A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy

Nature Genetics

Volumn 44, Issue 2, 2012, Pages 178-182

  Yu, Xue Qing ^a,b   Li, Ming ^a,b   Zhang, Hong ^c   Low, Hui Qi ^d   Wei, Xin ^a,b   Wang, Jin Quan ^e   Sun, Liang Dan ^f,g   Sim, Kar Seng ^d   Li, Yi ^d   Foo, Jia Nee ^d   Wang, Wei ^a,b   Li, Zhi Jian ^a,b   Yin, Xian Yong ^f,g   Tang, Xue Qing ^a,b   Fan, Li ^a,b   Chen, Jian ^h   Li, Rong Shan ⁱ   Wan, Jian Xin ^j   Liu, Zhang Suo ^k   Lou, Tan Qi ^a   Zhu, Li ^c   Huang, Xiao Jun ^l   Zhang, Xue Jun ^f,g   Liu, Zhi Hong ^e   Liu, Jian Jun ^d,f   more..

^a SUN YAT SEN UNIVERSITY   (China)

^b BEIJING HOSPITAL   (China)

^c PEKING UNIVERSITY FIRST HOSPITAL   (China)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

^e NANJING GENERAL HOSPITAL OF NANJING MILITARY COMMAND   (China)

^f ANHUI MEDICAL UNIVERSITY   (China)

^g State Key Laboratory Incubation Base of Dermatology   (China)

^h FUZHOU GENERAL HOSPITAL   (China)

ⁱ SHANXI MEDICAL UNIVERSITY   (China)

^j FUJIAN MEDICAL UNIVERSITY   (China)

^k THE FIRST AFFILIATED HOSPITAL OF ZHENGZHOU UNIVERSITY   (China)

^l PEKING UNIVERSITY PEOPLE S HOSPITAL   (China)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA DEFENSIN; HLA DR ANTIGEN; IMMUNOGLOBULIN A; TUMOR NECROSIS FACTOR;

ADULT; ARTICLE; CONTROLLED STUDY; ETHNIC GROUP; FEMALE; FOLLOW UP; GENE LOCUS; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENOTYPE; HAN CHINESE; HEMATURIA; HUMAN; IMMUNOGLOBULIN A NEPHROPATHY; IMMUNOGLOBULIN BLOOD LEVEL; INFLAMMATION; INNATE IMMUNITY; LINKAGE ANALYSIS; MAJOR CLINICAL STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; NEPHROTIC SYNDROME; PRIORITY JOURNAL; PROTEINURIA; SINGLE NUCLEOTIDE POLYMORPHISM;

ALPHA-DEFENSINS; ASIAN CONTINENTAL ANCESTRY GROUP; CASE-CONTROL STUDIES; FEMALE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GLOMERULONEPHRITIS, IGA; HUMANS; IMMUNOGLOBULIN A; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINURIA; TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13;

EID: 84856277654     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.1047     Document Type: Article

References (54)

