1. BirdA (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6–21.
2. ListerR, PelizzolaM, DowenRH, HawkinsRD, HonG, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315–322.
3. RobertsonKD, WolffeAP (2000) DNA methylation in health and disease. Nat Rev Genet 1: 11–19.
4. ChongS, WhitelawE (2004) Epigenetic germline inheritance. Curr Opin Genet Dev 14: 692–696.
5. AnwayMD, CuppAS, UzumcuM, SkinnerMK (2005) Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science 308: 1466–1469.
6. KaminskyZA, TangT, WangSC, PtakC, OhGH, et al. (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 41: 240–245.
7. OllikainenM, SmithKR, JooEJ, NgHK, AndronikosR, et al. (2010) DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome. Hum Mol Genet 19: 4176–4188.
8. ZhangD, ChengL, BadnerJA, ChenC, ChenQ, et al. (2010) Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet 86: 411–419.
9. GibbsJR, van der BrugMP, HernandezDG, TraynorBJ, NallsMA, et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: e1000952.
10. NumataS, YeT, HydeTM, Guitart-NavarroX, TaoR, et al. (2012) DNA methylation signatures in development and aging of the human prefrontal cortex. Am J Hum Genet 90: 260–272.
11. DrongAW, NicholsonG, HedmanAK, MeduriE, GrundbergE, et al. (2013) The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue. PLoS One 8: e55923.
12. GrundbergE, MeduriE, SandlingJK, HedmanAK, KeildsonS, et al. (2013) Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet 93: 876–890.
13. Gutierrez-ArcelusM, LappalainenT, MontgomerySB, BuilA, OngenH, et al. (2013) Passive and active DNA methylation and the interplay with genetic variation in gene regulation. eLife 2: e00523.
14. WagnerJR, BuscheS, GeB, KwanT, PastinenT, et al. (2014) The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol 15: R37.
15. BarrettJC, ClaytonDG, ConcannonP, AkolkarB, CooperJD, et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 41: 703–707.
16. BradfieldJP, QuHQ, WangK, ZhangH, SleimanPM, et al. (2011) A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. PLoS Genet 7: e1002293.
17. BurrenOS, AdlemEC, AchuthanP, ChristensenM, CoulsonRM, et al. (2011) T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. Nucleic Acids Res 39: D997–1001.
18. FungEY, SmythDJ, HowsonJM, CooperJD, WalkerNM, et al. (2009) Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus. Genes Immun 10: 188–191.
19. GrantSF, QuHQ, BradfieldJP, MarchandL, KimCE, et al. (2009) Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Diabetes 58: 290–295.
20. GroopL, PociotF (2013) Genetics of diabetes - Are we missing the genes or the disease? Mol Cell Endocrinol 382: 726–739.
21. HakonarsonH, GrantSF, BradfieldJP, MarchandL, KimCE, et al. (2007) A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature 448: 591–594.
22. LoweCE, CooperJD, BruskoT, WalkerNM, SmythDJ, et al. (2007) Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes. Nat Genet 39: 1074–1082.
23. PociotF, AkolkarB, ConcannonP, ErlichHA, JulierC, et al. (2010) Genetics of type 1 diabetes: what's next? Diabetes 59: 1561–1571.
24. QuHQ, GrantSF, BradfieldJP, KimC, FrackeltonE, et al. (2009) Association of RASGRP1 with type 1 diabetes is revealed by combined follow-up of two genome-wide studies. J Med Genet 46: 553–554.
25. SaxenaR, VoightBF, LyssenkoV, BurttNP, de BakkerPI, et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316: 1331–1336.
26. ScottLJ, MohlkeKL, BonnycastleLL, WillerCJ, LiY, et al. (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316: 1341–1345.
27. SladekR, RocheleauG, RungJ, DinaC, ShenL, et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445: 881–885.
28. SteinthorsdottirV, ThorleifssonG, ReynisdottirI, BenediktssonR, JonsdottirT, et al. (2007) A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. Nat Genet 39: 770–775.
29. ZegginiE, WeedonMN, LindgrenCM, FraylingTM, ElliottKS, et al. (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316: 1336–1341.
30. ProkopenkoI, PoonW, MagiR, PrasadBR, SalehiSA, et al. (2014) A central role for GRB10 in regulation of islet function in man. PLoS Genet 10: e1004235.
