A Weighted False Discovery Rate Control Procedure Reveals Alleles at FOXA2 that Influence Fasting Glucose Levels

American Journal of Human Genetics

Volumn 86, Issue 3, 2010, Pages 440-446

  Xing, Chao ^a   Cohen, Jonathan C ^a   Boerwinkle, Eric ^b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE; HEPATOCYTE NUCLEAR FACTOR 3BETA;

AFRICAN AMERICAN; ANALYTIC METHOD; ARTICLE; ATHEROSCLEROSIS; DIET RESTRICTION; EFFECT SIZE; EUROPEAN AMERICAN; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; GENOTYPE; GLUCOSE BLOOD LEVEL; HUMAN; MAJOR CLINICAL STUDY; POPULATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICAN AMERICANS; ALLELES; BIOSTATISTICS; BLOOD GLUCOSE; EUROPEAN CONTINENTAL ANCESTRY GROUP; FASTING; GENE FREQUENCY; GENOME-WIDE ASSOCIATION STUDY; HEPATOCYTE NUCLEAR FACTOR 3-BETA; HUMANS; LINKAGE DISEQUILIBRIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77649237725     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2010.01.025     Document Type: Article

References (49)

1. Hindorff, L.A., Junkins, H.A., Mehta, J.P., and Manolio, T.A. A Catalog of Published Genome-wide Association Studies.
2. Altshuler D., Daly M.J., and Lander E.S. Genetic mapping in human disease. Science 322 (2008) 881-888
3. Frazer K.A., Murray S.S., Schork N.J., and Topol E.J. Human genetic variation and its contribution to complex traits. Nat. Rev. Genet. 10 (2009) 241-251
4. McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P., and Hirschhorn J.N. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9 (2008) 356-369
5. Ioannidis J.P., Thomas G., and Daly M.J. Validating, augmenting and refining genome-wide association signals. Nat. Rev. Genet. 10 (2009) 318-329
6. Goldstein D.B. Common genetic variation and human traits. N. Engl. J. Med. 360 (2009) 1696-1698
7. Frazer K.A., Ballinger D.G., Cox D.R., Hinds D.A., Stuve L.L., Gibbs R.A., Belmont J.W., Boudreau A., Hardenbol P., Leal S.M., et al., International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (2007) 851-861
8. International HapMap Consortium. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
9. Holm S. A Simple Sequentially Rejective Multiple Test Procedure. Scand. J. Stat. 6 (1979) 65-70
10. Dalmasso C., Génin E., and Trégouet D.A. A weighted-Holm procedure accounting for allele frequencies in genomewide association studies. Genetics 180 (2008) 697-702
11. Benjamini Y., and Hochberg Y. Multiple Hypotheses Testing with Weights. Scand. J. Stat. 24 (1997) 407-418
12. The ARIC Investigators. The Atherosclerosis Risk in Communities (ARIC) Study: design and objectives. The ARIC investigators. Am. J. Epidemiol. 129 (1989) 687-702
13. McCarroll S.A., Kuruvilla F.G., Korn J.M., Cawley S., Nemesh J., Wysoker A., Shapero M.H., de Bakker P.I., Maller J.B., Kirby A., et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40 (2008) 1166-1174
14. International HapMap Consortium. The International HapMap Project. Nature 426 (2003) 789-796
15. Wigginton J.E., Cutler D.J., and Abecasis G.R. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 76 (2005) 887-893
16. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C.R., Lim E.P., Kalyanaraman N., et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22 (1999) 231-238
17. Wong G.K., Yang Z., Passey D.A., Kibukawa M., Paddock M., Liu C.R., Bolund L., and Yu J. A population threshold for functional polymorphisms. Genome Res. 13 (2003) 1873-1879
18. Gorlov I.P., Gorlova O.Y., Sunyaev S.R., Spitz M.R., and Amos C.I. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am. J. Hum. Genet. 82 (2008) 100-112
19. Devlin B., and Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29 (1995) 311-322
20. Price A.L., Butler J., Patterson N., Capelli C., Pascali V.L., Scarnicci F., Ruiz-Linares A., Groop L., Saetta A.A., Korkolopoulou P., et al. Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. 4 (2008) e236
21. Tian C., Plenge R.M., Ransom M., Lee A., Villoslada P., Selmi C., Klareskog L., Pulver A.E., Qi L., Gregersen P.K., and Seldin M.F. Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 4 (2008) e4
22. Smith M.W., Patterson N., Lautenberger J.A., Truelove A.L., McDonald G.J., Waliszewska A., Kessing B.D., Malasky M.J., Scafe C., Le E., et al. A high-density admixture map for disease gene discovery in african americans. Am. J. Hum. Genet. 74 (2004) 1001-1013
23. Price A.L., Patterson N.J., Plenge R.M., Weinblatt M.E., Shadick N.A., and Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38 (2006) 904-909
24. Box G., and Cox D. An analysis of transformations (with discussions). J. R. Stat. Soc., B 26 (1964) 211-254
