Identification of novel risk genes associated with type 1 diabetes mellitus using a genome-wide gene-based association analysis

Journal of Diabetes Investigation

Volumn 5, Issue 6, 2014, Pages 649-656

  Qiu, Ying Hua ^a   Deng, Fei Yan ^a   Li, Min Jing ^a   Lei, Shu Feng ^a  

^a MEDICAL COLLEGE OF SOOCHOW UNIVERSITY   (China)

Author keywords

Genome wide gene based association study; Knowledge based mining system for genome wide genetic studies; Type 1 diabetes mellitus

Indexed keywords

ARTICLE; BCAR1 GENE; CHROMOSOME 6P; CONTROLLED STUDY; FYN GENE; GENE; GENE CLUSTER; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE ONTOLOGY; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENOME ANALYSIS; HLA J GENE; HUMAN; HUMAN CELL; INSULIN DEPENDENT DIABETES MELLITUS; MAJOR CLINICAL STUDY; MONOCYTE; MYL2 GENE; PERIPHERAL BLOOD MONONUCLEAR CELL; PPP1R11 GENE; PRIORITY JOURNAL; RASIP1 GENE; RISK ASSESSMENT; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; STRN4 GENE;

EID: 84911410681     PISSN: 20401116     EISSN: 20401124     Source Type: Journal    
DOI: 10.1111/jdi.12228     Document Type: Article

References (37)