31. VoightBF, ScottLJ, SteinthorsdottirV, MorrisAP, DinaC, et al. (2010) Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 42: 579–589.
32. MillsteinJ, ZhangB, ZhuJ, SchadtEE (2009) Disentangling molecular relationships with a causal inference test. BMC Genet 10: 23.
33. ChenYA, LemireM, ChoufaniS, ButcherDT, GrafodatskayaD, et al. (2013) Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 8: 203–209.
34. DoiA, ParkIH, WenB, MurakamiP, AryeeMJ, et al. (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41: 1350–1353.
35. IrizarryRA, Ladd-AcostaC, WenB, WuZ, MontanoC, et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: 178–186.
36. LindgrenCM, MahtaniMM, WidenE, McCarthyMI, DalyMJ, et al. (2002) Genomewide search for type 2 diabetes mellitus susceptibility loci in Finnish families: the Botnia study. American journal of human genetics 70: 509–516.
37. PociotF, McDermottMF (2002) Genetics of type 1 diabetes mellitus. Genes Immun 3: 235–249.
38. ShiinaT, InokoH, KulskiJK (2004) An update of the HLA genomic region, locus information and disease associations: 2004. Tissue Antigens 64: 631–649.
39. BibikovaM, BarnesB, TsanC, HoV, KlotzleB, et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics 98: 288–295.
40. YangBT, DayehTA, VolkovPA, KirkpatrickCL, MalmgrenS, et al. (2012) Increased DNA methylation and decreased expression of PDX-1 in pancreatic islets from patients with type 2 diabetes. Mol Endocrinol 26: 1203–1212.
41. SandoviciI, SmithNH, NitertMD, Ackers-JohnsonM, Uribe-LewisS, et al. (2011) Maternal diet and aging alter the epigenetic control of a promoter-enhancer interaction at the Hnf4a gene in rat pancreatic islets. Proc Natl Acad Sci U S A 108: 5449–5454.
42. ParkerSC, StitzelML, TaylorDL, OrozcoJM, ErdosMR, et al. (2013) Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A 110: 17921–17926.
43. PasqualiL, GaultonKJ, Rodriguez-SeguiSA, MularoniL, Miguel-EscaladaI, et al. (2014) Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet 46: 136–143.
44. BirdA (2007) Perceptions of epigenetics. Nature 447: 396–398.
45. GiladY, RifkinSA, PritchardJK (2008) Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 24: 408–415.
46. MantelN (1967) The detection of disease clustering and a generalized regression approach. Cancer research 27: 209–220.
47. BekrisLM, ShephardC, PetersonM, HoehnaJ, Van YserlooB, et al. (2005) Glutathione-s-transferase M1 and T1 polymorphisms and associations with type 1 diabetes age-at-onset. Autoimmunity 38: 567–575.
48. CircuML, AwTY (2008) Glutathione and apoptosis. Free Radic Res 42: 689–706.
49. RobertsonRP, HarmonJS (2007) Pancreatic islet beta-cell and oxidative stress: the importance of glutathione peroxidase. FEBS Lett 581: 3743–3748.
50. HarashimaSI, HarashimaC, NishimuraT, HuY, NotkinsAL (2007) Overexpression of the autoantigen IA-2 puts beta cells into a pre-apoptotic state: autoantigen-induced, but non-autoimmune-mediated, tissue destruction. Clin Exp Immunol 150: 49–60.
51. NguyenVD, SaaranenMJ, KaralaAR, LappiAK, WangL, et al. (2011) Two endoplasmic reticulum PDI peroxidases increase the efficiency of the use of peroxide during disulfide bond formation. J Mol Biol 406: 503–515.
52. PengD, BelkhiriA, HuT, ChaturvediR, AsimM, et al. (2012) Glutathione peroxidase 7 protects against oxidative DNA damage in oesophageal cells. Gut 61: 1250–1260.
53. UtomoA, JiangX, FurutaS, YunJ, LevinDS, et al. (2004) Identification of a novel putative non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase (NPGPx) essential for alleviating oxidative stress generated from polyunsaturated fatty acids in breast cancer cells. J Biol Chem 279: 43522–43529.
54. LuJ, LiQ, XieH, ChenZJ, BorovitskayaAE, et al. (1996) Identification of a second transmembrane protein tyrosine phosphatase, IA-2beta, as an autoantigen in insulin-dependent diabetes mellitus: precursor of the 37-kDa tryptic fragment. Proc Natl Acad Sci U S A 93: 2307–2311.
