Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix

Heredity

Volumn 95, Issue 3, 2005, Pages 221-227

  Li, J ^a   Ji, L ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

Experiment wise significant level; False discovery rate; Multilocus analysis; Multiple testing

Indexed keywords

EIGENVALUE;

ARTICLE; BIOLOGICAL MODEL; GENETIC PREDISPOSITION; GENETIC SCREENING; MEDICAL GENETICS; METHODOLOGY; STATISTICAL ANALYSIS;

DATA INTERPRETATION, STATISTICAL; GENETIC PREDISPOSITION TO DISEASE; GENETIC SCREENING; GENETICS, MEDICAL; MODELS, GENETIC; RESEARCH DESIGN;

EID: 30744434862     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800717     Document Type: Article

References (28)

1. Benjamini Y, Hochberg Y (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc Ser B (Methodological) 57: 289-300.
2. Benjamini Y, Liu W (1999). A step-down multiple hypotheses testing procedure that controls the false discovery rate under independence. J Stat Plan Infer 82: 163.
3. Benjamini Y, Yekutieli D (2001). The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165-1188.
4. Cheverud JM (2001). A simple correction for multiple comparisons in interval mapping genome scans. Heredity 87: 52-58.
5. Cheverud JM, Vaughn TT, Pletscher LS, Peripato AC, Adams ES, Erikson CF et al (2001). Genetic architecture of adiposity in the cross of LG/J and SM/J inbred mice. Mamm Genome 12: 3-12.
6. Churchill GA, Doerge RW (1994). Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
7. Clarkson DB, Fan Y-a, Joe H (1993). A remark on algorithm 643: FEXACT: an algorithm for performing Fisher's exact test in r x c contingency tables. ACM Trans Math Software (TOMS) 19: 484-488.
8. 2 tests. Biometrics 10: 417-451.
9. Cordell HJ, Clayton DG (2002). A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. Am J Hum Genet 70: 124-141.
10. Cover TM, Thomas JA (1991). Elements of Information Theory. Wiley-Interscience: New York.
11. Hill WG, Robertson A (1968). Linkage disequilibrium in finite populations. Theoret Appl Genet 38: 226-231.
12. Hoh J, Ott J (2003). Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4: 701-709.
13. Hoh J, Wille A, Ott J (2001). Trimming, weighting, and grouping SNPs in human case-control association studies. Genome Res 11: 2115-2119.
14. Keavney B, McKenzie CA, Connell JM, Julier C, Ratcliffe PJ, Sobel E et al (1998). Measured haplotype analysis of the angiotensin-I converting enzyme gene. Hum Mol Genet 7: 1745-1751.
15. King TS, Chinchilli VM (2001). A generalized concordance correlation coefficient for continuous and categorical data. Stat Med 20: 2131-2147.
16. Lander E, Kruglyak L (1995). Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11: 241-247.
17. Lander ES, Botstein D (1989). Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
18. Nelson MR, Kardia SL, Ferrell RE, Sing CF (2001). A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 11: 458-470.
19. 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.
20. Page GP, George V, Go RC, Page PZ, Allison DB (2003). 'Are we there yet'? Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. Am J Hum Genet 73: 711-719.
21. Piepho H-P (2001). A quick method for computing approximate thresholds for quantitative trait loci detection. Genetics 157: 425-432.
22. Ritchie MD, Hahn LW, Moore JH (2003). Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemiol 24: 150-157.
23. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF et al (2001). Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69: 138-147.
24. Sidak Z (1967). Rectangular confidence regions for the means of multivariate normal distributions. J Am Stat Assoc 62: 626-633.
25. Storey JD (2002). A direct approach to false discovery rates. J Roy Stat Soc Ser B 64: 479-498.
26. Storey JD, Tibshirani R (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
27. Xu Q, Jia YB, Zhang BY, Zou K, Tao YB, Wang YP et al (2004). Association study of an SNP combination pattern in the dopaminergic pathway in paranoid schizophrenia: a novel strategy for complex disorders. Mol Psychiatry 9: 510-521.
28. Zhang H, Bonney G (2000). Use of classification trees for association studies. Genet Epidemiol 19: 323-332.