Genome-wide studies to identify risk factors for kidney disease with a focus on patients with diabetes

Nephrology Dialysis Transplantation

Volumn 30, Issue , 2015, Pages iv26-iv34

  Regele, Florina ^a   Jelencsics, Kira ^a   Shiffman, Dov ^b   Paré, Guillaume ^c   McQueen, Matthew J ^c   Mann, Johannes F E ^c,d   Oberbauer, Rainer ^a  

^a MEDICAL UNIVERSITY OF VIENNA   (Austria)

^b QUEST DIAGNOSTICS NICHOLS INSTITUTE   (United States)

^c MCMASTER UNIVERSITY   (Canada)

^d UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

chronic kidney disease; diabetes mellitus; genomewide association studies

Indexed keywords

ALBUMINURIA; CERS2 GENE; CHRONIC KIDNEY DISEASE; DIABETES MELLITUS; DIABETIC NEPHROPATHY; DISEASE COURSE; GENE; GENE FUNCTION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GLOMERULUS FILTRATION RATE; HUMAN; KIDNEY FAILURE; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; UMOD GENE; VALIDATION STUDY; CHRONIC KIDNEY FAILURE; GENETICS;

DIABETES MELLITUS; DIABETIC NEPHROPATHIES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RENAL INSUFFICIENCY, CHRONIC; RISK FACTORS;

EID: 84939624622     PISSN: 09310509     EISSN: 14602385     Source Type: Journal    
DOI: 10.1093/ndt/gfv087     Document Type: Review

References (70)

