Fast model-based estimation of ancestry in unrelated individuals
- 1 Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA;
- 2 Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California 90095, USA;
- 3 Department of Human Genetics and Department of Statistics, University of California at Los Angeles, Los Angeles, California 90095, USA
Abstract
Population stratification has long been recognized as a confounding factor in genetic association studies. Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification. One popular technique for estimation of ancestry is the model-based approach embodied by the widely applied programstructure. Another approach, implemented in the program EIGENSTRAT, relies on Principal Component Analysis rather than model-based estimation and does not directly deliver admixture fractions. EIGENSTRAT has gained in popularity in part owing to its remarkable speed in comparison tostructure. We present a new algorithm and a program, ADMIXTURE, for model-based estimation of ancestry in unrelated individuals. ADMIXTURE adopts the likelihood model embedded instructure. However, ADMIXTURE runs considerably faster, solving problems in minutes that takestructure hours. In many of our experiments, we have found that ADMIXTURE is almost as fast as EIGENSTRAT. The runtime improvements of ADMIXTURE rely on a fast block relaxation scheme using sequential quadratic programming for block updates, coupled with a novel quasi-Newton acceleration of convergence. Our algorithm also runs faster and with greater accuracy than the implementation of an Expectation-Maximization (EM) algorithm incorporated in the program FRAPPE. Our simulations show that ADMIXTURE's maximum likelihood estimates of the underlying admixture coefficients and ancestral allele frequencies are as accurate asstructure's Bayesian estimates. On real-world data sets, ADMIXTURE's estimates are directly comparable to those fromstructure and EIGENSTRAT. Taken together, our results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Footnotes
↵4 Corresponding author.
E-maildalexander{at}ucla.edu; fax (310) 825-8685.
[Supplemental material is available online athttp://www.genome.org. The ADMIXTURE program is freely available athttp://www.genetics.ucla.edu/software.]
Article published online before print. Article and publication date are athttp://www.genome.org/cgi/doi/10.1101/gr.094052.109.
- ReceivedApril 2, 2009.
- AcceptedJune 22, 2009.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
