Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study

Diabetes

Volumn 56, Issue 4, 2007, Pages 975-983

  Hanson, Robert L ^a   Craig, David W ^b   Millis, Meredith P ^b   Yeatts, Kimberly A ^b   Kobes, Sayuko ^a   Pearson, John V ^b   Lee, Anne M ^b   Knowler, William C ^a   Nelson, Robert G ^a   Wolford, Johanna K ^b  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; CONTROLLED STUDY; DISEASE PREDISPOSITION; EXON; GENE; GENE FREQUENCY; GENE TRANSLOCATION; GENETIC PREDISPOSITION; GENOME; GENOTYPE; HUMAN; INTRON; KIDNEY FAILURE; MAJOR CLINICAL STUDY; NON INSULIN DEPENDENT DIABETES MELLITUS; PLASMACYTOMA; PRIORITY JOURNAL; PROMOTER REGION; PVT1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM;

ARIZONA; DIABETES MELLITUS, TYPE 2; DIABETIC NEPHROPATHIES; GENE FREQUENCY; GENOME, HUMAN; HUMANS; INDIANS, NORTH AMERICAN; KIDNEY FAILURE, CHRONIC; LONGITUDINAL STUDIES; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; VARIATION (GENETICS);

EID: 34047098737     PISSN: 00121797     EISSN: 00121797     Source Type: Journal    
DOI: 10.2337/db06-1072     Document Type: Article

References (44)