1. Coresh J, Selvin E, Stevens LA et al. Prevalence of chronic kidney disease in the United States. JAMA 2007; 298: 2038-2047
2. Eckardt KU, Coresh J, Devuyst O et al. Evolving importance of kidney disease: from subspecialty to global health burden. Lancet 2013; 382: 158-169
3. Gross JL, de Azevedo MJ, Silveiro SP et al. Diabetic nephropathy: diagnosis, prevention, and treatment. Diabetes Care 2005; 28: 164-176
4. Adler AI, Stevens RJ, Manley SE et al. Development and progression of nephropathy in type 2 diabetes: the United Kingdom Prospective Diabetes Study (UKPDS 64). Kidney Int 2003; 63: 225-232
5. Macisaac RJ, Ekinci EI, Jerums G. Markers of and risk factors for the development and progression of diabetic kidney disease. Am J Kidney Dis 2014; 63(2 Suppl 2): S39-S62
6. Satko SG, Sedor JR, Iyengar SK et al. Familial clustering of chronic kidney disease. Semin Dial 2007; 20: 229-236
7. O'Seaghdha CM, Fox CS. Genetics of chronic kidney disease. Nephron Clin Pract 2011; 118: c55-c63
8. International HapMap C. The International HapMap Project. Nature 2003; 426: 789-796
9. Igarashi P, Somlo S. Genetics and pathogenesis of polycystic kidney disease. J Am Soc Nephrol 2002; 13: 2384-2398
10. Bush WS, Moore JH. Chapter 11: genome-wide association studies. PLoS Comput Biol 2012; 8: e1002822
11. Laird NM, Lange C. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 2006; 7: 385-394
12. Boger CA, Heid IM. Chronic kidney disease: novel insights from genome-wide association studies. Kidney Blood Press Res 2011; 34: 225-234
13. Li Y, Shiffman D, Oberbauer R. Analysis of single nucleotide polymorphisms in case-control studies. Methods Mol Biol 2011; 719: 219-234
14. Turner S, Armstrong LL, Bradford Y et al. Quality control procedures for genome-wide association studies. Curr Protoc Hum Genet 2011; Supplement 68, Unit 1.19, p1.19.1-1.19.8
15. Wittke-Thompson JK, Pluzhnikov A, Cox NJ. Rational inferences about departures from Hardy-Weinberg equilibrium. Am J Hum Genet 2005; 76: 967-986
16. Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nat Rev Genet 2009; 10: 681-690
17. Pe'er I, Yelensky R, Altshuler D et al. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol 2008; 32: 381-385
18. Hoggart CJ, Clark TG, De Iorio M et al. Genome-wide significance for dense SNP and resequencing data. Genet Epidemiol 2008; 32: 179-185
19. Mayer G, Heinze G, Mischak H et al. Omics-bioinformatics in the context of clinical data. Methods Mol Biol 2011; 719: 479-497
20. Sham PC, Purcell SM. Statistical power and significance testing in large-scale genetic studies. Nat Rev Genet 2014; 15: 335-346
21. Zollner S, Pritchard JK. Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet 2007; 80: 605-615
22. Köttgen A, Glazer NL, Dehghan A et al. Multiple loci associated with indices of renal function and chronic kidney disease. Nat Genet 2009; 41: 712-717
23. Köttgen A, Pattaro C, Boger CA et al. New loci associated with kidney function and chronic kidney disease. Nat Genet 2010; 42: 376-384
24. Hart TC, Gorry MC, Hart PS et al. Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy. J Med Genet 2002; 39: 882-892
25. Serafini-Cessi F, Malagolini N, Cavallone D. Tamm-Horsfall glycoprotein: biology and clinical relevance. Am J Kidney Dis 2003; 42: 658-676
26. Deshmukh HA, Palmer CN, Morris AD et al. Investigation of known estimated glomerular filtration rate loci in patients with type 2 diabetes. Diabet Med 2013; 30: 1230-1235
27. Shiffman D, Pare G, Oberbauer R et al. A gene variant in CERS2 Is associated with rate of increase in albuminuria in patients with diabetes from ONTARGET and TRANSCEND. PLoS ONE 2014; 9: e106631
28. Investigators OtGilbert RE, Mann JF, Hanefeld M et al. Basal insulin glargine and microvascular outcomes in dysglycaemic individuals: results of the Outcome Reduction with an Initial Glargine Intervention (ORIGIN) trial. Diabetologia 2014; 57: 1325-1331
29. Shimazaki A, Kawamura Y, Kanazawa A et al. Genetic variations in the gene encoding ELMO1 are associated with susceptibility to diabetic nephropathy. Diabetes 2005; 54: 1171-1178
30. Pezzolesi MG, Katavetin P, Kure M et al. Confirmation of genetic associations at ELMO1 in the GoKinD collection supports its role as a susceptibility gene in diabetic nephropathy. Diabetes 2009; 58: 2698-2702
31. Leak TS, Perlegas PS, Smith SG et al. Variants in intron 13 of the ELMO1 gene are associated with diabetic nephropathy in African Americans. Ann Hum Genet 2009; 73: 152-159
32. Shimazaki A, Tanaka Y, Shinosaki T et al. ELMO1 increases expression of extracellular matrix proteins and inhibits cell adhesion to ECMs. Kidney Int 2006; 70: 1769-1776
33. Niu W, Qi Y. An updated meta-analysis of methylenetetrahydrofolate reductase gene 677C/T polymorphism with diabetic nephropathy and diabetic retinopathy. Diabetes Res Clin Pract 2012; 95: 110-118
34. Wrone EM, Zehnder JL, Hornberger JM et al. An MTHFR variant, homocysteine, and cardiovascular comorbidity in renal disease. Kidney Int 2001; 60: 1106-1113
35. Kopp JB, Smith MW, Nelson GW et al. MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet 2008; 40: 1175-1184
36. Kao WH, Klag MJ, Meoni LA et al. MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet 2008; 40: 1185-1192
37. Genovese G, Friedman DJ, Ross MD et al. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 2010; 329: 841-845
38. Parsa A, Kao WH, Xie D et al. APOL1 risk variants, race, and progression of chronic kidney disease. N Engl J Med 2013; 369: 2183-2196
39. Freedman BI, Hicks PJ, Bostrom MA et al. Non-muscle myosin heavy chain 9 gene MYH9 associations in African Americans with clinically diagnosed type 2 diabetes mellitus-associated ESRD. Nephrol Dial Transplant 2009; 24: 3366-3371
