ArticleHeredity2011
Investigating population stratification and admixture using eigenanalysis of dense genotypes.
Article in Heredity, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Analyses of genome wide association data, cytokines, and gene expression in African-Americans with benign ethnic neutropenia.PloS one · 2018Trial
- Population Genomics Reveals Local Adaptation Related to Temperature Variation in Two Stream Frog Species: Implications for Vulnerability to Climate Warming.Molecular ecology · 2025Article
- Impact of Bronchiectasis on COPD Severity and Alpha-1 Antitrypsin Deficiency as a Risk Factor in Individuals with a Heavy Smoking History.Chronic obstructive pulmonary diseases (Miami, Fla.) · 2023Article
- Article
- Genome-wide mapping of quantitative trait loci in admixed populations using mixed linear model and Bayesian multiple regression analysis.Genetics, selection, evolution : GSE · 2018Article
- Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2017Article
- SNP-based heritability estimates of the personality dimensions and polygenic prediction of both neuroticism and major depression: findings from CONVERGE.Translational psychiatry · 2016Article
- Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach.BMC genomics · 2016Article
- Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome.BMC plant biology · 2015Article
- F-box/LRR-repeat protein 7 is genetically associated with Alzheimer's disease.Annals of clinical and translational neurology · 2015Article
- APOL1 G1 genotype modifies the association between HDLC and kidney function in African Americans.BMC genomics · 2015Article
- Genome-wide association studies in Africans and African Americans: expanding the framework of the genomics of human traits and disease.Public health genomics · 2015Review
- Phenotypic variance explained by local ancestry in admixed African Americans.Frontiers in genetics · 2015Article
- Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry.Scientific reports · 2014Article
- Pharmacogenomics, ancestry and clinical decision making for global populations.The pharmacogenomics journal · 2014Article
- On the association of common and rare genetic variation influencing body mass index: a combined SNP and CNV analysis.BMC genomics · 2014Article
- Two genomic regions contribute disproportionately to geographic differentiation in wild barley.G3 (Bethesda, Md.) · 2014Article
- Gene-based sequencing identifies lipid-influencing variants with ethnicity-specific effects in African Americans.PLoS genetics · 2014Article
- Breed-specific ancestry studies and genome-wide association analysis highlight an association between the MYH9 gene and heat tolerance in Alaskan sprint racing sled dogs.Mammalian genome : official journal of the International Mammalian Genome Society · 2012Article
- Article
Corrections and comments
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1 author.
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Abstract
Principal components analysis of genetic data is used to avoid inflation in type I error rates in association testing due to population stratification by covariate adjustment using the top eigenvectors and to estimate cluster or group membership independent of self-reported or ethnic identities. Eigendecomposition transforms correlated variables into an equal number of uncorrelated variables. Numerous stopping rules have been developed to identify which principal components should be retained. Recent developments in random matrix theory have led to a formal hypothesis test of the top eigenvalue, providing another way to achieve dimension reduction. In this study, I compare Velicer's minimum average partial test to a test on the basis of Tracy-Widom distribution as implemented in EIGENSOFT, the most widely used implementation of principal components analysis in genome-wide association analysis. By computer simulation of vicariance on the basis of coalescent theory, EIGENSOFT systematically overestimates the number of significant principal components. Furthermore, this overestimation is larger for samples of admixed individuals than for samples of unadmixed individuals. Overestimating the number of significant principal components can potentially lead to a loss of power in association testing by adjusting for unnecessary covariates and may lead to incorrect inferences about group differentiation. Velicer's minimum average partial test is shown to have both smaller bias and smaller variance, often with a mean squared error of 0, in estimating the number of principal components to retain. Velicer's minimum average partial test is implemented in R code and is suitable for genome-wide genotype data with or without population labels.
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Registered trials
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.