55. NotkinsAL, LernmarkA (2001) Autoimmune type 1 diabetes: resolved and unresolved issues. J Clin Invest 108: 1247–1252.
56. McCarthyMI (2010) Genomics, type 2 diabetes, and obesity. N Engl J Med 363: 2339–2350.
57. HindorffLA, SethupathyP, JunkinsHA, RamosEM, MehtaJP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362–9367.
58. JohnsonAD, HandsakerRE, PulitSL, NizzariMM, O'DonnellCJ, et al. (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24: 2938–2939.
59. MorrisAP, VoightBF, TeslovichTM, FerreiraT, SegreAV, et al. (2012) Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 44: 981–990.
60. DupuisJ, LangenbergC, ProkopenkoI, SaxenaR, SoranzoN, et al. (2010) New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet 42: 105–116.
61. SaxenaR, HivertMF, LangenbergC, TanakaT, PankowJS, et al. (2010) Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. Nat Genet 42: 142–148.
62. SoranzoN, SannaS, WheelerE, GiegerC, RadkeD, et al. (2010) Common variants at 10 genomic loci influence hemoglobin A(1)(C) levels via glycemic and nonglycemic pathways. Diabetes 59: 3229–3239.
63. StrawbridgeRJ, DupuisJ, ProkopenkoI, BarkerA, AhlqvistE, et al. (2011) Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes 60: 2624–2634.
64. ManningAK, HivertMF, ScottRA, GrimsbyJL, Bouatia-NajiN, et al. (2012) A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Nat Genet 44: 659–669.
65. DayehTA, OlssonAH, VolkovP, AlmgrenP, RonnT, et al. (2013) Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets. Diabetologia 56: 1036–1046.
66. JonesPA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484–492.
67. LingC, GroopL (2009) Epigenetics: a molecular link between environmental factors and type 2 diabetes. Diabetes 58: 2718–2725.
68. YangBT, DayehTA, KirkpatrickCL, TaneeraJ, KumarR, et al. (2011) Insulin promoter DNA methylation correlates negatively with insulin gene expression and positively with HbA(1c) levels in human pancreatic islets. Diabetologia 54: 360–367.
69. LingC, Del GuerraS, LupiR, RonnT, GranhallC, et al. (2008) Epigenetic regulation of PPARGC1A in human type 2 diabetic islets and effect on insulin secretion. Diabetologia 51: 615–622.
70. LingC, PoulsenP, SimonssonS, RonnT, HolmkvistJ, et al. (2007) Genetic and epigenetic factors are associated with expression of respiratory chain component NDUFB6 in human skeletal muscle. J Clin Invest 117: 3427–3435.
71. NitertMD, DayehT, VolkovP, ElgzyriT, HallE, et al. (2012) Impact of an exercise intervention on DNA methylation in skeletal muscle from first-degree relatives of patients with type 2 diabetes. Diabetes 61: 3322–3332.
72. RonnT, VolkovP, DavegardhC, DayehT, HallE, et al. (2013) A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue. PLoS Genet 9: e1003572.
73. VolkmarM, DedeurwaerderS, CunhaDA, NdlovuMN, DefranceM, et al. (2012) DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J 31: 1405–1426.
74. ToddJA, WalkerNM, CooperJD, SmythDJ, DownesK, et al. (2007) Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 39: 857–864.
75. MooreF, ColliML, CnopM, EsteveMI, CardozoAK, et al. (2009) PTPN2, a candidate gene for type 1 diabetes, modulates interferon-gamma-induced pancreatic beta-cell apoptosis. Diabetes 58: 1283–1291.
76. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661–678.
77. SmythDJ, PlagnolV, WalkerNM, CooperJD, DownesK, et al. (2008) Shared and distinct genetic variants in type 1 diabetes and celiac disease. N Engl J Med 359: 2767–2777.
78. de BakkerPI, McVeanG, SabetiPC, MirettiMM, GreenT, et al. (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 38: 1166–1172.
79. ZegginiE, ScottLJ, SaxenaR, VoightBF, MarchiniJL, et al. (2008) Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 40: 638–645.
80. JacobsenSC, BronsC, Bork-JensenJ, Ribel-MadsenR, YangB, et al. (2012) Effects of short-term high-fat overfeeding on genome-wide DNA methylation in the skeletal muscle of healthy young men. Diabetologia 55: 3341–3349.
