Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models

Lloyd-Jones, Luke R., Robinson, Matthew R., Moser, Gerhard, Zeng, Jian, Beleza, Sandra, Barsh, Gregory S., Tang, Hua and Visscher, Peter M. (2017) Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models. Genetics, 206 2: 1113-1126. doi:10.1534/genetics.116.193383


Author Lloyd-Jones, Luke R.
Robinson, Matthew R.
Moser, Gerhard
Zeng, Jian
Beleza, Sandra
Barsh, Gregory S.
Tang, Hua
Visscher, Peter M.
Title Inference on the genetic basis of eye and skin color in an admixed population via Bayesian linear mixed models
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
1943-2631
Publication date 2017-06-01
Sub-type Article (original research)
DOI 10.1534/genetics.116.193383
Open Access Status Not yet assessed
Volume 206
Issue 2
Start page 1113
End page 1126
Total pages 14
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Language eng
Formatted 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).
Keyword Admixed populations
Genome-wide association studies
Bayesian linear mixed models
Eye and skin color
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Brain Institute Publications
Institute for Molecular Bioscience - Publications
 
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