ArticleGenetics2019
A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis.
Article in Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A generalized test of genotype-phenotype causality in population-sampled nuclear families.PLoS genetics · 2026Article
- Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding.Nature communications · 2026Article
- Extensive photophysiological variation in wild barley is linked to environmental origin.The New phytologist · 2026Article
- Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution.PLoS computational biology · 2025Article
- Mutational landscape of triple-negative breast cancer in African American women.Nature genetics · 2025Article
- Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Revealing the range of equally likely estimates in the admixture model.G3 (Bethesda, Md.) · 2025Article
- Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patterns.Genome biology · 2025Article
- Estimation of genetic admixture proportions via haplotypes.Computational and structural biotechnology journal · 2024Article
- Neural ADMIXTURE for rapid genomic clustering.Nature computational science · 2023Article
- Limitations of principal components in quantitative genetic association models for human studies.eLife · 2023Article
- AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap.Scientific data · 2023Article
- Weak gene-gene interaction facilitates the evolution of gene expression plasticity.BMC biology · 2023Article
- Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Unsupervised discovery of ancestry-informative markers and genetic admixture proportions in biobank-scale datasets.American journal of human genetics · 2023Article
- Inferring population structure in biobank-scale genomic data.American journal of human genetics · 2022Article
- Article
- Portability of 245 polygenic scores when derived from the UK Biobank and applied to 9 ancestry groups from the same cohort.American journal of human genetics · 2022Article
- Inference of population history using coalescent HMMs: review and outlook.Current opinion in genetics & development · 2018Review
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2 authors.
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Abstract
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.
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