Periconceptional folate consumption is associated with neonatal DNA methylation modifications in neural crest regulatory and cancer development genes

Epigenetics

Volumn 10, Issue 12, 2015, Pages 1166-1176

  Gonseth, Semira ^a   Roy, Ritu ^b   Houseman, E Andres ^c   de Smith, Adam J ^a   Zhou, Mi ^a   Lee, Seung Tae ^d   Nusslé, Sébastien ^e   Singer, Amanda W ^e   Wrensch, Margaret R ^a   Metayer, Catherine ^e   Wiemels, Joseph L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c OREGON STATE UNIVERSITY   (United States)

^d Yonsei University College of Medicine   (South Korea)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cancer prevention; developmental origin of health and disease; DNA methylation; epigenetics; folate; neural tube defects

Indexed keywords

CYSTINE; FOLIC ACID; ZINC FINGER PROTEIN; CYS1 PROTEIN, HUMAN; MEMBRANE PROTEIN; STX11 PROTEIN, HUMAN; SYNTAXIN; TFAP2A PROTEIN, HUMAN; TRANSCRIPTION FACTOR AP 2;

ARTICLE; CONTROLLED STUDY; CPG ISLAND; CYS1 GENE; DNA METHYLATION; DNA MODIFICATION; DNA REPLICATION; EPIGENETICS; FEMALE; FOOD FREQUENCY QUESTIONNAIRE; GENE; GENE EXPRESSION; HUMAN; MALE; NEURAL TUBE DEFECT; STX11 GENE; TFAP2A GENE; DIETARY SUPPLEMENT; EMBRYOLOGY; FERTILIZATION; FOLIC ACID DEFICIENCY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NEURAL CREST; NEWBORN; PREGNANCY; PRENATAL EXPOSURE; RETROSPECTIVE STUDY; TIME FACTOR; TUMOR GENE;

DIETARY SUPPLEMENTS; DNA METHYLATION; EPIGENOMICS; FEMALE; FERTILIZATION; FOLIC ACID; FOLIC ACID DEFICIENCY; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, NEOPLASM; HUMANS; INFANT, NEWBORN; MEMBRANE PROTEINS; NEURAL CREST; NEURAL TUBE DEFECTS; PREGNANCY; PRENATAL EXPOSURE DELAYED EFFECTS; QA-SNARE PROTEINS; RETROSPECTIVE STUDIES; TIME FACTORS; TRANSCRIPTION FACTOR AP-2;

EID: 84961572509     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.1080/15592294.2015.1117889     Document Type: Article

References (75)