81. GillbergL, JacobsenSC, RonnT, BronsC, VaagA (2014) PPARGC1A DNA methylation in subcutaneous adipose tissue in low birth weight subjects - impact of 5days of high-fat overfeeding. Metabolism 63: 263–271.
82. BronsC, JacobsenS, NilssonE, RonnT, JensenCB, et al. (2010) Deoxyribonucleic acid methylation and gene expression of PPARGC1A in human muscle is influenced by high-fat overfeeding in a birth-weight-dependent manner. J Clin Endocrinol Metab 95: 3048–3056.
83. FlorezJC (2008) Newly identified loci highlight beta cell dysfunction as a key cause of type 2 diabetes: where are the insulin resistance genes? Diabetologia 51: 1100–1110.
84. RosengrenAH, BraunM, MahdiT, AnderssonSA, TraversME, et al. (2012) Reduced insulin exocytosis in human pancreatic beta-cells with gene variants linked to type 2 diabetes. Diabetes 61: 1726–1733.
85. RuchatSM, ElksCE, LoosRJ, VohlMC, WeisnagelSJ, et al. (2009) Association between insulin secretion, insulin sensitivity and type 2 diabetes susceptibility variants identified in genome-wide association studies. Acta Diabetol 46: 217–226.
86. CooperJD, SmythDJ, SmilesAM, PlagnolV, WalkerNM, et al. (2008) Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet 40: 1399–1401.
87. PerryJR, VoightBF, YengoL, AminN, DupuisJ, et al. (2012) Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. PLoS Genet 8: e1002741.
88. SantinI, EizirikDL (2013) Candidate genes for type 1 diabetes modulate pancreatic islet inflammation and beta-cell apoptosis. Diabetes Obes Metab 15 Suppl 3: 71–81.
89. KanetoH, MiyatsukaT, KawamoriD, YamamotoK, KatoK, et al. (2008) PDX-1 and MafA play a crucial role in pancreatic beta-cell differentiation and maintenance of mature beta-cell function. Endocr J 55: 235–252.
90. DuttaS, GannonM, PeersB, WrightC, Bonner-WeirS, et al. (2001) PDX:PBX complexes are required for normal proliferation of pancreatic cells during development. Proc Natl Acad Sci U S A 98: 1065–1070.
91. DayehT, VolkovP, SaloS, HallE, NilssonE, et al. (2014) Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion. PLoS Genet 10: e1004160.
92. CaromileLA, OganesianA, CoatsSA, SeifertRA, Bowen-PopeDF (2010) The neurosecretory vesicle protein phogrin functions as a phosphatidylinositol phosphatase to regulate insulin secretion. J Biol Chem 285: 10487–10496.
93. DoiA, ShonoT, NishiM, FurutaH, SasakiH, et al. (2006) IA-2beta, but not IA-2, is induced by ghrelin and inhibits glucose-stimulated insulin secretion. Proc Natl Acad Sci U S A 103: 885–890.
94. CaiT, HiraiH, ZhangG, ZhangM, TakahashiN, et al. (2011) Deletion of Ia-2 and/or Ia-2beta in mice decreases insulin secretion by reducing the number of dense core vesicles. Diabetologia 54: 2347–2357.
95. ToriiS, SaitoN, KawanoA, HouN, UekiK, et al. (2009) Gene silencing of phogrin unveils its essential role in glucose-responsive pancreatic beta-cell growth. Diabetes 58: 682–692.
96. LiuY, AryeeMJ, PadyukovL, FallinMD, HesselbergE, et al. (2013) Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 31: 142–147.
97. StorlingJ, OvergaardAJ, BrorssonCA, PivaF, Bang-BerthelsenCH, et al. (2013) Do post-translational beta cell protein modifications trigger type 1 diabetes? Diabetologia 56: 2347–2354.
98. KellyC, McClenaghanNH, FlattPR (2011) Role of islet structure and cellular interactions in the control of insulin secretion. Islets 3: 41–47.
99. SabraG, DubielEA, KuehnC, KhalfaouiT, BeaulieuJF, et al. (2013) INS-1 cell glucose-stimulated insulin secretion is reduced by the downregulation of the 67 kDa laminin receptor. Journal of tissue engineering and regenerative medicine 10.1002/term.1689.
