ArticleG3 (Bethesda, Md.)2016
Genome-Wide Association Studies with a Genomic Relationship Matrix: A Case Study with Wheat and Arabidopsis.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- A novel rare variants association test for binary traits in family-based designs via copulas.Statistical methods in medical research · 2023Article
- Inference about quantitative traits under selection: a Bayesian revisitation for the post-genomic era.Genetics, selection, evolution : GSE · 2022Article
- Gene-Based Association Testing of Dichotomous Traits With Generalized Functional Linear Mixed Models Using Extended Pedigrees: Applications to Age-Related Macular Degeneration.Journal of the American Statistical Association · 2021Article
- Genome-Wide Association Studies of Mineral Content in Common Bean.Frontiers in plant science · 2021Article
- Article
- Fast Algorithms for Conducting Large-Scale GWAS of Age-at-Onset Traits Using Cox Mixed-Effects Models.Genetics · 2020Article
- Association analysis of loci implied in "buffering" epistasis.Journal of animal science · 2020Article
- A Multiple-Trait Bayesian Lasso for Genome-Enabled Analysis and Prediction of Complex Traits.Genetics · 2020Article
- Genome-Wide Association Study for Milk Fatty Acids in Holstein Cattle Accounting for theAnimals : an open access journal from MDPI · 2019Article
- WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants.Genome biology · 2019Article
- A certain invariance property of BLUE in a whole-genome regression context.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2019Article
- Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation.Scientific reports · 2019Article
- Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny.Scientific reports · 2019Article
- Including Phenotypic Causal Networks in Genome-Wide Association Studies Using Mixed Effects Structural Equation Models.Frontiers in genetics · 2018Article
- Prediction of Complex Traits: Robust Alternatives to Best Linear Unbiased Prediction.Frontiers in genetics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Standard genome-wide association studies (GWAS) scan for relationships between each of p molecular markers and a continuously distributed target trait. Typically, a marker-based matrix of genomic similarities among individuals ( G: ) is constructed, to account more properly for the covariance structure in the linear regression model used. We show that the generalized least-squares estimator of the regression of phenotype on one or on m markers is invariant with respect to whether or not the marker(s) tested is(are) used for building G,: provided variance components are unaffected by exclusion of such marker(s) from G: The result is arrived at by using a matrix expression such that one can find many inverses of genomic relationship, or of phenotypic covariance matrices, stemming from removing markers tested as fixed, but carrying out a single inversion. When eigenvectors of the genomic relationship matrix are used as regressors with fixed regression coefficients, e.g., to account for population stratification, their removal from G: does matter. Removal of eigenvectors from G: can have a noticeable effect on estimates of genomic and residual variances, so caution is needed. Concepts were illustrated using genomic data on 599 wheat inbred lines, with grain yield as target trait, and on close to 200 Arabidopsis thaliana accessions.
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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.