1. H.J.Blom, G.M.Shaw, M.den Heijer, R.H.Finnell. Neural tube defects and folate: case far from closed. Nat Rev Neurosci 2006; 7:724-31; PMID:16924261; http://dx.doi.org/10.1038/nrn1986
2. P.A.Mossey, J.Little, R.G.Munger, M.J.Dixon, W.C.Shaw. Cleft lip and palate. Lancet 2009; 374:1773-85; PMID:19747722; http://dx.doi.org/10.1016/S0140-6736(09)60695-4
3. S.Hernández-Díaz, M.M.Werler, A.M.Walker, A.A.Mitchell. Folic Acid Antagonists during Pregnancy and the Risk of Birth Defects. N Engl J Med 2000; 343:1608-14; http://dx.doi.org/10.1056/NEJM200011303432204
4. C.Metayer, E.Milne, J.D.Dockerty, J.Clavel, M.S.Pombo-de-Oliveira, C.Wesseling, L.G.Spector, J.Schüz, E.Petridou, S.Ezzat, et al. Maternal Supplementation with Folic Acid and Other Vitamins and Risk of Leukemia in Offspring: A Childhood Leukemia International Consortium Study. Epidemiol Camb Mass 2014; 25:811-22; http://dx.doi.org/10.1097/EDE.0000000000000141
5. A.E.Beaudin, P.J.Stover. Folate-mediated one-carbon metabolism and neural tube defects: Balancing genome synthesis and gene expression. Birth Defects Res. Part C Embryo Today Rev 2007; 81:183-203; http://dx.doi.org/10.1002/bdrc.20100
6. E.Alonso-Aperte, N.Ubeda, M.Achon, J.Perez-Miguelsanz, G.Varela-Moreiras. Impaired methionine synthesis and hypomethylation in rats exposed to valproate during gestation. Neurol March 10 1999 1999; 52:750-6
7. R.H.Finnell, O.Spiegelstein, B.Wlodarczyk, A.Triplett, I.P.Pogribny, S.Melnyk, J.S.James. DNA Methylation in Folbp1 Knockout Mice Supplemented with Folic Acid during Gestation. J Nutr 2002; 132:2457S-61S; PMID:12163711
8. R.A.Waterland, R.L.Jirtle. Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation. Mol Cell Biol 2003; 23:5293-300; http://dx.doi.org/10.1128/MCB.23.15.5293-5300.2003
9. K.A.Lillycrop, E.S.Phillips, A.A.Jackson, M.A.Hanson, G.C.Burdge. Dietary Protein Restriction of Pregnant Rats Induces and Folic Acid Supplementation Prevents Epigenetic Modification of Hepatic Gene Expression in the Offspring. J Nutr 2005; 135:1382-6; PMID:15930441
10. R.A.Waterland, D.C.Dolinoy, J.R.Lin, C.A.Smith, X.Shi, K.G.Tahiliani. Maternalmethyl supplements increase offspring DNA methylation at Axin fused. Genesis 2006; 44:401-6; PMID:16868943; http://dx.doi.org/10.1002/dvg.20230
11. C.A.Maloney, S.M.Hay, W.D.Rees. Folate deficiency during pregnancy impacts on methyl metabolism without affecting global DNA methylation in the rat fetus. Br J Nutr 2007; 97:1090-8; PMID:17433124; http://dx.doi.org/10.1017/S0007114507670834
12. D.C.Dolinoy, D.Huang, R.L.Jirtle. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc Natl Acad Sci USA 2007; 104:13056-61; PMID:17670942; http://dx.doi.org/10.1073/pnas.0703739104
13. K.D.Sinclair, C.Allegrucci, R.Singh, D.S.Gardner, S.Sebastian, J.Bispham, A.Thurston, J.F.Huntley, W.D.Rees, C.A.Maloney, et al. DNA methylation, insulin resistance, and blood pressure in offspring determined by maternal periconceptional B vitamin and methionine status. Proc Natl Acad Sci USA 2007; 104:19351-6; PMID:18042717; http://dx.doi.org/10.1073/pnas.0707258104
14. K.A.Lillycrop, E.S.Phillips, C.Torrens, M.A.Hanson, A.A.Jackson, G.C.Burdge. Feeding pregnant rats a protein-restricted diet persistently alters the methylation of specific cytosines in the hepatic PPAR? promoter of the offspring. Br J Nutr 2008; 100:278-82; PMID:18186951; http://dx.doi.org/10.1017/S0007114507894438
15. J.M.Kim, K.Hong, J.H.Lee, S.Lee, N.Chang. Effect of folate deficiency on placental DNA methylation in hyperhomocysteinemic rats. J Nutr Biochem 2009; 20:172-6; PMID:18547797; http://dx.doi.org/10.1016/j.jnutbio.2008.01.010
