Experimental designs for robust detection of effects in genome-wide case-control studies

Genetics

Volumn 189, Issue 4, 2011, Pages 1497-1514

  Ball, Roderick D ^a  

^a SCION   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN E;

ALZHEIMER DISEASE; ARTICLE; CASE CONTROL STUDY; CROHN DISEASE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC MODEL; GENOTYPE; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM;

BAYES THEOREM; CASE-CONTROL STUDIES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; RESEARCH DESIGN;

EID: 83655182972     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.131698     Document Type: Article

References (40)

1. Altshuler, D., J. N. Hirschhorn, M. Klannemark, C. M. Lindgren, M.-C. Vohl et al., 2000 The common PPARg Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat. Genet. 26: 76-80.
2. Ball, R. D., 2001 Bayesian methods for quantitative trait loci mapping based on model selection: approximate analysis using the Bayesian information criterion. Genetics 159: 1351-1364.
3. Ball, R. D., 2004 ldDesign-Design of experiments for detection of linkage disequilibrium. Available at: http://cran.r-project.org/ web/packages/ldDesign/index.html. Accessed November 2, 2011.
4. Ball, R. D., 2005 Experimental designs for reliable detection of linkage disequilibrium in unstructured random population association studies. Genetics 170: 859-873.
5. Ball, R. D., 2007a Statistical analysis and experimental design, pp. 133-196 in Association Mapping in Plants, edited by N. C.
6. Oraguzie, E. H. A. Rikkerink, S. E. Gardiner, and H. N. DeSilva. Springer-Verlag, New York.
7. Ball, R. D., 2007b Quantifying evidence for candidate gene polymorphisms-Bayesian analysis combining sequence-specific and QTL co-location information. Genetics 177: 2399-2416.
8. Benjamini, Y., and Y. Hochberg, 1995 Controlling the false discovery rate a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 159-165.
9. Berger, J., and D. Berry, 1988 Statistical analysis and the illusion of objectivity. Am. Sci. 76: 159-165.
10. De Groot, M. H., 1970 Optimal Statistical Decisions. McGraw-Hill, New York.
11. Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, 2007 Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316: 1331-1336.
12. Dickey, J. M., 1971 The weighted likelihood ratio, linear hypothesis on normal location parameters. Ann. Math. Stat. 42: 204-223.
13. Dudbridge, F., and A. Gusnato, 2008 Estimation of significance thresholds for genomewide association scans. Genet. Epidemiol. 32: 227-234.
14. Emahazion, T., L. Feuk, M. Jobs, S. L. Sawyer, D. Fredman et al., 2001 SNP association studies in Alzheimer's disease highlight problems for complex disease analysis. Trends Genet. 17: 407-413.
15. Fisher, R. A. 1959 Statistical Methods and Scientific Inference, Ed. 2. Oliver and Boyd, Edinburgh and London.
16. Gudbjartsson, D. F., G. B. Walters, G. Thorleifsson, H. Stefansson, B. V. Halldorsson et al., 2008 Many sequence variants affecting diversity of adult human height. Nat. Genet. 40: 609-615.
17. Hindorff, L., H. Junkins, P. Hall, J. Mehta, and T. Manolio, 2011 A Catalog of Published Genome-Wide Association Studies. Available at: http://www.genome.gov/gwastudies. Accessed: May 16, 2011.
18. Johnson, V., 2005 Bayes factors based on test statistics. J. R. Stat. Soc. Ser. B Stat. Methodol. 67: 689-701.
19. Johnson, V., 2008 Properties of Bayes factors based on test statistics. Scand. J. Stat. 35: 354-368.
20. Lango Allen, H., K. Estrada, G. Lettre, S. I. Berndt, M. N. Weedon et al., 2010 Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467: 832-838.
21. Lettre, G., A. U. Jackson, C. Geiger, F. R. Schumacher, S. Berndt et al., 2008 Identification of ten loci associated with height highlights new biological pathways in human growth. Nat. Genet. 40: 584-591.
22. Lindley, D. V., 1957 A statistical paradox. Biometrika 44: 187-192.
23. Luo, Z. W., 1998 Linkage disequilibrium in a two-locus model. Heredity 80: 198-208.
24. Menashe, I., and P. Rosenberg, and B. Chen, 2008 PGA: power calculator for case-control genetic association analyses. BMC Genet. 9: 36.
25. Miller, A., 1990 Subset Selection in Regression (Monographs on Statistics and Applied Probability 40). Chapman & Hall, London.
26. Nielsen, D., and B. Weir, 2001 Association studies under general disease models. Theor. Popul. Biol. 60: 253-263.
27. O'Hagan, A., C. Buck, A. Daneshkhah, J. R. Eiser, P. H. Garthwaite et al., 2006 Uncertain Judgements: Eliciting Experts' Probabilities. Wiley, Hoboken, NJ.
28. Purcell, S., S. S. Cherny, and P. C. Sham, 2003 Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19: 149-150. Available at: http://pngu.mgh.harvard.edu/~purcell/gpc/cc2.html. Accessed: November 2, 2011.
29. Sellke, T., M. J. Bayarri, and J. O. Berger, 2001 Calibration of pvalues for testing precise null hypotheses. Am. Stat. 55: 62-71.
30. Sillanpää, M. J., and J. Corander, 2002 Model choice in gene mapping: what and why. Trends Genet. 18: 301-307.
31. Spiegelhalter, D., and A. F. M. Smith, 1982 Bayes factors for linear and log-linear models with vague prior information. J. R. Stat. Soc. B 44(3): 377-387.
32. Stephens, M., and D. J. Balding, 2009 Bayesian statistical methods for association studies. Nat. Rev. Genet. 10: 681-690.
33. Strittmatter, W., and A. Roses, 1996 Apolipoprotein E and Alzheimer's disease. Annu. Rev. Neurosci. 19: 53-77.
34. Terwilliger, J., and K. Weiss, 1998 Linkage disequilibrium mapping of complex disease: Fantasy or reality? Curr. Opin. Biotechnol. 9: 578-594.
35. Visscher, P., 2008 Sizing up human height variation. Nat. Genet. 40: 489-490.
36. Wakefield, J., 2007 A Bayesian measure of the probability of false discovery in genetic epidemiology studies. Am. J. Hum. Genet. 81: 208-227.
37. Weedon, M., H. Lango, C. Lindgren, C. Wallace, D. Evans et al., 2008 Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet. 40: 575-583.
38. Wellcome Trust Case Control Consortium, 2007 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
39. Wellcome Trust Case Control Consortium, 2010 Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464: 713-722.
40. Yang, J., B. Beben, D. McEvoy, S. Gordon, A. Henders et al., 2010 Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42: 565-569, 608.