Control of Population Stratification by Correlation-Selected Principal Components

Biometrics

Volumn 67, Issue 3, 2011, Pages 967-974

  Lee, Seunggeun ^a   Wright, Fred A ^a   Zou, Fei ^a  

^a IL   (United States)

Author keywords

Genomic control; GWAS; PCA; Population stratification

Indexed keywords

EIGENVALUES AND EIGENFUNCTIONS; GENES; POPULATION STATISTICS; PRINCIPAL COMPONENT ANALYSIS; STATISTICAL TESTS;

COMPONENT BASED; EIGEN-VALUE; GENOME-WIDE ASSOCIATION STUDIES; GENOMIC CONTROL; GENOMICS; GWAS; PCA; POPULATION STRATIFICATION; PRINCIPAL COMPONENTS; TEST STATISTICS;

GENOME;

CORRELATION; DATA SET; EIGENVALUE; ERROR ANALYSIS; GENOME; GENOMICS; GENOTYPE; PHENOTYPE; POPULATION STRUCTURE; PRECISION; PRINCIPAL COMPONENT ANALYSIS; STRATIFICATION; TESTING METHOD;

EID: 80052814052     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2010.01520.x     Document Type: Article

References (22)

1. Balding, D. and Nichols, R. (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96, 3-12.
2. Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B (Methodological) 57, 289-300.
3. Devlin, B. and Roeder, K. (1999). Genomic control for association studies. Biometrics 55, 997-1004.
4. Devlin, B., Roeder, K., and Wasserman, L. (2001). Genomic control, a new approach to genetic-based association studies. Theoretical Population Biology 60, 155-166.
5. Devlin, B., Bacanu, S., and Roeder, K. (2004). Genomic control to the extreme. Nature Genetics 36, 1129-1130.
6. Epstein, M., Allen, A., and Satten, G. (2007). A simple and improved correction for population stratification in case-control studies. The American Journal of Human Genetics 80, 921-930.
7. Epstein, M., Allen, A., and Satten, G. (2008). Response to Lee et al. The American Journal of Human Genetics 82, 526-528.
8. Fellay, J., Shianna, K., Ge, D., Colombo, S., Ledergerber, B., Weale, M., Zhang, K., Gumbs, C., Castagha, A., Cossarizza, A., Cozzi-Lepri, A., De Luca, A., Easterbrook, P., Francioli, P., Mallal, S., Martinez-Picado, J., Miro, J. M., Obel, N., Smith, J. P., Wyniger, J., Descombes, P., Antonarakis, S. E., Letvin, N. L., McMichael, A. J., Haynes, B. F., Telenti, A., and Goldstein, D. B. (2007). A whole-genome association study of major determinants for host control of HIV-1. Science 317, 944-947.
9. Fisher, R. (1921). On the probable error of a coefficient of correlation deduced from a small sample. Metron 1, 3-32.
10. Johnstone, I. (2001). On the distribution of the largest eigenvalue in principal components analysis. Annals of Statistics 29, 295-327.
11. Kimmel, G., Jordan, M., Halperin, E., Shamir, R., and Karp, R. (2007). A randomization test for controlling population stratification in whole-genome association studies. The American Journal of Human Genetics 81, 895-905.
12. Lee, S., Sullivan, P., Zou, F., and Wright, F. (2008). Comment on a simple and improved correction for population stratification. The American Journal of Human Genetics 82, 524-526.
13. Lubin, J. (1981). An empirical evaluation of the use of conditional and unconditional likelihoods for case-control data. Biometrika 68, 567-571.
14. Marchini, J., Cardon, L., Phillips, M., and Donnelly, P. (2004). The effects of human population structure on large genetic association studies. Nature Genetics 36, 512-517.
15. Patterson, N., Price, A., and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genetics 2, e190.
16. Price, A., Butler, J., Patterson, N., Capelli, C., Pascali, V., Scarnicci, F., Ruiz-Linares, A., Groop, L., Saetta, A., Korkolopoulou, P., Seligsohn, U., Waliszewska, A., Schirmer, C., Ardlie, K., Ramos, A., Nemesh, J., Arbeitman, L., Goldstein, D. B., Reich, D., and Hirschhorn, J. N. (2008). Discerning the ancestry of European Americans in genetic association studies. PLoS Genetics 4, e236.
17. Price, A., Patterson, N., Plenge, R., Weinblatt, M., Shadick, N., and Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38, 904-909.
18. Reich, D. and Goldstein, D. (2001). Detecting association in a case-control study while correcting for population stratification. Genetic Epidemiology 20, 4-16.
19. Sanders, A., Duan, J., Levinson, D., Shi, J., He, D., Hou, C., Burrell, G., Rice, J., Nertney, D., Olincy, A., Rozic, P., Vinogradov, S., Buccola, N. G., Mowry, B. J., Freedman, R., Amin, F., Black, D. W., Silverman, J. M., Byerley, W. F., Crowe, R. R., Cloninger, C. R., Martinez, M., and Gejman, P. V. (2008). No significant association of 14 candidate genes with schizophrenia in a large European ancestry sample: Implications for psychiatric genetics. American Journal of Psychiatry 165, 497-506.
20. Sullivan, P., Lin, D., Tzeng, J., van den Oord, E., Perkins, D., Stroup, T., Wagner, M., Lee, S., Wright, F., Zou, F., Liu, W., Downing, A. M., Lieberman, J., and Close, S, L. (2008). Genomewide association for schizophrenia in the CATIE study: Results of stage 1. Molecular Psychiatry 13, 570-584.
21. Zhao, H., Rebbeck, T., and Mitra, N. (2009). A propensity score approach to correction for bias due to population stratification using genetic and non-genetic factors. Genetic Epidemiology 33, 679-690.
22. Zou, F., Lee, S., Knowles, M., and Wright, F. (2010). Quantification of population structure using correlated SNPs by shrinkage principal components. Human Heredity 70, 9-22.