40. Cooke JN, Bostrom MA, Hicks PJ et al. Polymorphisms in MYH9 are associated with diabetic nephropathy in European Americans. Nephrol Dial Transplant 2012; 27: 1505-1511
41. McKnight AJ, Duffy S, Fogarty DG et al. Association of MYH9/APOL1 with chronic kidney disease in a UK population. Nephrol Dial Transplant 2012; 27: 3660; author reply 660-661
42. Sandholm N, Salem RM, McKnight AJ et al. New susceptibility loci associated with kidney disease in type 1 diabetes. PLoS Genet 2012; 8: e1002921
43. Sandholm N, McKnight AJ, Salem RM et al. Chromosome 2q31.1 associates with ESRD in women with type 1 diabetes. J Am Soc Nephrol 2013; 24: 1537-1543
44. Wang F, Fang Q, Yu N et al. Association between genetic polymorphism of the angiotensin-converting enzyme and diabetic nephropathy: a meta-analysis comprising 26,580 subjects. J Renin Angiotensin Aldosterone Syst 2012; 13: 161-174
45. Ding W, Wang F, Fang Q et al. Association between two genetic polymorphisms of the renin-angiotensin-aldosterone system and diabetic nephropathy: a meta-analysis. Mol Biol Rep 2012; 39: 1293-1303
46. Tang SC, Leung VT, Chan LY et al. The acetyl-coenzyme A carboxylase beta (ACACB) gene is associated with nephropathy in Chinese patients with type 2 diabetes. Nephrol Dial Transplant 2010; 25: 3931-3934
47. Maeda S, Kobayashi MA, Araki S et al. A single nucleotide polymorphism within the acetyl-coenzyme A carboxylase beta gene is associated with proteinuria in patients with type 2 diabetes. PLoS Genet 2010; 6: e1000842
48. Palmer ND, Ng MC, Hicks PJ et al. Evaluation of candidate nephropathy susceptibility genes in a genome-wide association study of African American diabetic kidney disease. PLoS ONE 2014; 9: e88273
49. Yin YW, Qiao L, Sun QQ et al. Influence of apolipoprotein E gene polymorphism on development of type 2 diabetes mellitus in Chinese Han population: a meta-analysis of 29 studies. Metabolism 2014; 63: 532-541
50. Palmer ND, McDonough CW, Hicks PJ et al. A genome-wide association search for type 2 diabetes genes in African Americans. PLoS ONE 2012; 7: e29202
51. Boger CA, Chen MH, Tin A et al. CUBN is a gene locus for albuminuria. J Am Soc Nephrol 2011; 22: 555-570
52. Pezzolesi MG, Poznik GD, Mychaleckyj JC et al. Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes. Diabetes 2009; 58: 1403-1410
53. Wu HY, Wang Y, Chen M et al. Association of ELMO1 gene polymorphisms with diabetic nephropathy in Chinese population. J Endocrinol Invest 2013; 36: 298-302
54. Williams WW, Salem RM, McKnight AJ et al. Association testing of previously reported variants in a large case-control meta-analysis of diabetic nephropathy. Diabetes 2012; 61: 2187-2194
55. Tanaka N, Babazono T, Saito S et al. Association of solute carrier family 12 (sodium/chloride) member 3 with diabetic nephropathy, identified by genome-wide analyses of single nucleotide polymorphisms. Diabetes 2003; 52: 2848-2853
56. Nishiyama K, Tanaka Y, Nakajima K et al. Polymorphism of the solute carrier family 12 (sodium/chloride transporters) member 3, SLC12A3, gene at exon 23 (+78G/A: Arg913Gln) is associated with elevation of urinary albumin excretion in Japanese patients with type 2 diabetes: a 10-year longitudinal study. Diabetologia 2005; 48: 1335-1338
57. Abu Seman N, He B, Ojala JR et al. Genetic and biological effects of sodium-chloride cotransporter (SLC12A3) in diabetic nephropathy. Am J Nephrol 2014; 40: 408-416
58. Zhou TB, Jiang ZP, Qin YH et al. Association of transforming growth factor-beta1 T869C gene polymorphism with diabetic nephropathy risk. Nephrology (Carlton) 2014; 19: 107-115
59. Stanescu HC, Arcos-Burgos M, Medlar A et al. Risk HLA-DQA1 and PLA (2)R1 alleles in idiopathic membranous nephropathy. N Engl J Med 2011; 364: 616-626
60. Genovese G, Tonna SJ, Knob AU et al. A risk allele for focal segmental glomerulosclerosis in African Americans is located within a region containing APOL1 and MYH9. Kidney Int 2010; 78: 698-704
61. Gharavi AG, Kiryluk K, Choi M et al. Genome-wide association study identifies susceptibility loci for IgA nephropathy. Nat Genet 2011; 43: 321-327
62. Placha G, Canani LH, Warram JH et al. Evidence for different susceptibility genes for proteinuria and ESRD in type 2 diabetes. Adv Chronic Kidney Dis 2005; 12: 155-169
63. Köttgen A, Hwang SJ, Larson MG et al. Uromodulin levels associate with a common UMOD variant and risk for incident CKD. J Am Soc Nephrol 2010; 21: 337-344
64. Imgrund S, Hartmann D, Farwanah H et al. Adult ceramide synthase 2 (CERS2)-deficient mice exhibit myelin sheath defects, cerebellar degeneration, and hepatocarcinomas. J Biol Chem 2009; 284: 33549-33560
65. Pewzner-Jung Y, Brenner O, Braun S et al. A critical role for ceramide synthase 2 in liver homeostasis: II. Insights into molecular changes leading to hepatopathy. J Biol Chem 2010; 285: 10911-10923
66. Manolio TA, Collins FS, Cox NJ et al. Finding the missing heritability of complex diseases. Nature 2009; 461: 747-753
67. Zuk O, Hechter E, Sunyaev SR et al. The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci USA 2012; 109: 1193-1198
68. Clayton DG. Prediction and interaction in complex disease genetics: experience in type 1 diabetes. PLoS Genet 2009; 5: e1000540
69. Macisaac RJ, Jerums G. Diabetic kidney disease with and without albuminuria. Curr Opin Nephrol Hypertens 2011; 20: 246-257
70. Steinke JM, Sinaiko AR, Kramer MS et al. The early natural history of nephropathy in Type 1 diabetes: III. Predictors of 5-year urinary albumin excretion rate patterns in initially normoalbuminuric patients. Diabetes 2005; 54: 2164-2171