16. A.K.Lawrance, L.Deng, R.Rozen. Methylenetetrahydrofolate reductase deficiency and low dietary folate reduce tumorigenesis in Apcmin/+ mice. Gut 2009; 58:805-11; PMID:19174418; http://dx.doi.org/10.1136/gut.2007.143107
17. L.Gong, Y.X.Pan, H.Chen. Gestational low protein diet in the rat mediates Igf2 gene expression in male offspring via altered hepatic DNA methylation. Epigenetics Off J DNA Methylation Soc 2010; 5:619-26; http://dx.doi.org/10.4161/epi.5.7.12882
18. C.Downing, T.E.Johnson, C.Larson, T.I.Leakey, R.N.Siegfried, T.M.Rafferty, C.A.Cooney. Subtle Decreases in DNA Methylation and Gene Expression at the Mouse Igf2 Locus Following Prenatal Alcohol Exposure: Effects of a Methyl-Supplemented Diet. Alcohol Fayettev N 2011; 45:65-71; http://dx.doi.org/10.1016/j.alcohol.2010.07.006
19. T.D.Schaible, R.A.Harris, S.E.Dowd, C.W.Smith, R.Kellermayer. Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes. Hum Mol Genet 2011; 20:1687-96; PMID:21296867; http://dx.doi.org/10.1093/hmg/ddr044
20. A.Kulkarni, K.Dangat, A.Kale, P.Sable, P.Chavan-Gautam, S.Joshi. Effects of Altered Maternal Folic Acid, Vitamin B12 and Docosahexaenoic Acid on Placental Global DNA Methylation Patterns in Wistar Rats. PLoS One 2011; 6:e17706; PMID:21423696; http://dx.doi.org/10.1371/journal.pone.0017706
21. A.Chmurzynska, M.Stachowiak, E.Pruszynska-Oszmalek. Maternal protein and folic acid intake during gestation does not program leptin transcription or serum concentration in rat progeny. Genes Nutr 2012; 7:217-22; PMID:21735287; http://dx.doi.org/10.1007/s12263-011-0239-5
22. W.N.Cooper, B.Khulan, S.Owens, C.E.Elks, V.Seidel, A.M.Prentice, G.Belteki, K.K.Ong, N.A.Affara, M.Constância, et al. DNA methylation profiling at imprinted loci after periconceptional micronutrient supplementation in humans: results of a pilot randomized controlled trial. FASEB J 2012; 26:1782-90; PMID:22267336; http://dx.doi.org/10.1096/fj.11-192708
23. P.Dominguez-Salas, S.E.Moore, M.S.Baker, A.W.Bergen, S.E.Cox, R.A.Dyer, A.J.Fulford, Y.Guan, E.Laritsky, M.J.Silver, et al. Maternal nutrition at conception modulates DNA methylation of human metastable epialleles. Nat Commun 2014; 5:3746; PMID:24781383; http://dx.doi.org/10.1038/ncomms4746
24. A.A.Fryer, T.M.Nafee, K.M.K.Ismail, W.D.Carroll,, R.D.Emes, W.E.Farrell. LINE-1 DNA methylation is inversely correlated with cord plasma homocysteine in man: a preliminary study. Epigenetics 2009; 4:394-8; PMID:19755846; http://dx.doi.org/10.4161/epi.4.6.9766
25. A.A.Fryer, R.D.Emes, K.M.Ismail, K.E.Haworth, C.Mein, W.D.Carroll, W.E.Farrell. Quantitative, high-resolution epigenetic profiling of CpG loci identifies associations with cord blood plasma homocysteine and birth weight in humans. Epigenetics 2011; 6:86-94; PMID:20864804; http://dx.doi.org/10.4161/epi.6.1.13392
26. R.P.Steegers-Theunissen, S.A.Obermann-Borst, D.Kremer, J.Lindemans, C.Siebel, E.A.Steegers, P.E.Slagboom, B.T.Heijmans. Periconceptional Maternal Folic Acid Use of 400 µg per Day Is Related to Increased Methylation of the IGF2 Gene in the Very Young Child. PLoS One 2009; 4:e7845; PMID:19924280; http://dx.doi.org/10.1371/journal.pone.0007845
27. Y.Ba, H.Yu, F.Liu, X.Geng, C.Zhu,, Q.Zhu,, T.Zheng,, S.Ma,, G.Wang,, Z.Li,, et al. Relationship of folate, vitamin B12 and methylation of insulin-like growth factor-II in maternal and cord blood. Eur J Clin Nutr 2011; 65:480-5; PMID:21245875; http://dx.doi.org/10.1038/ejcn.2010.294
28. H.Chang, T.Zhang, Z.Zhang, R.Bao, C.Fu, Z.Wang, Y.Bao, Y.Li, L.Wu, X.Zheng. Tissue-specific distribution of aberrant DNA methylation associated with maternal low-folate status in human neural tube defects. J Nutr Biochem 2011; 22:1172-7; PMID:21333513; http://dx.doi.org/10.1016/j.jnutbio.2010.10.003