1. D'Amico, G. The commonest glomerulonephritis in the world: IgA nephropathy. Q. J. Med. 64, 709-727 (1987). (Pubitemid 18047151)
2. Barratt, J. & Feehally, J. IgA nephropathy. J. Am. Soc. Nephrol. 16, 2088-2097 (2005). (Pubitemid 41716440)
3. Donadio, J.V. & Grande, J.P. IgA nephropathy. N. Engl. J. Med. 347, 738-748 (2002). (Pubitemid 35203906)
4. Levy, M. & Berger, J. Worldwide perspective of IgA nephropathy. Am. J. Kidney Dis. 12, 340-347 (1988).
5. Tsukamoto, Y. et al. Report of the Asian Forum of Chronic Kidney Disease Initiative (AFCKDI) 2007. "Current status and perspective of CKD in Asia": diversity and specificity among Asian countries. Clin. Exp. Nephrol. 13, 249-256 (2009).
6. Hsu, S.I., Ramirez, S.B., Winn, M.P., Bonventre, J.V. & Owen, W.F. Evidence for genetic factors in the development and progression of IgA nephropathy. Kidney Int. 57, 1818-1835 (2000). (Pubitemid 30252274)
7. Hsu, S.I. Racial and genetic factors in IgA nephropathy. Semin. Nephrol. 28, 48-57 (2008).
8. Beerman, I., Novak, J., Wyatt, R.J., Julian, B.A. & Gharavi, A.G. The genetics of IgA nephropathy. Nat. Clin. Pract. Nephrol. 3, 325-338 (2007). (Pubitemid 46834885)
9. Izzi, C. et al. Familial aggregation of primary glomerulonephritis in an Italian population isolate: Valtrompia study. Kidney Int. 69, 1033-1040 (2006). (Pubitemid 43372178)
10. Scolari, F. Inherited forms of IgA nephropathy. J. Nephrol. 16, 317-320 (2003). (Pubitemid 37304093)
11. Kiryluk, K. et al. Genetic studies of IgA nephropathy: past, present, and future. Pediatr. Nephrol. 25, 2257-2268 (2010).
12. Bisceglia, L. et al. Genetic heterogeneity in Italian families with IgA nephropathy: suggestive linkage for two novel IgA nephropathy loci. Am. J. Hum. Genet. 79, 1130-1134 (2006). (Pubitemid 44853485)
13. Gharavi, A.G. et al. IgA nephropathy, the most common cause of glomerulonephritis, is linked to 6q22-23. Nat. Genet. 26, 354-357 (2000).
14. Paterson, A.D. et al. Genome-wide linkage scan of a large family with IgA nephropathy localizes a novel susceptibility locus to chromosome 2q36. J. Am. Soc. Nephrol. 18, 2408-2415 (2007). (Pubitemid 47203857)
15. Cao, H.X. et al. Human leukocyte antigen DRB1 alleles predict risk and disease progression of immunoglobulin A nephropathy in Han Chinese. Am. J. Nephrol. 28, 684-691 (2008).
16. Fennessy, M. et al. HLA-DQ gene polymorphism in primary IgA nephropathy in three European populations. Kidney Int. 49, 477-480 (1996). (Pubitemid 26051831)
17. Raguénès, O., Mercier, B., Cledes, J., Whebe, B. & Ferec, C. HLA class II typing and idiopathic IgA nephropathy (IgAN): DQB1*0301, a possible marker of unfavorable outcome. Tissue Antigens 45, 246-249 (1995).
18. Yu, H.H. et al. Genetics and immunopathogenesis of IgA nephropathy. Clin. Rev. Allergy Immunol. 41, 198-213 (2011).
19. Gharavi, A.G. et al. Genome-wide association study identifies susceptibility loci for IgA nephropathy. Nat. Genet. 43, 321-327 (2011).
20. Alexopoulos, E., Apostolos, K. & Papadimitriou, M. Increased glomerular and interstitial LFA-1 expression in proteinuric immunoglobulin A nephropathy. Am. J. Kidney Dis. 27, 327-333 (1996). (Pubitemid 26075840)
21. Gupta, S.K. et al. Proteinuria, creatinine clearance, and immune activation in antiretroviral-naive HIV-infected subjects. J. Infect. Dis. 200, 614-618 (2009).
22. Ganz, T. Defensins: antimicrobial peptides of innate immunity. Nat. Rev. Immunol. 3, 710-720 (2003). (Pubitemid 41070812)
23. Rehaume, L.M. & Hancock, R.E. Neutrophil-derived defensins as modulators of innate immune function. Crit. Rev. Immunol. 28, 185-200 (2008).
24. Yokoyama, H. et al. Urinary levels of chemokines (MCAF/MCP-1, IL-8) reflect distinct disease activities and phases of human IgA nephropathy. J. Leukoc. Biol. 63, 493-499 (1998). (Pubitemid 28163190)
25. Stangou, M. et al. Urinary levels of epidermal growth factor, interleukin-6 and monocyte chemoattractant protein-1 may act as predictor markers of renal function outcome in immunoglobulin A nephropathy. Nephrology (Carlton) 14, 613-620 (2009).