25. Devlin B., and Roeder K. Genomic control for association studies. Biometrics 55 (1999) 997-1004
26. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57 (1995) 289-300
27. Benjamini Y., and Yekutieli D. The Control of the False Discovery Rate in Multiple Testing under Dependency. Ann. Stat. 29 (2001) 1165-1188
28. Prokopenko I., Langenberg C., Florez J.C., Saxena R., Soranzo N., Thorleifsson G., Loos R.J., Manning A.K., Jackson A.U., Aulchenko Y., et al. Variants in MTNR1B influence fasting glucose levels. Nat. Genet. 41 (2009) 77-81
29. Chen W.M., Erdos M.R., Jackson A.U., Saxena R., Sanna S., Silver K.D., Timpson N.J., Hansen T., Orrù M., Grazia Piras M., et al. Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels. J. Clin. Invest. 118 (2008) 2620-2628
30. Bouatia-Naji N., Bonnefond A., Cavalcanti-Proença C., Sparsø T., Holmkvist J., Marchand M., Delplanque J., Lobbens S., Rocheleau G., Durand E., et al. A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. Nat. Genet. 41 (2009) 89-94
31. Bouatia-Naji N., Rocheleau G., Van Lommel L., Lemaire K., Schuit F., Cavalcanti-Proença C., Marchand M., Hartikainen A.L., Sovio U., De Graeve F., et al. A polymorphism within the G6PC2 gene is associated with fasting plasma glucose levels. Science 320 (2008) 1085-1088
32. Lyssenko V., Nagorny C.L., Erdos M.R., Wierup N., Jonsson A., Spégel P., Bugliani M., Saxena R., Fex M., Pulizzi N., et al. Common variant in MTNR1B associated with increased risk of type 2 diabetes and impaired early insulin secretion. Nat. Genet. 41 (2009) 82-88
33. Sabatti C., Service S.K., Hartikainen A.L., Pouta A., Ripatti S., Brodsky J., Jones C.G., Zaitlen N.A., Varilo T., Kaakinen M., et al. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat. Genet. 41 (2009) 35-46
34. Orho-Melander M., Melander O., Guiducci C., Perez-Martinez P., Corella D., Roos C., Tewhey R., Rieder M.J., Hall J., Abecasis G., et al. Common missense variant in the glucokinase regulatory protein gene is associated with increased plasma triglyceride and C-reactive protein but lower fasting glucose concentrations. Diabetes 57 (2008) 3112-3121
35. Victor R.G., Haley R.W., Willett D.L., Peshock R.M., Vaeth P.C., Leonard D., Basit M., Cooper R.S., Iannacchione V.G., Visscher W.A., et al., Dallas Heart Study Investigators. The Dallas Heart Study: a population-based probability sample for the multidisciplinary study of ethnic differences in cardiovascular health. Am. J. Cardiol. 93 (2004) 1473-1480
36. Romeo S., Kozlitina J., Xing C., Pertsemlidis A., Cox D., Pennacchio L.A., Boerwinkle E., Cohen J.C., and Hobbs H.H. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat. Genet. 40 (2008) 1461-1465
37. Blair S.N., Kohl III H.W., Paffenbarger Jr. R.S., Clark D.G., Cooper K.H., and Gibbons L.W. Physical fitness and all-cause mortality. A prospective study of healthy men and women. JAMA 262 (1989) 2395-2401
38. Hedges L.V. Meta-Analysis. J. Educ. Stat. 17 (1992) 279-296
39. Friedman J.R., and Kaestner K.H. The Foxa family of transcription factors in development and metabolism. Cell. Mol. Life Sci. 63 (2006) 2317-2328
40. Dupuis J., Langenberg C., Prokopenko I., Saxena R., Soranzo N., Jackson A.U., Wheeler E., Glazer N.L., Bouatia-Naji N., Gloyn A.L., et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat. Genet. 42 (2010) 105-116
41. Chapman J.M., Cooper J.D., Todd J.A., and Clayton D.G. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered. 56 (2003) 18-31
42. Spencer C.C., Su Z., Donnelly P., and Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet. 5 (2009) e1000477
43. Benjamini Y., and Yekutieli D. Quantitative trait Loci analysis using the false discovery rate. Genetics 171 (2005) 783-790
44. Genovese C.R., Roeder K., and Wasserman L. False discovery rate control with p value weighting. Biometrika 93 (2006) 509-524
45. Hoggart C.J., Clark T.G., De Iorio M., Whittaker J.C., and Balding D.J. Genome-wide significance for dense SNP and resequencing data. Genet. Epidemiol. 32 (2008) 179-185
46. Dudbridge F., and Gusnanto A. Estimation of significance thresholds for genomewide association scans. Genet. Epidemiol. 32 (2008) 227-234
47. Pe'er I., Yelensky R., Altshuler D., and Daly M.J. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet. Epidemiol. 32 (2008) 381-385
48. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447 (2007) 661-678
49. Wakefield J. Bayes factors for genome-wide association studies: comparison with P values. Genet. Epidemiol. 33 (2008) 79-86