title: Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models.
abstract: Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n= 625) and skin (n= 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia l.lloydjones@uq.edu.au.
authors.forename: Luke R
authors.initials: LR
authors.lastname: Lloyd-Jones
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Robinson
authors.affiliation: Central Queensland University, Bellbowrie, Brisbane, Queensland 4070, Australia.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Moser
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia.
authors.forename: Jian
authors.initials: J
authors.lastname: Zeng
authors.affiliation: Department of Genetics, University of Leicester, LE1 7RH, United Kingdom.
authors.forename: Sandra
authors.initials: S
authors.lastname: Beleza
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806.|Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia.
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Barsh
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, California 94305.
authors.forename: Hua
authors.initials: H
authors.lastname: Tang
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia.|Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Visscher
mesh_terms: D000354:Africa, Western; D001499:Bayes Theorem; D003116:Color; D005123:Eye; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D006801:Humans; D010860:Pigments, Biological / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci; D012880:Skin Pigmentation / Q000235:genetics*
chemical_list: D010860:Pigments, Biological
keywords: Bayesian linear mixed models; admixed populations; eye and skin color; genome-wide association studies