26. Saraheimo, M. et al. Increased levels of alpha-defensin (-1,-2 and-3) in type 1 diabetic patients with nephropathy. Nephrol. Dial. Transplant. 23, 914-918 (2008). (Pubitemid 351767570)
27. Vordenbäumen, S. et al. Elevated levels of human beta-defensin 2 and human neutrophil peptides in systemic lupus erythematosus. Lupus 19, 1648-1653 (2010).
28. Stein, J.V. et al. APRIL modulates B and T cell immunity. J. Clin. Invest. 109, 1587-1598 (2002). (Pubitemid 34663521)
29. Castigli, E. et al. Impaired IgA class switching in APRIL-deficient mice. Proc. Natl. Acad. Sci. USA 101, 3903-3908 (2004). (Pubitemid 38381075)
30. He, B. et al. Intestinal bacteria trigger T cell-independent immunoglobulin A2 class switching by inducing epithelial-cell secretion of the cytokine APRIL. Immunity 26, 812-826 (2007). (Pubitemid 46915505)
31. Neusser, M.A. et al. Intrarenal production of B-cell survival factors in human lupus nephritis. Mod. Pathol. 24, 98-107 (2011).
32. Ramanujam, M. et al. Similarities and differences between selective and nonselective BAFF blockade in murine SLE. J. Clin. Invest. 116, 724-734 (2006). (Pubitemid 43326881)
33. Maruhashi, Y. et al. Analysis of macrophages in urine sediments in children with IgA nephropathy. Clin. Nephrol. 62, 336-343 (2004). (Pubitemid 39480839)
34. Hei, A.L. et al. Analysis of high-resolution HLA-A,-B,-Cw,-DRB1, and-DQB1 alleles and haplotypes in 718 Chinese marrow donors based on donor-recipient confirmatory typings. Int. J. Immunogenet. 36, 275-282 (2009).
35. Trachtenberg, E. et al. HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China. Tissue Antigens 70, 455-463 (2007). (Pubitemid 350075785)
36. Kawabata, Y. et al. Differential association of HLA with three subtypes of type 1 diabetes: fulminant, slowly progressive and acute-onset. Diabetologia 52, 2513-2521 (2009).
37. Tsuchiya, N., Kobayashi, S., Hashimoto, H., Ozaki, S. & Tokunaga, K. Association of HLA-DRB1*0901-DQB1*0303 haplotype with microscopic polyangiitis in Japanese. Genes Immun. 7, 81-84 (2006).
38. Geetha, D. & Seo, P. Renal transplantation in the ANCA-associated vasculitides. Am. J. Transplant. 7, 2657-2662 (2007). (Pubitemid 350045766)
39. Berthoux, F.C. et al. HLA-Bw35 and mesangial IgA glomerulonephritis. N. Engl. J. Med. 298, 1034-1035 (1978).
40. Berthoux, F.C., Alamartine, E., Pommier, G. & Lepetit, J.C. HLA and IgA nephritis revisited 10 years later: HLA-B35 antigen as a prognostic factor. N. Engl. J. Med. 319, 1609-1610 (1988). (Pubitemid 19003435)
41. Chen, J., Niaudet, P. & Levy, M. Schonlein-Henoch purpura and IgA nephropathy. in Renal Pathology (eds. C. Tisher & B. Brenner) 507-508 (Lippincott, Philadelphia, 1994).
42. Niaudet, P. & Levy, M. Schonlein-Henoch purpura and IgA nephropathy. in Renal Pathology (Tisher, C. & Brenner, B., eds.) 507-508 (Lippincott, Philadelphia, 1994).
43. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007). (Pubitemid 47330214)
44. Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006). (Pubitemid 44141658)
45. Steinhaus, H. Sur la division des corps matériels en parties. Bull. Acad. Polon. Sci. (in French) 4, 801-804 (1957).
46. Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005). (Pubitemid 40202029)
47. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing (Vienna, 2008).
48. Browning, S.R. & Browning, B.L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084-1097 (2007). (Pubitemid 47580259)
49. de Bakker, P.I. et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat. Genet. 38, 1166-1172 (2006). (Pubitemid 44470362)
50. Pereyra, F. et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330, 1551-1557 (2010).
51. Howie, B.N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).
52. Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913 (2007). (Pubitemid 47014502)
53. International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
54. -1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).