100. SmithGC, KonychevaG, DziadekMA, RavelichSR, PatelS, et al. (2011) Pre- and postnatal methyl deficiency in the rat differentially alters glucose homeostasis. Journal of nutrigenetics and nutrigenomics 4: 175–191.
101. CnopM, WelshN, JonasJC, JornsA, LenzenS, et al. (2005) Mechanisms of pancreatic beta-cell death in type 1 and type 2 diabetes: many differences, few similarities. Diabetes 54 Suppl 2: S97–107.
102. LernmarkA, LarssonHE (2013) Immune therapy in type 1 diabetes mellitus. Nat Rev Endocrinol 9: 92–103.
103. YangSN, BerggrenPO (2005) Beta-cell CaV channel regulation in physiology and pathophysiology. Am J Physiol Endocrinol Metab 288: E16–28.
104. CalderonB, CarreroJA, UnanueER (2014) The central role of antigen presentation in islets of Langerhans in autoimmune diabetes. Current opinion in immunology 26: 32–40.
105. GuoY, ZhuLR, LuG, WangH, HongJY (2012) Selective expression of CYP2A13 in human pancreatic alpha-islet cells. Drug metabolism and disposition: the biological fate of chemicals 40: 1878–1882.
106. In't VeldPA, PipeleersDG (1988) In situ analysis of pancreatic islets in rats developing diabetes. Appearance of nonendocrine cells with surface MHC class II antigens and cytoplasmic insulin immunoreactivity. J Clin Invest 82: 1123–1128.
107. StandopJ, SchneiderM, UlrichA, BuchlerMW, PourPM (2003) Differences in immunohistochemical expression of xenobiotic-metabolizing enzymes between normal pancreas, chronic pancreatitis and pancreatic cancer. Toxicologic pathology 31: 506–513.
108. TsoTK, HuangHY, ChangCK, LiaoYJ, HuangWN (2004) Clinical evaluation of insulin resistance and beta-cell function by the homeostasis model assessment in patients with systemic lupus erythematosus. Clinical rheumatology 23: 416–420.
109. VerganiA, FotinoC, D'AddioF, TezzaS, PodettaM, et al. (2013) Effect of the purinergic inhibitor oxidized ATP in a model of islet allograft rejection. Diabetes 62: 1665–1675.
110. ZengYJ, ZengFQ, DaiL, YangC, LinBZ, et al. (2011) [Insulin sensitivity and beta cell function in female systemic lupus erythematosus patients]. Zhonghua nei ke za zhi 50: 18–22.
111. ZhangL, Moffatt-BruceSD, GaughanAA, WangJJ, RajabA, et al. (2009) An anti-CD103 immunotoxin promotes long-term survival of pancreatic islet allografts. American journal of transplantation: official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 9: 2012–2023.
112. QuonG, LippertC, HeckermanD, ListgartenJ (2013) Patterns of methylation heritability in a genome-wide analysis of four brain regions. Nucleic Acids Res 41: 2095–2104.
113. BellJT, PaiAA, PickrellJK, GaffneyDJ, Pique-RegiR, et al. (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 12: R10.
114. NilssonE, JanssonPA, PerfilyevA, VolkovP, PedersenM, et al. (2014) Altered DNA methylation and differential expression of genes influencing metabolism and inflammation in adipose tissue from subjects with type 2 diabetes. Diabetes 63: 2962–2976.
115. SmemoS, TenaJJ, KimKH, GamazonER, SakabeNJ, et al. (2014) Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 507: 371–375.
116. JjingoD, ConleyAB, YiSV, LunyakVV, JordanIK (2012) On the presence and role of human gene-body DNA methylation. Oncotarget 3: 462–474.
117. ZhiD, AslibekyanS, IrvinMR, ClaasSA, BoreckiIB, et al. (2013) SNPs located at CpG sites modulate genome-epigenome interaction. Epigenetics 8: 802–806.
118. ReynardLN, BuiC, SyddallCM, LoughlinJ (2014) CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383. Hum Genet 133: 1059–1073.
119. TaqiMM, BazovI, WatanabeH, SheedyD, HarperC, et al. (2011) Prodynorphin CpG-SNPs associated with alcohol dependence: elevated methylation in the brain of human alcoholics. Addiction biology 16: 499–509.
120. ParkJH, LeeJ, KimCH, LeeS (2014) The polymorphism (−600 C>A) of CpG methylation site at the promoter region of CYP17A1 and its association of male infertility and testosterone levels. Gene 534: 107–112.