1. Maahs DM, West NA, Lawrence JM, et al. Epidemiology of type 1 diabetes. Endocrinol Metab Clin North Am 2010; 393: 481-497.
2. Noble JA, Valdes AM. Genetics of the HLA region in the prediction of type 1 diabetes. Curr Diab Rep 2011; 116: 533-542.
3. Park Y, Eisenbarth GS. Genetic susceptibility factors of Type 1 diabetes in Asians. Diabetes Metab Res Rev 2001; 171: 2-11.
4. Sugihara S. Genetic susceptibility of childhood type 1 diabetes mellitus in Japan. Pediatr Endocrinol Rev 2012; 10(Suppl. 1): 62-71.
5. Mosaad YM, Auf FA, Metwally SS, et al. HLA-DQB1* alleles and genetic susceptibility to type 1 diabetes mellitus. World J Diabetes 2012; 38: 149-155.
6. Paterson AD, Waggott D, Boright AP, et al. A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose. Diabetes 2010; 592: 539-549.
7. Barrett JC, Clayton DG, Concannon P, et al. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 2009; 416: 703-707.
8. Buil A, Martinez-Perez A, Perera-Lluna A, et al. A new gene-based association test for genome-wide association studies. BMC Proc 2009; 3(Suppl. 7): S130.
9. Mueller PW, Rogus JJ, Cleary PA, et al. Genetics of Kidneys in Diabetes (GoKinD) study: a genetics collection available for identifying genetic susceptibility factors for diabetic nephropathy in type 1 diabetes. J Am Soc Nephrol 2006; 177: 1782-1790.
10. Pezzolesi MG, Poznik GD, Mychaleckyj JC, et al. Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes. Diabetes 2009; 586: 1403-1410.
11. Paterson AD, Lopes-Virella MF, Waggott D, et al. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Arterioscler Thromb Vasc Biol 2009; 2911: 1958-1967.
12. Li MX, Gui HS, Kwan JS, et al. GATES: a rapid and powerful gene-based association test using extended Simes procedure. Am J Hum Genet 2011; 883: 283-293.
13. Beyan H, Drexhage RC, van der Heul Nieuwenhuijsen L, et al. Monocyte gene-expression profiles associated with childhood-onset type 1 diabetes and disease risk: a study of identical twins. Diabetes 2010; 597: 1751-1755.
14. Levy H, Wang X, Kaldunski M, et al. Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. Genes Immun 2012; 138: 593-604.
15. Irvine KM, Gallego P, An X, et al. Peripheral blood monocyte gene expression profile clinically stratifies patients with recent-onset type 1 diabetes. Diabetes 2012; 615: 1281-1290.
16. Stechova K, Kolar M, Blatny R, et al. Healthy first degree relatives of patients with type 1 diabetes exhibit significant differences in basal gene expression pattern of immunocompetent cells compared to controls: expression pattern as predeterminant of autoimmune diabetes. Scand J Immunol 2011; 75: 210-219.
17. Sherman BT, da Huang W, Tan Q, et al. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 2007; 8: 426.
18. Tarone RE. A modified Bonferroni method for discrete data. Biometrics 1990; 462: 515-522.
19. Hochberg Y, Benjamini Y. More powerful procedures for multiple significance testing. Stat Med 1990; 97: 811-818.
20. Todd JA, Walker NM, Cooper JD, et al. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 2007; 397: 857-864.
21. Cooper JD, Smyth DJ, Smiles AM, et al. Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet 2008; 4012: 1399-1401.
22. Plagnol V, Howson JM, Smyth DJ, et al. Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. PLoS Genet 2011; 78: e1002216.
23. Hakonarson H, Qu HQ, Bradfield JP, et al. A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study. Diabetes 2008; 574: 1143-1146.
24. Howard TD, Koppelman GH, Xu J, et al. Gene-gene interaction in asthma: IL4RA and IL13 in a Dutch population with asthma. Am J Hum Genet 2002; 701: 230-236.
25. Liu JZ, McRae AF, Nyholt DR, et al. A versatile gene-based test for genome-wide association studies. Am J Hum Genet 2010; 871: 139-145.
26. Baranzini SE, Galwey NW, Wang J, et al. Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum Mol Genet 2009; 1811: 2078-2090.
27. Bugawan TL, Klitz W, Alejandrino M, et al. The association of specific HLA class I and II alleles with type 1 diabetes among Filipinos. Tissue Antigens 2002; 596: 452-469.
28. Sheehy MJ, Scharf SJ, Rowe JR, et al. A diabetes-susceptible HLA haplotype is best defined by a combination of HLA-DR and -DQ alleles. J Clin Invest 1989; 833: 830-835.
29. Harder MN, Ribel-Madsen R, Justesen JM, et al. Type 2 diabetes risk alleles near BCAR1 and in ANK1 associate with decreased beta-cell function whereas risk alleles near ANKRD55 and GRB14 associate with decreased insulin sensitivity in the Danish Inter99 cohort. J Clin Endocrinol Metab 2013; 984: E801-E806.
30. Sun J, Matthias G, Mihatsch MJ, et al. Lack of the transcriptional coactivator OBF-1 prevents the development of systemic lupus erythematosus-like phenotypes in Aiolos mutant mice. J Immunol 2003; 1704: 1699-1706.
31. Hu SJ, Wen LL, Hu X, et al. IKZF1: a critical role in the pathogenesis of systemic lupus erythematosus? Mod Rheumatol 2013; 232: 205-209.
32. Landego I, Jayachandran N, Wullschleger S, et al. Interaction of TAPP adapter proteins with phosphatidylinositol (3, 4)-bisphosphate regulates B-cell activation and autoantibody production. Eur J Immunol 2012; 4210: 2760-2770.
33. Liu X, Lindberg R, Xiao BG, et al. CD24 and myosin light polypeptide 2 are involved in prevention of experimental autoimmune encephalomyelitis by myelin basic protein-pulsed dendritic cells. J Neuroimmunol 2006; 1721-2: 137-144.
34. Klune JR, Dhupar R, Cardinal J, et al. HMGB1: endogenous danger signaling. Mol Med 2008; 147-8: 476-484.
35. Yin YW, Hu AM, Sun QQ, et al. Association between interleukin 10 gene -1082 A/G polymorphism and the risk of type 2 diabetes mellitus: a meta-analysis of 4250 subjects. Cytokine 2013; 622: 226-231.
36. Martinez A, Santiago JL, Cenit MC, et al. IFIH1-GCA-KCNH7 locus: influence on multiple sclerosis risk. Eur J Hum Genet 2008; 167: 861-864.
37. Smyth DJ, Cooper JD, Howson JM, et al. FUT2 nonsecretor status links type 1 diabetes susceptibility and resistance to infection. Diabetes 2011; 6011: 3081-3084.