Hidden population substructures in an apparently homogeneous population bias association studies

European Journal of Human Genetics

Volumn 14, Issue 2, 2006, Pages 236-244

  Berger, Mario ^a   Stassen, Hans H ^b   Köhler, Karola ^c   Krane, Vera ^a   Mönks, Detlev ^a   Wanner, Christoph ^a   Hoffmann, Katrin ^d   Hoffmann, Michael M ^e   Zimmer, Michael ^a   Bickeböller, Heike ^c   Lindner, Tom M ^a,f  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

^d HUMBOLDT UNIVERSITY   (Germany)

^e UNIVERSITY OF FREIBURG   (Germany)

^f UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

Association study; Calpain 10; End stage diabetic nephropathy; Haplotypes; Population structure analysis; Type 2 diabetes mellitus

Indexed keywords

CALPAIN 10;

ADULT; AGED; ALLELE; ARTICLE; CONTROLLED STUDY; DIABETIC NEPHROPATHY; ETHNOLOGY; FEMALE; GENE FREQUENCY; GENE LOCUS; GENE VECTOR; GENETIC ANALYSIS; GENETIC MARKER; GENOTYPE; HAPLOTYPE; HUMAN; INTRON; MAJOR CLINICAL STUDY; MALE; MICROSATELLITE MARKER; NON INSULIN DEPENDENT DIABETES MELLITUS; POPULATION GENETICS; POPULATION STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

BIAS (EPIDEMIOLOGY); CALPAIN; DIABETES MELLITUS, TYPE 2; DNA PRIMERS; FEMALE; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOTYPE; GERMANY; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 31344454230     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201546     Document Type: Article

References (50)