121. MaunakeaAK, NagarajanRP, BilenkyM, BallingerTJ, D'SouzaC, et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253–257.
122. DeatonAM, BirdA (2011) CpG islands and the regulation of transcription. Genes Dev 25: 1010–1022.
123. DeatonAM, WebbS, KerrAR, IllingworthRS, GuyJ, et al. (2011) Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res 21: 1074–1086.
124. ShuklaS, KavakE, GregoryM, ImashimizuM, ShutinoskiB, et al. (2011) CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479: 74–79.
125. SigurdssonMI, SmithAV, BjornssonHT, JonssonJJ (2009) HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. Genome Res 19: 581–589.
126. RakyanVK, BeyanH, DownTA, HawaMI, MaslauS, et al. (2011) Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis. PLoS Genet 7: e1002300.
127. ChenH, KazemierHG, de GrooteML, RuitersMH, XuGL, et al. (2014) Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 42: 1563–1574.
128. ChristensenDP, DahllofM, LundhM, RasmussenDN, NielsenMD, et al. (2011) Histone deacetylase (HDAC) inhibition as a novel treatment for diabetes mellitus. Molecular medicine 17: 378–390.
129. ChristensenDP, GysemansC, LundhM, DahllofMS, NoesgaardD, et al. (2014) Lysine deacetylase inhibition prevents diabetes by chromatin-independent immunoregulation and beta-cell protection. Proc Natl Acad Sci U S A 111: 1055–1059.
130. KrusU, KingBC, NagarajV, GandasiNR, SjolanderJ, et al. (2014) The complement inhibitor CD59 regulates insulin secretion by modulating exocytotic events. Cell Metab 19: 883–890.
131. MahdiT, HanzelmannS, SalehiA, MuhammedSJ, ReinbotheTM, et al. (2012) Secreted frizzled-related protein 4 reduces insulin secretion and is overexpressed in type 2 diabetes. Cell Metab 16: 625–633.
132. TaneeraJ, LangS, SharmaA, FadistaJ, ZhouY, et al. (2012) A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets. Cell Metab 16: 122–134.
133. OlssonAH, YangBT, HallE, TaneeraJ, SalehiA, et al. (2011) Decreased expression of genes involved in oxidative phosphorylation in human pancreatic islets from patients with type 2 diabetes. Eur J Endocrinol 165: 589–595.
134. StahleMU, BrandhorstD, KorsgrenO, KnutsonF (2011) Pathogen inactivation of human serum facilitates its clinical use for islet cell culture and subsequent transplantation. Cell Transplant 20: 775–781.
135. PurcellS, NealeB, Todd-BrownK, ThomasL, FerreiraMA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559–575.
136. TeschendorffAE, MenonU, Gentry-MaharajA, RamusSJ, GaytherSA, et al. (2009) An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One 4: e8274.
137. DuP, KibbeWA, LinSM (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24: 1547–1548.
138. DuP, ZhangX, HuangCC, JafariN, KibbeWA, et al. (2010) Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11: 587.
139. BolstadBM, IrizarryRA, AstrandM, SpeedTP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185–193.
140. JohnsonWE, LiC, RabinovicA (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118–127.
141. ShabalinAA (2012) Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28: 1353–1358.
142. HohmeierHE, MulderH, ChenG, Henkel-RiegerR, PrentkiM, et al. (2000) Isolation of INS-1-derived cell lines with robust ATP-sensitive K+ channel-dependent and -independent glucose-stimulated insulin secretion. Diabetes 49: 424–430.
143. WeissT, GrellM, HessabiB, BourteeleS, MullerG, et al. (1997) Enhancement of TNF receptor p60-mediated cytotoxicity by TNF receptor p80: requirement of the TNF receptor-associated factor-2 binding site. J Immunol 158: 2398–2404.
144. MalmgrenS, SpegelP, DanielssonAP, NagornyCL, AnderssonLE, et al. (2013) Coordinate changes in histone modifications, mRNA levels, and metabolite profiles in clonal INS-1 832/13 beta-cells accompany functional adaptations to lipotoxicity. J Biol Chem 288: 11973–11987.
145. O'ConnellJ, GurdasaniD, DelaneauO, PirastuN, UliviS, et al. (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet 10: e1004234.
146. HowieBN, DonnellyP, MarchiniJ (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5: e1000529.