elm E, Gamble C, Ghersi D, Ioannidis JP, Simes J, Williamson PR: Systematic review of the empirical evidence of study publication bias and outcome reporting bias.PLoS One 2008, 3:e3081..
40. Kyzas PA, Denaxa-Kyza D, Ioannidis JP. Almost all articles on cancer prognostic markers report statistically significant results. Eur J Cancer 2007, 43:2559-2579. 10.1016/j.ejca.2007.08.030, 17981458.
41. Shaw GM, Lu W, Zhu H, Yang W, Briggs FB, Carmichael SL, Barcellos LF, Lammer EJ, Finnell RH: 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects.BMC Med Genet 2009, 10:49..
42. Lu W, Guzman AR, Yang W, Chapa CJ, Shaw GM, Greene RM, Pisano MM, Lammer EJ, Finnell RH, Zhu H: Genes encoding critical transcriptional activators for murine neural tube development and human spina bifida: a case-control study.BMC Med Genet 2010, 11:141..
43. Martinez CA, Northrup H, Lin JI, Morrison AC, Fletcher JM, Tyerman GH, Au KS. Genetic association study of putative functional single nucleotide polymorphisms of genes in folate metabolism and spina bifida. Am J Obstet Gynecol 2009, 201(394):e311-e391.
44. Carter TC, Pangilinan F, Troendle JF, Molloy AM, VanderMeer J, Mitchell A, Kirke PN, Conley MR, Shane B, Scott JM, Brody LC, Mills JL. Evaluation of 64 candidate single nucleotide polymorphisms as risk factors for neural tube defects in a large Irish study population. Am J Med Genet A 2011, 155A:14-21. 10.1002/ajmg.a.33755, 21204206.
45. Pangilinan F, Molloy AM, Mills JL, Troendle JF, Parle-McDermott A, Signore C, O'Leary VB, Chines P, Seay JM, Geiler-Samerotte K, Mitchell A, VanderMeer JE, Krebs KM, Sanchez A, Cornman-Homonoff J, Stone N, Conley M, Kirke PN, Shane B, Scott JM, Brody LC: Evaluation of common genetic variants in 82 candidate genes as risk factors for neural tube defects.BMC Med Genet 2012, 13:62..
46. Spielman RS, McGinnis RE, Ewens WJ. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 1993, 52:506-516. 8447318.
47. Pangilinan F, Mitchell A, VanderMeer J, Molloy AM, Troendle J, Conley M, Kirke PN, Sutton M, Sequeira JM, Quadros EV, Scott JM, Mills JL, Brody LC. Transcobalamin II receptor polymorphisms are associated with increased risk for neural tube defects. J Med Genet 2010, 47:677-685. 10.1136/jmg.2009.073775, 20577008.
48. Hol FA, van der Put NM, Geurds MP, Heil SG, Trijbels FJ, Hamel BC, Mariman EC, Blom HJ. Molecular genetic analysis of the gene encoding the trifunctional enzyme MTHFD (methylenetetrahydrofolate-dehydrogenase, methenyltetrahydrofolate-cyclohydrolase, formyltetrahydrofolate synthetase) in patients with neural tube defects. Clin Genet 1998, 53:119-125. 10.1111/j.1399-0004.1998.tb02658.x, 9611072.
49. Saavedra-Matiz CA, Isabelle JT, Biski CK, Duva SJ, Sweeney ML, Parker AL, Young AJ, Diantonio LL, Krein LM, Nichols MJ, Caggana M. Cost-effective and scalable DNA extraction method from dried blood spots. Clin Chem 2013, 59:1045-1051. 10.1373/clinchem.2012.198945, 23509109.
50. Browne ML, Carter TC, Kay DM, Kuehn D, Brody LC, Romitti PA, Liu A, Caggana M, Druschel CM, Mills JL. Evaluation of genes involved in limb development, angiogenesis, and coagulation as risk factors for congenital limb deficiencies. Am J Med Genet A 2012, 158A:2463-2472. 10.1002/ajmg.a.35565, 22965740.
51. Gorroochurn P, Hodge SE, Heiman GA, Durner M, Greenberg DA. Non-replication of association studies: " pseudo-failures" to replicate?. Genet Med 2007, 9:325-331. 10.1097/GIM.0b013e3180676d79, 17575498.
52. Zollner S, Pritchard JK. Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet 2007, 80:605-615. 10.1086/512821, 17357068.
53. Au KS, Ashley-Koch A, Northrup H. Epidemiologic and genetic aspects of spina bifida and other neural tube defects. Dev Disabil Res Rev 2010, 16:6-15. 10.1002/ddrr.93, 20419766.
54. Shaw GM, Rozen R, Finnell RH, Wasserman CR, Lammer EJ. Maternal vitamin use, genetic variation of infant methylenetetrahydrofolate reductase, and risk for spina bifida. Am J Epidemiol 1998, 148:30-37. 10.1093/oxfordjournals.aje.a009555, 9663401.
55. Volcik KA, Shaw GM, Zhu H, Lammer EJ, Laurent C, Finnell RH. Associations between polymorphisms within the thymidylate synthase gene and spina bifida. Birth Defects Res A Clin Mol Teratol 2003, 67:924-928. 10.1002/bdra.10029, 14745930.
56. Lupo PJ, Canfield MA, Chapa C, Lu W, Agopian AJ, Mitchell LE, Shaw GM, Waller DK, Olshan AF, Finnell RH, Zhu H. Diabetes and obesity-related genes and the risk of neural tube defects in the national birth defects prevention study. Am J Epidemiol 2012, 176:1101-1109. 10.1093/aje/kws190, 23132673.
57. Ubbink JB, Christianson A, Bester MJ, Van Allen MI, Venter PA, Delport R, Blom HJ, van der Merwe A, Potgieter H, Vermaak WJ. Folate status, homocysteine metabolism, and methylene tetrahydrofolate reductase genotype in rural South African blacks with a history of pregnancy complicated by neural tube defects. Metabolism 1999, 48:269-274. 10.1016/S0026-0495(99)90046-X, 10024094.
58. Yan L, Zhao L, Long Y, Zou P, Ji G, Gu A, Zhao P: Association of the maternal MTHFR C677T polymorphism with susceptibility to neural tube defects in offsprings: evidence from 25 case-control studies.PLoS One 2012, 7:e41689..
59. van der Put NM, Eskes TK, Blom HJ. Is the common 677C- > T mutation in the methylenetetrahydrofolate reductase gene a risk factor for neural tube defects? A meta-analysis. QJM 1997, 90:111-115. 10.1093/qjmed/90.2.111, 9068801.
60. Ouyang S, Li Y, Liu Z, Chang H, Wu J. Association between MTR A2756G and MTRR A66G polymorphisms and maternal risk for neural tube defects: a meta-analysis. Gene 2013, 515:308-312. 10.1016/j.gene.2012.11.070, 23266814.
61. van der Linden IJ, den Heijer M, Afman LA, Gellekink H, Vermeulen SH, Kluijtmans LA, Blom HJ. The methionine synthase reductase 66A > G polymorphism is a maternal risk factor for spina bifida. J Mol Med (Berl) 2006, 84:1047-1054. 10.1007/s00109-006-0093-x.
62. Ouyang S, Liu Z, Li Y, Wu J. Meta-analyses on the association of MTR A2756G and MTRR A66G polymorphisms with neural tube defect risks in Caucasian children. J Matern Fetal Neonatal Med 2013, 26(12):1166-1170. 10.3109/14767058.2013.777699, 23425389.