Roles of Genetic Polymorphisms in the Folate Pathway in Childhood Acute Lymphoblastic Leukemia Evaluated by Bayesian Relevance and Effect Size Analysis

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Lautner Csorba, Orsolya ^a   Gézsi, András ^a   Erdélyi, Dániel J ^b   Hullám, Gábor ^c   Antal, Péter ^c   Semsei, Ágnes F ^a   Kutszegi, Nóra ^a   Kovács, Gábor ^b   Falus, András ^a   Szalai, Csaba ^a,d,e  

^a SEMMELWEIS UNIVERSITY   (Hungary)

^b SEMMELWEIS UNIVERSITY   (Hungary)

^c BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

^d HEIM PÁL CHILDREN S HOSPITAL   (Hungary)

^e Csertex Research Laboratory   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

FOLIC ACID;

ABCB1 GENE; ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ARTICLE; B CELL LEUKEMIA; BAYES THEOREM; CANCER RISK; CANCER SURVIVAL; CHILD; CHILDHOOD LEUKEMIA; CONTROLLED STUDY; DHFR GENE; DIPLOIDY; EFFECT SIZE; FEMALE; FOLATE GENE; FPGS GENE; GENE; GENE FUNCTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC RISK; GGH GENE; HAPLOTYPE; HUMAN; HUNGARY; MAJOR CLINICAL STUDY; MALE; MTHFD1 GENE; MTR GENE; MTRR GENE; PRESCHOOL CHILD; SHMT1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SLC19A1 GENE; SLC22A8 GENE; SLCO1B1 GENE; SURVIVAL RATE; TPMT GENE; TYMS GENE;

ADOLESCENT; ADULT; BAYES THEOREM; CHILD; CHILD, PRESCHOOL; FEMALE; FOLIC ACID; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HAPLOTYPES; HUMANS; INFANT; MALE; METHYLENETETRAHYDROFOLATE DEHYDROGENASE (NADP); MIDDLE AGED; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; SURVIVAL RATE; YOUNG ADULT;

EID: 84881114492     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0069843     Document Type: Article

References (57)

