ArticlePloS one2013
Correcting for population structure and kinship using the linear mixed model: theory and extensions.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
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- A candidate-variant association study of self-reported asthma in mothers of the Cebu Longitudinal Health and Nutrition Survey (CLHNS) cohort.BMC genomic data · 2026Article
- Method for the Dissection of Genomic Loci Associated with Chickpea Root Penetration Traits in Compact Soil.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Fast Probabilistic Whitening Transformation for Ultra-High Dimensional Genetic Data.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide association study reveals the QTLs and candidate genes associated with seed longevity in soybean (Glycine max (L.) Merrill).BMC plant biology · 2025Article
- Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs.Animals : an open access journal from MDPI · 2025Article
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- A Litmus Test for Confounding in Polygenic Scores.bioRxiv : the preprint server for biology · 2025Article
- Hierarchical selection of genetic and gene by environment interaction effects in high-dimensional mixed models.Statistical methods in medical research · 2025Review
- Identification of favorable alleles from exotic Upland cotton lines for fiber quality improvement using multiple association models.Frontiers in plant science · 2025Article
- A brief guide to analyzing expression quantitative trait loci.Molecules and cells · 2024Review
- Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations.PLoS biology · 2024Article
- Detecting inbreeding depression in structured populations.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach.Plants (Basel, Switzerland) · 2024Article
- Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia.Frontiers in genetics · 2024Article
- Bayesian LASSO for population stratification correction in rare haplotype association studies.Statistical applications in genetics and molecular biology · 2024Article
- Population stratification correction using Bayesian shrinkage priors for genetic association studies.Annals of human genetics · 2023Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Population structure and kinship are widespread confounding factors in genome-wide association studies (GWAS). It has been standard practice to include principal components of the genotypes in a regression model in order to account for population structure. More recently, the linear mixed model (LMM) has emerged as a powerful method for simultaneously accounting for population structure and kinship. The statistical theory underlying the differences in empirical performance between modeling principal components as fixed versus random effects has not been thoroughly examined. We undertake an analysis to formalize the relationship between these widely used methods and elucidate the statistical properties of each. Moreover, we introduce a new statistic, effective degrees of freedom, that serves as a metric of model complexity and a novel low rank linear mixed model (LRLMM) to learn the dimensionality of the correction for population structure and kinship, and we assess its performance through simulations. A comparison of the results of LRLMM and a standard LMM analysis applied to GWAS data from the Multi-Ethnic Study of Atherosclerosis (MESA) illustrates how our theoretical results translate into empirical properties of the mixed model. Finally, the analysis demonstrates the ability of the LRLMM to substantially boost the strength of an association for HDL cholesterol in Europeans.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.