A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis.

Publisher: Oxford University Press Country of Publication: United States NLM ID: 0374636 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1943-2631 (Electronic) Linking ISSN: 00166731 NLM ISO Abbreviation: Genetics Subsets: MEDLINE

Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Austin, Tex. [etc.]

Algorithms* ; Computational Biology* ; Genetics, Population* ; Likelihood Functions* ; Models, Genetic*; Datasets as Topic ; Genome, Human ; Humans ; Principal Component Analysis

We introduce a simple and computationally efficient method for fitting the admixture model of genetic population structure, called ALStructure The strategy of ALStructure is to first estimate the low-dimensional linear subspace of the population admixture components, and then search for a model within this subspace that is consistent with the admixture model's natural probabilistic constraints. Central to this strategy is the observation that all models belonging to this constrained space of solutions are risk-minimizing and have equal likelihood, rendering any additional optimization unnecessary. The low-dimensional linear subspace is estimated through a recently introduced principal components analysis method that is appropriate for genotype data, thereby providing a solution that has both principal components and probabilistic admixture interpretations. Our approach differs fundamentally from other existing methods for estimating admixture, which aim to fit the admixture model directly by searching for parameters that maximize the likelihood function or the posterior probability. We observe that ALStructure typically outperforms existing methods both in accuracy and computational speed under a wide array of simulated and real human genotype datasets. Throughout this work, we emphasize that the admixture model is a special case of a much broader class of models for which algorithms similar to ALStructure may be successfully employed.
(Copyright © 2019 Cabreros and Storey.)

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R01 HG006448 United States HG NHGRI NIH HHS; T32 HG003284 United States HG NHGRI NIH HHS

Keywords: PCA; admixture; genetic structure; logistic factor analysis; method of moments; nonparametric; population stratification; population structure; unifying

Date Created: 20190428 Date Completed: 20200108 Latest Revision: 20240720

20240720

PMC6707457

10.1534/genetics.119.302159

31028112