1. Ansari M, Krajinovic M, (2007) Pharmacogenomics of acute leukemia. Pharmacogenomics 8: 817-834.
2. Krajinovic M, Labuda D, Sinnett D, (2001) Childhood acute lymphoblastic leukemia: Genetic determinants of susceptibility and disease outcome. Reviews on Environmental Health 16: 263-279.
3. Pui CH, (2000) Genetic studies in acute lymphoblastic leukemia. Acta Paediatrica Taiwanica 41: 303-307.
4. Zingg JM, Jones PA, (1997) Genetic and epigenetic aspects of DNA methylation on genome expression, evolution, mutation and carcinogenesis. Carcinogenesis 18: 869-882.
5. Küppers R, Klein U, Hansmann M-L, Rajewsky K, (1999) Cellular Origin of Human B-Cell Lymphomas. New England Journal of Medicine 341: 1520-1529.
6. Shane B, (1989) Folylpolyglutamate synthesis and role in the regulation of one-carbon metabolism. Vitamins and Hormones 45: 263-335.
7. Schwahn B, Rozen R, (2001) Polymorphisms in the methylenetetrahydrofolate reductase gene: clinical consequences. Am J Pharmacogenomics 1: 189-201.
8. Krajinovic M, Lamothe S, Labuda D, Lemieux-Blanchard É, Théorêt Y, et al. (2004) Role of MTHFR genetic polymorphisms in the susceptibility to childhood acute lymphoblastic leukemia. Blood 103: 252-257.
9. Krajinovic M, Lemieux-Blanchard É, Chiasson S, Primeau M, Costea I, et al. (2004) Role of polymorphism in MTHFR and MTHFD1 genes in the outcome of childhood acute lymphoblastic leukemia. Pharmacogenomics Journal 4: 66-72.
10. Krajinovic M, (2008) MTHFD1 gene: role in disease susceptibility and pharmacogenetics. Pharmacogenomics 9: 829-832.
11. Vijayakrishnan J, Houlston RS, (2010) Candidate gene association studies and risk of childhood acute lymphoblastic leukemia: a systematic review and meta-analysis. Haematologica 95: 1405-1414.
12. Han D, Shen C, Meng X, Bai J, Chen F, et al. (2012) Methionine synthase reductase A66G polymorphism contributes to tumor susceptibility: evidence from 35 case-control studies. Molecular Biology Reports 39: 805-816.
13. Zhong R, Liu L, Zou L, Sheng W, Zhu B, et al. (2013) Genetic variations in the TGFβ signaling pathway, smoking and risk of colorectal cancer in a Chinese population. Carcinogenesis 34: 936-942.
14. Liu L, Wu C, Wang Y, Zhong R, Wang F, et al. (2011) Association of candidate genetic variations with gastric cardia adenocarcinoma in Chinese population: a multiple interaction analysis. Carcinogenesis 32: 336-342.
15. Hahn LW, Ritchie MD, Moore JH, (2003) Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19: 376-382.
16. Antal P, Millinghoffer A, Hullám G, Hajós G, Szalai C, et al. (2010) A bioinformatic platform for a Bayesian, multiphased, multilevel analysis in immunogenomics. In: Flower D, Davies M, Ranganathan S, editors. Bioinformatics for Immunomics, Immunomics reviews. New York, USA: Springer. pp. 157-185.
17. Antal P, Millinghoffer A,33 Hullam G, Szalai C, Falus A (2008) A Bayesian view of challenges in feature selection: feature aggregation, multiple targets, redundancy and interaction. JMLR Workshop and Conference Proceedings: New challenges for feature selection in data mining and knowledge discovery. Antwerpen, Belgium. pp. 74-89.
18. Hullám G, Antal P, Szalai C, Falus A, (2010) Evaluation of a Bayesian model-based approach in GA studies. Journal of Machine Learning in Systems Biology, Workshop and Conference Proceedings 8: 30-43.
19. Hullam G, Antal P (2012) Estimation of effect size posterior using model averaging over Bayesian network structures and parameters. Proceedings of the Sixth European Workshop on Probabilistic Graphical Models. Granada, Spain. pp. 147-154.
20. Lautner-Csorba O, Gezsi A, Semsei A, Antal P, Edelyi D, et al. (2012) Candidate gene association study in pediatric acute lymphoblastic leukemia evaluated by Bayesian network based Bayesian multilevel analysis of relevance. BMC Medical Genomics 5: 42 doi:10.1186/1755-8794-1185-1142.
