Your browser doesn't support javascript.
loading
The benefits of permutation-based genome-wide association studies.
John, Maura; Korte, Arthur; Grimm, Dominik G.
Afiliação
  • John M; Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Petersgasse 18, 94315 Straubing, Germany.
  • Korte A; Weihenstephan-Triesdorf University of Applied Sciences, Bioinformatics, Petersgasse 18, 94315 Straubing, Germany.
  • Grimm DG; University of Würzburg, Faculty of Biology, Julius-von-Sachs Institute, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany.
J Exp Bot ; 75(17): 5377-5389, 2024 Sep 11.
Article em En | MEDLINE | ID: mdl-38954539
ABSTRACT
Linear mixed models (LMMs) are a commonly used method for genome-wide association studies (GWAS) that aim to detect associations between genetic markers and phenotypic measurements in a population of individuals while accounting for population structure and cryptic relatedness. In a standard GWAS, hundreds of thousands to millions of statistical tests are performed, requiring control for multiple hypothesis testing. Typically, static corrections that penalize the number of tests performed are used to control for the family-wise error rate, which is the probability of making at least one false positive. However, it has been shown that in practice this threshold is too conservative for normally distributed phenotypes and not stringent enough for non-normally distributed phenotypes. Therefore, permutation-based LMM approaches have recently been proposed to provide a more realistic threshold that takes phenotypic distributions into account. In this work, we discuss the advantages of permutation-based GWAS approaches, including new simulations and results from a re-analysis of all publicly available Arabidopsis phenotypes from the AraPheno database.
Assuntos
Palavras-chave

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Fenótipo / Arabidopsis / Estudo de Associação Genômica Ampla Idioma: En Ano de publicação: 2024 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Fenótipo / Arabidopsis / Estudo de Associação Genômica Ampla Idioma: En Ano de publicação: 2024 Tipo de documento: Article