The impact of population stratification on commonly used statistical procedures in population-based QTL association studies

Random Walk, Sequential Analysis and Related Topics: A Festschrift in Honor of Yuan-Shih Chow

Volumn , Issue , 2006, Pages 311-333

  Qin, Hong ^a,c   Zhang, Hong ^b,c   Li, Zhaohai ^c,d  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c GEORGE WASHINGTON UNIVERSITY   (United States)

^d NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Association study; Case control design; False positive rate; Population structure; Quantitative trait locus (QTL); Regression analysis

Indexed keywords

CUTOFF FREQUENCY; REGRESSION ANALYSIS; STATISTICAL TESTS;

ASSOCIATION ANALYSIS; CASE-CONTROL; FALSE POSITIVE RATES; POPULATION STRATIFICATION; POPULATION STRUCTURES; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAITS; SIMULATION STUDIES;

POPULATION STATISTICS;

EID: 77954807603     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789812772558_0021     Document Type: Chapter

References (25)

1. Bacanu, S. A., Devlin, B. and Roeder, K. (2000). The power of genomic control. American Journal of Human Genetics 28, 782-793.
2. Devlin, B. and Roeder, K. (1999). Genomic control for association studies, Biometrics 55, 997-1004.
3. Devlin, B., Roeder, K. and Wasserman, L. (2001). Genomic control, a new approach to genetic-based association studies. Theoretical Population Biology 60, 155-166.
4. Ewens, W. J. and Spielman, R. (1995). The Transmission/Disequilibrium test: history, subdivision, and admixture. American Journal of Human Genetics 57, 455-464.
5. Li, C. C. (1969). Population subdivision with respect to multiple alleles. Annals of Human Genetic 33, 23-29.
6. Li, Z., Gail, M. H., Pee, D. and Gastwirth, J. L. (2001). Statistical properties of Teng and Risch’s sibship type tests for detecting an association between diseases and a candidate allele. Human Heredity 53, 114-129.
7. Li, Z., Zhang, H., Gastwirth J. L. and Gail, M. H. (2005). Excessive false positive rate caused by population stratification and disease rate heterogeneity in case-control association studies. (Personal communication)
8. Morton, N. E. and Collins, A. (1998). Tests and estimates of allelic association in complex inheritance. Proceedings of the National Academy of Sciences of the United States of America 95, 11389-11393.
9. Ohashi, J., Yamamoto, S., Tsuchiya, N., Hatta, Y., Komata, T., Matsushita, M. and Tokunaga, K. (2001). Comparison of statistical power between 2 x2 allele frequency and allele positivity tables in case-control studies of complex disease genes. Annals of Human Genetic 65, 197-206.
10. Pritchard, J. K., Stephens, M., Donnelly, P. (2000a). Inference of population structure using multilocus genotype data. Genetics 65, 220-228.
11. Pritchard, J. K., Stephens, M., Rosenberg, N. A., Donnelly, P. (2000b). Association mapping in structured population. American Journal of Human Genetics 67, 170-181.
12. Rabinowitz, D. (1997). A transmission disequilibrium test for qauntitative trait loci. Human Heredity 47, 342-350.
13. Rannala, B. and Slatkin, M. (1998). Likelihood analysis of disequilibrium mapping, and related problems. American Journal of Human Genetics 62, 459-473.
14. Risch, N. (2000). Searching for genetic determinants in the new millennium. Nature 405, 847-856.
15. Risch, N. and Merikangas, K. (1996). The future of genetic studies of complex human diseases. Science 273, 1516-1517.
16. Risch, N. and Teng, J. (1998). The relative power of family-based and casecontrol designs for linkage disequilibrium studies of complex human diseases. I. DNA pooling, Genome Research 8, 1273-1288.
17. Satten, G. A., Flanders, W. D. and Yang, Q. (2001). Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model, American Journal of Human Genetics 68, 466-477.
18. Spielman, R. S., McGinnis, R. E. and Ewens, W. J. (1993). Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM), American Journal of Human Genetics, 52: 506-513.
19. Teng, J. and Risch, N. (1999). The relative power of family-based and casecontrol designs for linkage disequilibrium studies of complex human diseases. II. individual genotyping. Genome Research 9, 234-241.
20. Thompson, E. A. and Neel, J. V. (1997). Allelic disequilibrium and allele frequency distribution as a function of social and demographic history. American Journal of Human Genetics 60, 197-204.
21. van den Oord, E. J. C. G. (1999). A comparison between different designs and tests to detect QTLs in association studies. Behavior Genetics 29, 245-256.
22. Xiong, M. M., Fan, R. Z. and Jin, L. (2002). Linkage disequilibrium mapping of quantitative trait loci under truncation selection. Human Heredity 53, 158-172.
23. Xiong, M. M. and Guo, S. W. (1997). Fine-scale genetic mapping based on linkage disequilibrium: theory and application. American Journal of Human Genetics 60, 1513-1531.
24. Zhang, S. L., Kidd, K. K. and Zhao, H. Y. (2002). Detecting genetic association in case-control studies using similarity-based association tests. Statistica Sinica 12, 337-359.
25. Zhang, S. L. and Zhao, H. Y. (2001). Quantitative similarity-based association tests using population samples. American Journal of Human Genetics 69, 601-614.