21. Ungvári I, Hullám G, Antal P, Kiszel P, Gézsi A, et al. (2012) Evaluation of a partial genome screening of two asthma susceptibility regions using Bayesian network based Bayesian multilevel analysis of relevance. PLoS ONE 7: e33573 doi:33510.31371/journal.pone.0033573.
22. Wiemels JL, Smith RN, Taylor GM, Eden OB, Alexander FE, et al. (2001) Methylenetetrahydrofolate reductase (MTHFR) polymorphisms and risk of molecularly defined subtypes of childhood acute leukemia. Proceedings of the National Academy of Sciences 98: 4004-4009.
23. de Deus DMV, de Lima ELS, Seabra Silva RM, Leite EP, Cartaxo Muniz MT, (2012) Influence of Methylenetetrahydrofolate Reductase C677T, A1298C, and G80A Polymorphisms on the Survival of Pediatric Patients with Acute Lymphoblastic Leukemia. Leukemia Research and Treatment 2012: 6.
24. Franco RF, Simões BP, Tone LG, Gabellini SM, Zago MA, et al. (2001) The methylenetetrahydrofolate reductase C677T gene polymorphism decreases the risk of childhood acute lymphocytic leukaemia. British Journal of Haematology 115: 616-618.
25. Pereira TV, Rudnicki M, Pereira AC, Pombo-de-Oliveira MS, Franco RF, (2006) 5,10-Methylenetetrahydrofolate Reductase Polymorphisms and Acute Lymphoblastic Leukemia Risk: A Meta-analysis. Cancer Epidemiology Biomarkers & Prevention 15: 1956-1963.
26. Lightfoot TJ, Johnston WT, Painter D, Simpson J, Roman E, et al. (2010) Genetic variation in the folate metabolic pathway and risk of childhood leukemia. Blood 115: 3923-3929.
27. Metayer C, Scélo G, Chokkalingam A, Barcellos L, Aldrich M, et al. (2011) Genetic variants in the folate pathway and risk of childhood acute lymphoblastic leukemia. Cancer Causes & Control 22: 1243-1258.
28. Carroll N, Pangilinan F, Molloy A, Troendle J, Mills J, et al. (2009) Analysis of the MTHFD1 promoter and risk of neural tube defects. Human Genetics 125: 247-256.
29. Yang L, Liu L, Wang J, Qiu L, Mi Y, et al. (2011) Polymorphisms in folate-related genes: impact on risk of adult acute lymphoblastic leukemia rather than pediatric in Han Chinese. Leukemia & Lymphoma 52: 1770-1776.
30. Chan JY-S, Ugrasena DG, Lum DW-K, Lu Y, Yeoh AE-J, (2011) Xenobiotic and folate pathway gene polymorphisms and risk of childhood acute lymphoblastic leukaemia in Javanese children. Hematological Oncology 29: 116-123.
31. Olteanu H, Munson T, Banerjee R, (2002) Differences in the Efficiency of Reductive Activation of Methionine Synthase and Exogenous Electron Acceptors between the Common Polymorphic Variants of Human Methionine Synthase Reductase†. Biochemistry 41: 13378-13385.
32. Erdelyi D, Kamory E, Csokay B, Andrikovics H, Tordai A, et al. (2008) Synergistic interaction of ABCB1 and ABCG2 polymorphisms predicts the prevalence of toxic encephalopathy during anticancer chemotherapy. Pharmacogenomics J 8: 321-327.
33. Semsei AF, Erdelyi DJ, Ungvari I, Kamory E, Csokay B, et al. (2008) Association of some rare haplotypes and genotype combinations in the MDR1 gene with childhood acute lymphoblastic leukaemia. Leukemia Research 32: 1214-1220.
34. Ongaro A, De Mattei M, Della Porta MG, Rigolin G, Ambrosio C, et al. (2009) Gene polymorphisms in folate metabolizing enzymes in adult acute lymphoblastic leukemia: effects on methotrexate-related toxicity and survival. Haematologica 94: 1391-1398.
35. de Jonge R, Hooijberg JH, van Zelst BD, Jansen G, van Zantwijk CH, et al. (2005) Effect of polymorphisms in folate-related genes on in vitro methotrexate sensitivity in pediatric acute lymphoblastic leukemia. Blood 106: 717-720.
36. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
37. Storey JD, (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64: 479-498.
38. Purcell S, Cherny SS, Sham PC, (2003) Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19: 149-150.
