Avoiding the high bonferroni penalty in genome-wide association studies

Genetic Epidemiology

Volumn 34, Issue 1, 2010, Pages 100-105

  Gao, Xiaoyi ^a   Becker, Lewis C ^b   Becker, Diane M ^b   Starmer, Joshua D ^c,d   Province, Michael A ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Genetic association studies; Genome wide significance; Multiple testing correction

Indexed keywords

ACETYLSALICYLIC ACID;

ARTICLE; CHROMOSOME; GENE FREQUENCY; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOME ANALYSIS; GENOTYPE; GOLD STANDARD; MUTATION; POPULATION; PRACTICE GUIDELINE; PUNISHMENT; QUALITY CONTROL; SAMPLE; THEORY; TREATMENT RESPONSE;

BIOMETRY; DATA INTERPRETATION, STATISTICAL; GENOME-WIDE ASSOCIATION STUDY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 75649151064     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20430     Document Type: Article

References (22)

1. Armitage P. 1955. Tests for linear trends in proportions and frequencies. Biometrics 11:375-386.
2. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
3. Browning SR, Browning BL. 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097.
4. Casella G, Berger RL. 2001. Statistical Inference. 2nd Edition. Pacific Grove, CA: Duxbury Press. p 230.
5. Cheverud JM. 2001. A simple correction for multiple comparisons in interval mapping genome scans. Heredity 87:52-58.
6. Churchill GA, Doerge RW. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
7. 2 tests. Biometrics 10:417-451.
8. Conneely KN, Boehnke M. 2007. So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. Am J Hum Genet 81:1158-1168.
9. Gao X, Starmer J, Martin ER. 2008. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genet Epidemiol 32:361-369.
10. Hastie T, Tibshirani R, Friedman J. 2001. The Elements of Statistical Learning. New York: Springer.
11. Li J, Ji L. 2005. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 95:221-227.
12. Li Y, Abecasis GR. 2006. Mach 1.0: rapid haplotype reconstruction and missing genotype inference. Am J Hum Genet S79:2290.
13. Lin DY. 2005. An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics 21:781-787.
14. Marchini J, Howie B, Myers S, McVean G, Donnelly P. 2007. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39:906-913.
15. Moskvina V, Schmidt KM. 2008. On multiple-testing correction in genome-wide association studies. Genet Epidemiol 32:567-573.
16. Nyholt DR. 2004. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am J Hum Genet 74:765-769.
17. Nyholt DR. 2005. Evaluation of Nyholt's procedure for multiple testing correction - author's reply. Hum Hered 60:61-62.
18. Salyakina D, Seaman SR, Browning BL, Dudbridge F, Muller-Myhsok B. 2005. Evaluation of Nyholt's procedure for multiple testing correction. Hum Hered 60:19-25, discussion 61-62.
19. Seaman SR, Müller-Myhsok B. 2005. Rapid simulation of P values for product methods and multiple-testing adjustment in association studies. Am J Hum Genet 76:399-408.
20. Servin B, Stephens M. 2007. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3:e114.
21. Ŝidák Z. 1967. Rectangular confidence regions for the means of multivariate normal distributions. J Am Stat Assoc 62:626-633.
22. Splansky GL, Corey D, Yang Q, Atwood LD, Cupples LA, Benjamin EJ, D'Agostino Sr RB, Fox CS, Larson MG, Murabito JM, O'Donnell CJ, Vasan RS, Wolf PA, Levy D. 2007. The third generation cohort of the National Heart, Lung, and Blood Institute's Framingham Heart Study: design, recruitment, and initial examination. Am J Epidemiol 165:1328-1335.