1. U.S. Renal Data System, USRDS Annual Data Report: Atlas of End-Stage Renal Disease in the United States. Bethesda, National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, 2002, p. 296-322
2. Nelson RG, Newman JM, Knowler WC, Sievers ML, Kunzelman CL, Pettitt DJ, Moffett CD, Teutsch SM, Bennett PH: Incidence of end-stage renal disease in type 2 (non-insulin-dependent) diabetes mellitus in Pima Indians. Diabetologia 31:730-736, 1988
3. Pettitt DJ, Saad MF, Bennett PH, Nelson RG, Knowler WC: Familial predisposition to renal disease in two generations of Pima Indians with type 2 (non-insulin-dependent) diabetes mellitus. Diabetologia 33:438-443, 1990
4. Seaquist ER, Goetz FC, Rich S, Barbosa J: Familial clustering of diabetic kidney disease: evidence for genetic susceptibility to diabetic nephropathy. N Engl J Med 320:1161-1165, 1989
5. Quinn M, Angelico MC, Warram JH, Krolewski AS: Familial factors determine the development of diabetic nephropathy in patients with IDDM. Diabetologia 39:940-945, 1996
6. Freedman BI, Tuttle AB, Spray BJ: Familial predisposition to nephropathy in African-Americans with non-insulin-dependent diabetes mellitus. Am J Kidney Dis 25:710-713, 1995
7. Spray BJ, Atassi NG, Tuttle AB, Freedman BI: Familial risk, age at onset, and cause of end-stage renal disease in white Americans. J Am Soc Nephrol 5:1806-1810, 1995
8. Canani LH, Gerchman F, Gross JL: Familial clustering of diabetic nephropathy in Brazilian type 2 diabetic patients. Diabetes 48:909-913, 1999
9. Faronato PP, Maioli M, Tonolo G, Brocco E, Noventa F, Piarulli F, Abaterusso C, Modena F, de Bigontina G, Velussi M, Inchiostro S, Santeusanio F, Bueti A, Nosadini R: Clustering of albumin excretion rate abnormalities in Caucasian patients with NIDDM: the Italian NIDDM Nephropathy Study Group. Diabetologia 40:816-823, 1997
10. Imperatore G, Knowler WC, Pettitt DJ, Kobes S, Bennett PH, Hanson RL: Segregation analysis of diabetic nephropathy in Pima Indians. Diabetes 49:1049-1056, 2000
11. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 273:1516-1517, 1996
12. Carlson CS, Eberle MA, Kruglyak L, Nickerson DA: Mapping complex disease loci in whole-genome association studies. Nature 429:446-452, 2004
13. Wang WY, Barratt BJ, Clayton DG, Todd JA: Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6:109-118, 2005
14. Brohede J, Dunne R, McKay JD, Hannan GN: PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays. Nucleic Acid Res 33:e142, 2005
15. Meaburn E, Butcher LM, Schalkwyk LC, Plomin R: Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans. Nucleic Acid Res 34:e27, 2006
16. Meaburn E, Butcher LM, Liu L, Fernandes C, Hansen V, Al-Chalabi A, Plomin R, Craig I, Schalkwyk LC: Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics 6:52, 2005
17. Craig I, Meaburn E, Butcher L, Hill L, Plomin R: Single-nucleotide polymorphism genotyping in DNA pools. Methods Mol Biol 311:147-164, 2005
18. Kirov G, Nikolov I, Georgieva L, Moskvina V, Owen MJ, O'Donovan MC: Pooled DNA genotyping on Affymetrix SNP genotyping arrays. BMC Genomics 7:27, 2006
19. Craig I, Plomin R: Quantitative trait loci for IQ and other complex traits: single-nucleotide polymorphism genotyping using pooled DNA and microarrays. Genes Brain Behav 5 (Suppl. 1):32-37, 2006
20. Liu QR, Drgon T, Walther D, Johnson C, Poleskaya O, Hess J, Uhl GR: Pooled association genome scanning: validation and use to identify addiction vulnerability loci in two samples. Proc Natl Acad Sci U S A 102:11864-11869, 2005
21. Butcher LM, Meaburn E, Dale PS, Sham P, Schalkwyk LC, Craig IW, Plomin R: Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms. Mol Psychiatry 10:384-392, 2005
22. Butcher LM, Meaburn E, Knight J, Sham PC, Schalkwyk LC, Craig IW, Plomin R: SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children. Hum Mol Genet 14:1315-1325, 2005
23. Knowler WC, Bennett PH, Hamman RF, Miller M: Diabetes incidence and prevalence in Pima Indians: a 19-fold greater incidence than in Rochester, Minnesota. Am J Epidemiol 108:497-505, 1978
24. Imperatore G, Hanson RL, Pettitt DJ, Kobes S, Bennett PH, Knowler WC: Sib-pair linkage analysis for susceptibility genes for microvascular complications among Pima Indians with type 2 diabetes: Pima Diabetes Genes Group. Diabetes 47:821-830, 1998
25. Hanson RL, Ehm MG, Pettitt DJ, Prochazka M, Thompson DB, Timberlake D, Foroud T, Kobes S, Baier L, Burns DK, Almasy L, Blangero J, Garvey WT, Bennett PH, Knowler WC: An autosomal genomic scan for loci linked to type II diabetes mellitus and body-mass index in Pima Indians. Am J Hum Genet 63:1130-1138, 1998
26. Wolford JK, Yeatts KA, Red Eagle AR, Nelson RG, Knowler WC, Hanson RL: Variants in the gene encoding aldose reductase (AKR1B1) and diabetic nephropathy in American Indians. Diabet Med 23:367-376, 2006
27. Lovmar L, Ahlford A, Jonsson M, Syvanen AC: Silhouette scores for assessment of SNP genotype clusters. BMC Genomics 6:35, 2005
28. Konheim YL, Wolford JK: Association of a promoter variant in the inducible cyclooxygenase-2 gene (PTGS2) with type 2 diabetes mellitus in Pima Indians. Hum Genet 113:377-381, 2003
29. Xie XO, Ott J: Testing linkage disequilibrium between a disease gene and marker loci. Am J Hum Genet 53:1107, 1993
30. Zondervan KT, Cardon LR: The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89-100, 2004
31. Maniatis N, Collins A, Xu CF, McCarthy LC, Hewett DR, Tapper W, Ennis S, Ke X, Morton NE: The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci U S A 99:2228-2233, 2002
32. MacQueen J: Some methods for classification and analysis of multivariate observations. In Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability. Berkeley, CA, University of California Press, 1965, p. 281-297
33. O'Connell JR: Zero-recombinant haplotyping: applications to fine mapping using SNPs. Genet Epidemiol 19 (Suppl. 1):S64-S70, 2000
34. Lathrop GM, Lalouel JM: Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet 36:460-465, 1984
35. Mantel N: Chi-square tests with one degree of freedom; extensions of the Mantel-Haenszel procedure. J Am Stat Assoc 58:690-700, 1963
36. Imperatore G, Knowler WC, Nelson RG, Hanson RL: Genetics of diabetic nephropathy in the Pima Indians. Curr Diab Rep 1:275-281, 2001
37. Graham M, Adams JM: Chromosome 8 breakpoint far 3 of the c-myc oncogene in a Burkitt's lymphoma 2;8 variant translocation is equivalent to the murine pvt-1 locus. Embo J 5:2845-2851, 1986
38. Shtivelman E, Bishop JM: The PVT gene frequently amplifies with MYC in tumor cells. Mol Cell Biol 9:1148-1154, 1989
39. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB: Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 99:4465-4470, 2002
40. Colhoun HM, McKeigue PM, Davey Smith G: Problems of reporting genetic associations with complex outcomes. Lancet 361:865-872, 2003
41. Manly KF: Reliability of statistical associations between genes and disease. Immunogenetics 57:549-558, 2005
42. Pe'er I, de Bakker PI, Maller J, Yelensky R, Altshuler D, Daly MJ: Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet 38:663-667, 2006
43. Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK: A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 38:1251-1260, 2006
44. Hanson RL, Looker HC, Ma L, Muller YL, Baier LJ, Knowler WC: Design and analysis of genetic association studies to finely map a locus identified by linkage analysis: sample size and power calculations. Ann Intern Med 70:332-349, 2006