39. Ungvári I, Hullám G, Antal P, Kiszel P, Gézsi A, et al. (2012) Evaluation of a partial genome screening of two asthma susceptibility regions using Bayesian network based Bayesian multilevel analysis of relevance. PLoS ONE 7: e33573.
40. Hullam G, Antal P. Estimation of effect size posterior using model averaging over Bayesian network structures and parameters; 2012; Granada, Spain. pp. 147-154.
41. Lautner-Csorba O, Gezsi A, Semsei A, Antal P, Edelyi D, et al. (2012) Candidate gene association study in pediatric acute lymphoblastic leukemia evaluated by Bayesian network based Bayesian multilevel analysis of relevance. BMC Medical Genomics 5: 42.
42. Wiemels JL, Smith RN, Taylor GM, Eden OB, Alexander FE, et al. (2001) Methylenetetrahydrofolate reductase (MTHFR) polymorphisms and risk of molecularly defined subtypes of childhood acute leukemia. Proceedings of the National Academy of Sciences of the United States of America 98: 4004-4009.
43. Franco RF, Simoes BP, Tone LG, Gabellini SM, Zago MA, et al. (2001) The methylenetetrahydrofolate reductase C677T gene polymorphism decreases the risk of childhood acute lymphocytic leukaemia. British Journal of Haematology 115: 616-618.
44. Pereira TV, Rudnicki M, Pereira AC, Pombo-De-Oliveira MS, Franco RF, (2006) 5,10-Methylenetetrahydrofolate reductase polymorphisms and acute lymphoblastic leukemia risk: A meta-analysis. Cancer Epidemiology Biomarkers and Prevention 15: 1956-1963.
45. Assaraf Y, (2007) Molecular basis of antifolate resistance. Cancer and Metastasis Reviews 26: 153-181.
46. Gaughan DJ, Kluijtmans LAJ, Barbaux S, McMaster D, Young IS, et al. (2001) The methionine synthase reductase (MTRR) A66G polymorphism is a novel genetic determinant of plasma homocysteine concentrations. Atherosclerosis 157: 451-456.
47. Geisel J, Zimbelmann I, Schorr H, Knapp J, Bodis M, et al. (2001) Genetic defects as important factors for moderate hyperhomocysteinemia. Clin Chem Lab Med 39: 698-704.
48. O'Leary VB, Parle-McDermott A, Molloy AM, Kirke PN, Johnson Z, et al. (2002) MTRR and MTHFR polymorphism: Link to Down syndrome? American Journal of Medical Genetics 107: 151-155.
49. Shaw G, Lu W, Zhu H, Yang W, Briggs F, et al. (2009) 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. BMC Medical Genetics 10: 49.
50. Erdélyi DJ, Kamory E, Csokay B, Andrikovics H, Tordai A, et al. (2008) Synergistic interaction of ABCB1 and ABCG2 polymorphisms predicts the prevalence of toxic encephalopathy during anticancer chemotherapy. Pharmacogenomics Journal 8: 321-327.
51. Hullam G, Antal P, Szalai C, Falus A. Evaluation of a Bayesian model-based approach in GA studies. In: Džeroski S, Geurts P, Rousu J, editors; 2010; Ljubljana, Slovenia. pp. 30-43.
52. Sherborne AL, Hemminki K, Kumar R, Bartram CR, Stanulla M, et al. (2011) Rationale for an international consortium to sztudy inherited genetic susceptibility to childhood acute lymphoblastic leukemia. Haematologica 96: 1049-1054.
53. Sherborne AL, Hosking FJ, Prasad RB, Kumar R, Koehler R, et al. (2010) Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat Genet 42: 492-494.
54. Zhang G, Candelaria P, Mäkelä JM, Khoo S-K, Hayden MC, et al. (2011) Disparity of innate immunity-related gene effects on asthma and allergy on Karelia. Pediatric Allergy and Immunology 22: 621-630.
55. Semsei AF, Antal P, Szalai C, (2010) Strengths and weaknesses of gene association studies in childhood acute lymphoblastic leukemia. Leukemia Research 34: 269-271.
56. de Jonge R, Tissing WJE, Hooijberg JH, Jansen G, Kaspers GJL, et al. (2009) Polymorphisms in folate-related genes and risk of pediatric acute lymphoblastic leukemia. Blood 113: 2284-2289.
57. Genagrid Homepage. Available: http://redmine.genagrid.eu/projects/bayeseyedownload/wiki Accessed: 2013 Jun 20.