29. C.Hoyo, A.P.Murtha, J.M.Schildkraut, R.Jirtle, W.Demark-Wahnefried, M.R.Forman, E.S.Iversen, J.Kurtzberg, F.Overcash, Z.Huang, et al. Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy. Epigenetics 2011; 6:928-36; PMID:21636975; http://dx.doi.org/10.4161/epi.6.7.16263
30. J.A.McKay, A.Groom, C.Potter, L.J.Coneyworth, D.Ford, J.C.Mathers, C.L.Relton. Genetic and Non-Genetic Influences during Pregnancy on Infant Global and Site Specific DNA Methylation: Role for Folate Gene Variants and Vitamin B12. Plos One 2012; 7:e33290; PMID:22479380; http://dx.doi.org/10.1371/journal.pone.0033290
31. P.Haggarty, G.Hoad, D.M.Campbell, G.W.Horgan, C.Piyathilake, G.McNeill. Folate in pregnancy and imprinted gene and repeat element methylation in the offspring. Am J Clin Nutr 2013; 97:94-9; PMID:23151531; http://dx.doi.org/10.3945/ajcn.112.042572
32. Y.J.Loke, J.C.Galati, R.Morley, E.J.H.Joo, B.Novakovic, X.Li, B.Weinrich, N.Carson, M.Ollikainen, H.K.Ng, et al Association of maternal and nutrient supply line factors with DNA methylation at the imprinted IGF2/H19 locus in multiple tissues of newborn twins. Epigenetics 2013; 8:1069-79; PMID:23917818; http://dx.doi.org/10.4161/epi.25908
33. K.S.Crider, T.P.Yang, R.J.Berry, L.B.Bailey, Folate and DNA methylation: a review of molecular mechanisms and the evidence for folate's role. Adv Nutr Int Rev J 2012; 3:21-38; http://dx.doi.org/10.3945/an.111.000992
34. M.Amarasekera, D.Martino, S.Ashley, H.Harb, D.Kesper, D.Strickland, R.Saffery, S.L.Prescott. Genome-wide DNA methylation profiling identifies a folate-sensitive region of differential methylation upstream of ZFP57-imprinting regulator in humans. FASEB J 2014; 28(9):4068-76; PMID:24891518; http://dx.doi.org/10.1096/fj.13-249029
35. G.Kelsey. Epigenome Changes During Development. In Epigenetic Epidemiology. Springer US, pp. 2012; 77-103
36. V.K.Rakyan, M.E.Blewitt, R.Druker, J.I.Preis, E.Whitelaw. Metastable epialleles in mammals. Trends Genet 2002; 18:348-51; PMID:12127774; http://dx.doi.org/10.1016/S0168-9525(02)02709-9
37. M.E.Price, A.M.Cotton, L.L.Lam, P.Farré, E.Emberly, C.J.Brown, W.P.Robinson, M.S.Kobor. Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin 2013; 6:4-4; PMID:23452981; http://dx.doi.org/10.1186/1756-8935-6-4
38. Y.Chen, M.Lemire, S.Choufani, D.T.Butcher, D.Grafodatskaya, B.W.Zanke, S.Gallinger, T.J.Hudson, R.Weksberg. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 2013; 8:203-9; PMID:23314698; http://dx.doi.org/10.4161/epi.23470
39. B.Karin. Michels Epigenetic Epidemiology
40. P.H.Westfall. Resampling-based multiple testing: Examples and methods for p-value adjustment John Wiley & Sons 1993
41. H.Hernandez-Vargas, J.Castelino, M.J.Silver, P.Dominguez-Salas, M.P.Cros, G.Durand, F.L.Calvez-Kelm, A.M.Prentice, C.P.Wild, S.E.Moore, et al. Exposure to aflatoxin B1 in utero is associated with DNA methylation in white blood cells of infants in The Gambia. Int J Epidemiol 2015; 44(4):1238-48; PMID:25855716; http://dx.doi.org/10.1093/ije/dyv027
42. M.J.Silver, N.J.Kessler, B.J.Hennig, P.Dominguez-Salas, E.Laritsky, M.S.Baker, C.Coarfa, H.Hernandez-Vargas, J.M.Castelino, M.N.Routledge, et al. Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment. Genome Biol 2015; 16:118; PMID:26062908; http://dx.doi.org/10.1186/s13059-015-0660-y
43. P.Dominguez-Salas, S.E.Moore, D.Cole, K.A.da Costa, S.E.Cox, R.A.Dyer, A.J.Fulford, S.M.Innis, R.A.Waterland, S.H.Zeisel, et al. DNA methylation potential: dietary intake and blood concentrations of one-carbon metabolites and cofactors in rural African women. Am J Clin Nutr 2013; 97:1217-27; PMID:23576045; http://dx.doi.org/10.3945/ajcn.112.048462
