Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Feb;16(2):290-6.
doi: 10.1101/gr.4346306. Epub 2005 Dec 14.

Logistic regression protects against population structure in genetic association studies

Efrosini Setakis  1 , Heide Stirnadel, David J Balding
Affiliations

Logistic regression protects against population structure in genetic association studies

Efrosini Setakis et al. Genome Res. 2006 Feb.

Abstract

We conduct an extensive simulation study to compare the merits of several methods for using null (unlinked) markers to protect against false positives due to cryptic substructure in population-based genetic association studies. The more sophisticated "structured association" methods perform well but are computationally demanding and rely on estimating the correct number of subpopulations. The simple and fast "genomic control" approach can lose power in certain scenarios. We find that procedures based on logistic regression that are flexible, computationally fast, and easy to implement also provide good protection against the effects of cryptic substructure, even though they do not explicitly model the population structure.

PubMed Disclaimer

References

    1. Bacanu, S.A., Devlin, B., and Roeder, K. 2000. The power of genomic control. Am. J. Hum. Genet. 66 1933-1944. - PMC - PubMed
    1. Balding, D.J. 2003. Likelihood-based inference for genetic correlation coefficients. Theoret. Pop. Biol. 63 221-230. - PubMed
    1. Campbell, C.D., Ogburn, E.L., Lunetta, K.L., Lyon, H.N., Freedman, M.L., Groop, L.C., Altshuler, D., Ardlie, K.G., and Hirschhorn, J.N. 2005. Demonstrating stratification in a European American population. Nat. Genet. 37 868-872. - PubMed
    1. Cardon, L.R. and Palmer, L.J. 2003. Population stratification and spurious allelic association. Lancet 361 598-604. - PubMed
    1. Cavalli-Sforza, L.L., Menozzi, P., and Piazza A. 1996. The history and geography of human genes. Princeton University Press, Princeton, NJ.

Publication types

LinkOut - more resources