A new approach to account for the correlations among single nucleotide polymorphisms in genome-wide association studies

Human Heredity

Volumn 72, Issue 1, 2011, Pages 1-9

  Chen, Zhongxue ^a   Liu, Qingzhong ^b  

^a UNIVERSITY OF TEXAS   (United States)

^b SAM HOUSTON STATE UNIVERSITY   (United States)

Author keywords

Effective number; Genome wide association studies; Multiple comparisons; Single nucleotide polymorphisms

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; BONFERRONI CORRECTION; COMPARATIVE STUDY; GENETIC ASSOCIATION; MATHEMATICAL ANALYSIS; SIDAK CORRECTION; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENETIC ASSOCIATION STUDIES; GENOME; GENOMICS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 80051655198     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000330135     Document Type: Article

References (26)

1. Šidák Z: Rectangular confidence regions for the means of multivariate normal distributions. J Am Stat Assoc 1967; 62: 626-633.
2. Bonferroni C: Il calcolo delle assicurazioni su gruppi di teste; in Studi in Onore del Professore Salvatore Ortu Carboni. Rome, 1935, pp 13-60.
3. Bonferroni C: Teoria statistica delle classi e calcolo delle probabilità. Firenze, R Istituto Superiore di Scienze Economiche e Commerciali, 1936, vol 8, pp 3-62.
4. Churchill GA, Doerge RW: Empirical threshold values for quantitative trait mapping. Genetics 1994; 138: 963-971. (Pubitemid 24337818)
5. Gao X, Starmer J, Martin ER: A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genet Epidemiol 2008; 32: 361-369. (Pubitemid 351656307)
6. Cheverud JM: A simple correction for multiple comparisons in interval mapping genome scans. Heredity 2001; 87: 52-58. (Pubitemid 32974332)
7. Gao X, Becker LC, Becker DM, Starmer JD, Province MA: Avoiding the high Bonferroni penalty in genome-wide association studies. Genet Epidemiol 2010; 34: 100-105.
8. Li J, Ji L: Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 2005; 95: 221-227. (Pubitemid 43093236)
9. Nyholt DR: A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am J Hum Genet 2004; 74: 765-769. (Pubitemid 38420107)
10. Nyholt DR: Evaluation of Nyholt's procedure for multiple testing correction-author's reply. Hum Hered 2005; 60: 61-62. (Pubitemid 41291519)
11. Moskvina V, Schmidt KM: On multiple-testing correction in genome-wide association studies. Genet Epidemiol 2008; 32: 567-573.
12. Dudbridge F, Gusnanto A: Estimation of significance thresholds for genomewide association scans. Genet Epidemiol 2008; 32: 227-234. (Pubitemid 351550369)
13. Han B, Kang HM, Eskin E: Rapid and accurate multiple testing correction and power estimation for millions of correlated markers. PLoS Genet 2009; 5:e1000456.
14. Peer I, Yelensky R, Altshuler D, Daly MJ: Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol 2008; 32: 381-385. (Pubitemid 351656309)
15. Salyakina D, Seaman SR, Browning BL, Dudbridge F, Muller-Myhsok B: Evaluation of Nyholt's procedure for multiple testing correction. Hum Hered 2005; 60: 19-25, discussion 61-12. (Pubitemid 41291516)
16. Armitage P: Tests for linear trends in proportions and frequencies. Biometrics 1955; 11: 375-386.
17. Cochran W: Some methods for strengthening the common chi-square tests. Biometrics 1954; 10: 417-451.
18. Schaid DJ: Linkage disequilibrium testing when linkage phase is unknown. Genetics 2004; 166: 505-512. (Pubitemid 38364735)
19. Weir BS, Hill WG, Cardon LR: Allelic association patterns for a dense SNP map. Genet Epidemiol 2004; 27: 442-450. (Pubitemid 39602326)
20. Zaykin DV: Bounds and normalization of the composite linkage disequilibrium coefficient. Genet Epidemiol 2004; 27: 252-257. (Pubitemid 39447247)
21. Zaykin DV, Meng Z, Ehm MG: Contrasting linkage-disequilibrium patterns between cases and controls as a novel associationmapping method. Am J Hum Genet 2006; 78: 737-746.
22. Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995; 12: 921-927.
23. Nielsen DM, Ehm MG, Weir BS: Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus. Am J Hum Genet 1998; 63: 1531-1540. (Pubitemid 30418550)
24. Wittke-Thompson JK, Pluzhnikov A, Cox NJ: Rational inferences about departures from Hardy-Weinberg equilibrium. Am J Hum Genet 2005; 76: 967-986. (Pubitemid 40705433)
25. Rinaldo A, Bacanu SA, Devlin B, Sonpar V, Wasserman L, Roeder K: Characterization of multilocus linkage disequilibrium. Genet Epidemiol 2005; 28: 193-206. (Pubitemid 40404574)
26. Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK: A worldwide survey of haploype variation and linkage disequilibrium in the human genome. Nat Genet 2006; 38: 1251-1260. (Pubitemid 44646287)