1. WacholdeB S, Rothman N, Caporaso N: Counterpoint: bias from population stratification is not a major threat to the validity of conclusions from epidemiological studies of common polymorphisms and cancer. Cancer Epidemiol Biomarkers Prev 2002; 11: 513-520.
2. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P: Association mapping in structured populations. Am J Hum Genet 2000; 67: 170-181.
3. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000; 155: 945-959.
4. Ardlie KG, Lunetta KL, Seielstad M: Testing for population subdivision and association in four case-control studies. Am J Hum Genet 2002; 71: 304-311.
5. Knowler WC, Williams RC, Pettitt DJ, Steinberg AG: Gm3;5,13,14 and type 2 diabetes mellitus: An association in American Indians with genetic admixture. Am J Hum Genet 1988; 43: 520-526.
6. Kittles RA, Chen W, Panguluri RK et al: CYP3A4-V and prostate cancer in African Americans: Causal or confounding association because of population stratification? Hum Genet 2002; 110: 553-560.
7. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN: Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet 2003; 33: 177-182.
8. Freedman ML, Reich D, Penney KL et al: Assessing the impact of population stratification on genetic association studies. Nat Genet 2004; 36: 388-393.
9. Helgason A, Yngvadottir B, Hrafnkelsson B, Gulcher J, Stefansson K: An Icelandic example of the impact of population structure on association studies. Nat Genet 2005; 37: 90-95.
10. Hanis CL, Boerwinkle E, Chakraborty R et al: A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2. Nat Genet 1996; 13: 161-166.
11. Horikawa Y, Oda N, Cox NJ et al: Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet 2000; 26: 163-175.
12. Weedon MN, Schwarz PE, Horikawa Y et al: Meta-analysis and a large association study confirm a role for calpain-10 variation in type 2 diabetes susceptibility. Am J Hum Genet 2003; 73: 1208-1212.
13. Baier LJ, Permana PA, Yang X et al: A calpain-10 gene polymorphism is associated with reduced muscle mRNA levels and insulin resistance. J Clin Invest 2000; 106: R69-73.
14. Chantrel F, Enache I, Bouiller M et al: Abysmal prognosis of patients with type 2 diabetes entering dialysis. Nephrol Dial Transplant 1999; 14: 129-136.
15. Ritz E: Nephropathy in type 2 diabetes. J Intern Med 1999; 245: 111-126.
16. Lindner TH, Monks D, Wanner C, Berger M: Genetic aspects of diabetic nephropathy. Kidney Int Suppl 2003; 84: S186-S191.
17. Wanner C, Krane V, Ruf G, Marz W, Ritz E: Rationale and design of a trial improving outcome of type 2 diabetics on hemodialysis. Die Deutsche Diabetes Dialyse Studie Investigators. Kidney Int Suppl 1999; 71: S222-226.
18. Berger M, Zschemisch S, Hocher B et al: Alternative approach for rapid and reliable single-nucleotide polymorphism typing with double restriction mutagenesis primer PCR. Clin Chem 2004; 50: 2376-2378.
19. Stassen HH, Hoffman K, Scharfetter C: Similarity by state/descent and genetic vector spaces: Analysis of a longitudinal family study. BMC Genet 2003; 4 (Suppl 1): S59.
20. Stassen HH, Meier M: Master.GEN: A program package for the multivariate analysis of genetic diversity. Mol Psychiatry 1999; 4 (Suppl 1): S62.
21. Stassen HH, Begleiter H, Porjesz B, Rice J, Scharfetter C, Reich T: Structural decomposition of genetic diversity in families with alcoholism. Genet Epidemiol 1999; 17 (Suppl 1): S325-S330.
22. Stassen HH, Begleiter H, Beirut L et al: Oligogenic approaches to the predisposition of alcohol dependence. A genome-wide search on 255 families. Neurol Psychiatr Brain Res 2004.
23. Stassen HH, Hoffmann K, Scharfetter C: Analysis of a longitudinal family study; In: Almasy L, Amos CI, Bailey-Wilson JE, Cantor RM, Jaquish CE, Martinez M, Neuman RJ, Olson JM, Palmer LJ, Rich SS, Spence MA, MacCluer JW (eds.): Genetic Analysis Workshop 13: Analysis of longitudinal family data for complex diseases and related risk factors: BMC Genet 2003, vol. 4: Pp S59, 51-56.
24. Stassen HH, Bridler R, Hell D, Weisbrod M, Scharfetter C: Ethnicity-independent genetic basis of functional psychoses. A genotype-to-phenotype approach. Neuropsychiatr Genet 2004; 124: 101-112.
25. Stassen HH, Begleiter H, Hergersberg M et al: A multivariate feature vector approach to quantifying genetic diversity. Mol Psychiatry 1999; 4 (Suppl. 1): S62.
26. Stassen HH, Scharfetter C: Oligogenic approaches to the predisposition of asthma in ethnically diverse populations. Genet Epidemiol 2001; 21 (Suppl 1): S284-S289.
27. Hoffmann K, Stassen HH, Reis A: Genkartierung in Isolatpopulationen. Medizinische Genetik 2000; 12: 428-437.
28. Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995; 29: 311-322.
29. Agresti A: An Introduction to Categorical Data Analysis. New York: John Wiley & Sons Inc., 1996, p section 7.3.5.
30. Suarez BK, Hampe CL, Van Eerdewegh P: Problems of replicating linkage claims in psychiatry; in: Gershon ES, Cloninger CR (eds).: Genetic Approaches to Mental Disorders. American Psychiatric Press, 1994.
31. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 1996; 273: 1516-1517.
32. Shima Y, Nakanishi K, Odawara M, Kobayashi T, Ohta H: Association of the SNP-19 genotype 22 in the calpain-10 gene with elevated body mass index and hemoglobin A1c levels in Japanese. Clin Chim Acta 2003; 336: 89-96.
33. Ehrmann DA, Schwarz PE, Hara M et al: Relationship of calpain-10 genotype to phenotypic features of polycystic ovary syndrome. J Clin Endocrinol Metab 2002; 87: 1669-1673.
34. Lynn S, Evans JC, White C et al: Variation in the calpain-10 gene affects blood glucose levels in the British population. Diabetes 2002; 51: 247-250.
35. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB: Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 1994; 91: 3166-3170.
36. Frayling TM, McCarthy MI, Walker M et al: No evidence for linkage at candidate type 2 diabetes susceptibility loci on chromosomes 12 and 20 in United Kingdom Caucasians. J Clin Endocrinol Metab 2000; 85: 853-857.
37. Frayling TM, WalkeA M, McCarthy MI et al: Parent-offspring trios: a resource to facilitate the identification of type 2 diabetes genes. Diabetes 1999; 48: 2475-2479.
38. Evans JC, Frayling TM, Cassell PG et al: Studies of association between the gene for calpain-10 and type 2 diabetes mellitus in the United Kingdom. Am J Hum Genet 2001; 69: 544-552.
39. Garant MJ, Kao WH, Brancati F et al: SNP43 of CAPN10 and the risk of type 2 diabetes in African-Americans: The Atherosclerosis Risk in Communities Study. Diabetes 2002; 51: 231-237.
40. Orho-Melander M, Klannemark M, Svensson MK, Ridderstrale M, Lindgren CM, Groop L: Variants in the calpain-10 gene predispose to insulin resistance and elevated free fatty acid levels. Diabetes 2002; 51: 2658-2664.
41. Sun HX, Zhang KX, Du WN et al: Single nucleotide polymorphisms in CAPN10 gene of Chinese people and its correlation with type 2 diabetes mellitus in Han people of northern China. Biomed Environ Sci 2002; 15: 75-82.
42. Chen LX, Ji LN, Han XY, Zhu F: Study on Calpain10 gene polymorphism in Chinese type 2 diabetes families. Zhonghua Yi Xue Za Zhi 2003; 83: 1856-1859.
43. Fingerlin TE, Erdos MR, Watanabe RM et al: Variation in three single nucleotide polymorphisms in the calpain-10 gene not associated with type 2 diabetes in a large Finnish cohort. Diabetes 2002; 51: 1644-1648.
44. Daimon M, Oizumi T, Saitoh T et al: Calpain 10 gene polymorphisms are related, not to type 2 diabetes, but to increased serum cholesterol in Japanese. Diabetes Res Clin Pract 2002; 56: 147-152.
45. Horikawa Y, Oda N, Yu L et al: Genetic variations in calpain-10 gene are not a major factor in the occurrence of type 2 diabetes in Japanese. J Clin Endocrinol Metab 2003; 88: 244-247.
46. del Bosque-Plata L, Aguilar-Salinas CA, Tusie-Luna MT et al: Association of the calpain-10 gene with type 2 diabetes mellitus in a Mexican population. Mol Genet Metab 2004; 81: 122-126.
47. Hegele RA, Harris SB, Zinman B, Hanley AJ, Cao H: Absence of association of type 2 diabetes with CAPN10 and PC-1 polymorphisms in Oji-Cree. Diabetes Care 2001; 24: 1498-1499.
48. Malecki MT, Moczulski DK, Klupa T et al: Homozygous combination of calpain 10 gene haplotypes is associated with type 2 diabetes mellitus in a Polish population. Eur J Endocrinol 2002; 146: 695-699.
49. Tsai HJ, Sun G, Weeks DE et al: Type 2 diabetes and three calpain-10 gene polymorphisms in Samoans: No evidence of association. Am J Hum Genet 2001; 69: 1236-1244.
50. Rasmussen SK, Urhammer SA, Berglund L et al: Variants within the calpain-10 gene on chromosome 2q37 (NIDDM1) and relationships to type 2 diabetes, insulin resistance, and impaired acute insulin secretion among Scandinavian Caucasians. Diabetes 2002; 51: 3561-3567.