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A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis.
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- المؤلفون: Cabreros I;Cabreros I; Storey JD; Storey JD
- المصدر:
Genetics [Genetics] 2019 Aug; Vol. 212 (4), pp. 1009-1029. Date of Electronic Publication: 2019 Apr 26.
- نوع النشر :
Evaluation Study; Journal Article; Research Support, N.I.H., Extramural
- اللغة:
English
- معلومة اضافية
- المصدر:
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
- بيانات النشر:
Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Austin, Tex. [etc.]
- الموضوع:
- نبذة مختصرة :
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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- Grant Information:
R01 HG006448 United States HG NHGRI NIH HHS; T32 HG003284 United States HG NHGRI NIH HHS
- Contributed Indexing:
Keywords: PCA; admixture; genetic structure; logistic factor analysis; method of moments; nonparametric; population stratification; population structure; unifying
- الموضوع:
Date Created: 20190428 Date Completed: 20200108 Latest Revision: 20240720
- الموضوع:
20240720
- الرقم المعرف:
PMC6707457
- الرقم المعرف:
10.1534/genetics.119.302159
- الرقم المعرف:
31028112
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