44. A.Barrallo-Gimeno, J.Holzschuh, W.Driever, E.W.Knapik. Neural crest survival and differentiation in zebrafish depends on mont blanc/tfap2a gene function. Development 2004; 131:1463-77; PMID:14985255; http://dx.doi.org/10.1242/dev.01033
45. T.I.Meshcheryakova, R.A.Zinchenko, T.A.Vasilyeva, A.V.Marakhonov, S.S.Zhylina, N.V.Petrova, T.V.Kozhanova, M.S.Belenikin, A.N.Petrin, G.R.Mutovin. A Clinical and Molecular Analysis of Branchio-Oculo-Facial Syndrome Patients in Russia Revealed New Mutations in TFAP2A. Ann Hum Genet 2015; 79(2):148-52; PMID:25590586; http://dx.doi.org/10.1111/ahg.12098
46. C.Gerth-Kahlert, K.Williamson, M.Ansari, J.K.Rainger, V.Hingst, T.Zimmermann, S.Tech, R.F.Guthoff, V.van Heyningen, D.R.FitzPatrick. Clinical and mutation analysis of 51 probands with anophthalmia and/or severe microphthalmia from a single center. Mol Genet Genomic Med 2013; 1:15-31; PMID:24498598; http://dx.doi.org/10.1002/mgg3.2
47. C.Di, S.Liao, D.C.Adamson, T.J.Parrett, D.K.Broderick, Q.Shi, C.Lengauer, J.M.Cummins, V.E.Velculescu, D.W.Fults, et al. Identification of OTX2 as a Medulloblastoma Oncogene Whose Product can be Targeted by All-Trans Retinoic Acid. Cancer Res 2005; 65:919-24; PMID:15705891
48. H.Moritake, S.Kamimura, H.Nunoi, H.Nakayama, A.Suminoe, H.Inada, J.Inagaki, F.Yanai, Y.Okamoto, Y.Shinkoda, et al. Clinical characteristics and genetic analysis of childhood acute lymphoblastic leukemia with hemophagocytic lymphohistiocytosis: a Japanese retrospective study by the Kyushu–Yamaguchi Children's Cancer Study Group. Int J Hematol 2014; 100:70-8; PMID:24827398; http://dx.doi.org/10.1007/s12185-014-1591-1
49. X.Hou, M.Mrug, B.K.Yoder, E.J.Lefkowitz, G.Kremmidiotis, P.D'Eustachio, D.R.Beier, L.M.Guay-Woodford. Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney disease. J Clin Invest 2002; 109:533-40; PMID:11854326; http://dx.doi.org/10.1172/JCI0214099
50. X.Wang, R.C.Southard, C.D.Allred, D.R.Talbert, M.E.Wilson, M.W.Kilgore. MAZ drives tumor-specific expression of PPAR gamma 1 in breast cancer cells. Breast Cancer Res Treat 2008; 111:103-11; PMID:17902047; http://dx.doi.org/10.1007/s10549-007-9765-7
51. L.Jiao, Y.Li, D.Shen, C.Xu, L.Wang, G.Huang, L.Chen, Y.Yang, C.Yang, Y.Yu, et al. The prostate cancer-up-regulated Myc-associated zinc-finger protein (MAZ) modulates proliferation and metastasis through reciprocal regulation of androgen receptor. Med Oncol Northwood Lond Engl 2013; 30:570; http://dx.doi.org/10.1007/s12032-013-0570-3
52. Institute of Medicine (US) Standing Committee on the Scientific Evaluation of Dietary Reference Intakes and its Panel on Folate, O.B.V. 1998 Folate
53. C.E.Boeke, A.Baccarelli, K.P.Kleinman, H.H.Burris, A.A.Litonjua, S.L.Rifas-Shiman, L.Tarantini, M.W.Gillman. Gestational intake of methyl donors and global LINE-1 DNA methylation in maternal and cord blood. Epigenetics 2012; 7:253-60; PMID:22430801; http://dx.doi.org/10.4161/epi.7.3.19082
54. M.Aarabi, M.C.S.Gabriel, D.Chan, N.A.Behan, M.Caron, T.Pastinen, G.Bourque, A.J.MacFarlane, A.Zini, J.Trasler. High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism. Hum Mol Genet 2015; 24(22):6301-13; PMID:26307085; http://dx.doi.org/10.1093/hmg/ddv338
55. A.M.Branum, R.Bailey, B.J.Singer. Dietary Supplement Use and Folate Status during Pregnancy in the United States. J Nutr 2013; 143:486-92; PMID:23365107; http://dx.doi.org/10.3945/jn.112.169987
56. J.Sobell, G.Block, P.Koslowe, J.Tobin, R.Andres. Validation of a retrospective questionnaire assessing diet 10-15 years ago. Am J Epidemiol 1989; 130:173-87; PMID:2741904
57. A.E.Teschendorff, J.Zhuang, M.Widschwendter. Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics 2011; 27:1496-505; PMID:21471010; http://dx.doi.org/10.1093/bioinformatics/btr171
58. J.T.Leek, J.D.Storey. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 2007; 3:1724-35; PMID:17907809; http://dx.doi.org/10.1371/journal.pgen.0030161
59. R.D.Knight, S.Nair, S.S.Nelson, A.Afshar, Y.Javidan, R.Geisler, G.J.Rauch, T.F.Schilling. lockjaw encodes a zebrafish tfap2a required for early neural crest. Development 2003; 130:5755-68; PMID:14534133; http://dx.doi.org/10.1242/dev.00575
60. E.Milne, K.R.Greenop, C.Bower, M.Miller, F.M.Bockxmeer, R.J.van Scott, N.H.Klerk, L.J.de Ashton, N.G.Gottardo, B.K.Armstrong. Maternal Use of Folic Acid and Other Supplements and Risk of Childhood Brain Tumors. Cancer Epidemiol Biomarkers Prev 2012; 21:1933-41; PMID:22941336; http://dx.doi.org/10.1158/1055-9965.EPI-12-0803
61. X.Zhang, T.Inukai, K.Hirose, K.Akahane, I.Kuroda, H.Honna-Oshiro, K.Kagami, K.Goi, K.Nakamura, M.Kobayashi, et al. Oncogenic fusion E2A-HLF sensitizes t(17;19)-positive acute lymphoblastic leukemia to TRAIL-mediated apoptosis by upregulating the expression of death receptors. Leukemia 2012; 26:2483-93; PMID:22743623; http://dx.doi.org/10.1038/leu.2012.139
62. SP1 Sp1 transcription factor [Homo sapiens (human)] - Gene - NCBI
63. LEF1 lymphoid enhancer-binding factor 1 [Homo sapiens (human)] - Gene - NCBI
64. C.D.Jensen, G.Block, P.Buffler, X.Ma, S.Selvin, S.Month. Maternal dietary risk factors in childhood acute lymphoblastic leukemia (United States). Cancer Causes Control CCC 2004; 15:559-70; PMID:15280635; http://dx.doi.org/10.1023/B:CACO.0000036161.98734.17
65. J.P.Fortin, A.Labbe, M.Lemire, B.W.Zanke, T.J.Hudson, E.J.Fertig, C.M.Greenwood, K.D.Hansen. Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biol 2014; 15(12):503; PMID:25599564; http://dx.doi.org/10.1186/s13059-014-0503-2
66. J.E.Joo, E.M.Wong, L.Baglietto, C.H.Jung, H.Tsimiklis, D.J.Park, N.C.Wong, D.R.English, J.L.Hopper, G.Severi, et al. The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array. BMC Biotechnol 2013; 13:23; PMID:23497093; http://dx.doi.org/10.1186/1472-6750-13-23
67. E.A.Houseman, W.P.Accomando, D.C.Koestler, B.C.Christensen, C.J.Marsit, H.H.Nelson, J.K.Wiencke, K.T.Kelsey. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 2012; 13:86; PMID:22568884; http://dx.doi.org/10.1186/1471-2105-13-86
68. B.Devlin, K.Roeder. Genomic Control for Association Studies. Biometrics 1999; 55:997-1004; PMID:11315092; http://dx.doi.org/10.1111/j.0006-341X.1999.00997.x
69. R Core Team, R: A Language and Environment for Statistical Computing 2013
70. M.E.Ritchie, B.Phipson, D.Wu, Y.Hu, C.W.Law, W.Shi, G.K.Smyth. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015; 43(7):e47; PMID:25605792; http://dx.doi.org/10.1093/nar/gkv007
71. F.Hahne, S.Durinck, R.Ivanek, A.Mueller, S.Lianoglou, G.Tan, L.P.Gviz. Plotting data and annotation information along genomic coordinates
72. H.K.Gjessing. Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes 2015
73. Institute of Medicine (US) Standing Committee on the Scientific Evaluation of Dietary Reference Intakes and its Panel on Folate, Other B Vitamins, and Choline. Dietary Reference Intakes for Thiamin, Riboflavin, Niacin, Vitamin B6, Folate, Vitamin B12, Pantothenic Acid, Biotin, and Choline National Academies Press (US), Washington (DC) 1998
74. A.Subramanian, P.Tamayo, V.K.Mootha, S.Mukherjee, B.L.Ebert, M.A.Gillette, A.Paulovich, S.L.Pomeroy, T.R.Golub, E.S.Lander, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005; 102:15545-50; PMID:16199517; http://dx.doi.org/10.1073/pnas.0506580102
75. V.K.Mootha, C.M.Lindgren, K.F.Eriksson, A.Subramanian, S.Sihag, J.Lehar, P.Puigserver, E.Carlsson, M.Ridderstråle, E.Laurila, et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003; 34:267-73; PMID:12808457; http://dx.doi.org/10.1038/ng1180