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Abstract
Previous studies have successfully identified genetic variants in several genes associated with human iris (eye) color; however, they all used simplified categorical trait information. Here, we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photographs and conducted a genome-wide association study on 5,951 Dutch Europeans from the Rotterdam Study. Three new regions, 1q42.3, 17q25.3, and 21q22.13, were highlighted meeting the criterion for genome-wide statistically significant association. The latter two loci were replicated in 2,261 individuals from the UK and in 1,282 from Australia. The LYST gene at 1q42.3 and the DSCR9 gene at 21q22.13 serve as promising functional candidates. A model for predicting quantitative eye colors explained over 50% of trait variance in the Rotterdam Study. Over all our data exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits.
Highlights
The iris functions as the diaphragm of the eye controlling the amount of light reaching the retina
We clearly identified 3 new loci, lysosomal trafficking regulator (LYST), 17q25.3, tetratricopeptide repeat domain 3 (TTC3)/Down Syndrome Critical Region 9 (DSCR9), in contributing to the natural and subtle eye color variation along multiple dimensions, providing new leads towards a more detailed understanding of the genetic basis of human eye color
Our quantitative prediction model explained over 50% of eye color variance, representing the highest accuracy achieved so far in genomic prediction of human complex and quantitative traits, with relevance for future forensic applications
Summary
The iris functions as the diaphragm of the eye controlling the amount of light reaching the retina. Genome-wide association studies in people of Europeans decent [4,5,6,7] have confirmed eye color as a polygenic trait, with the HERC2/OCA2 genes explaining the most of the blue and brown eye color inheritance, whereas other genes such as SLC2A4, TYR, TYRP1, SLC45A2, and IRF4 contribute to eye color variation, albeit with minor effects [8] These findings increased our understanding of the genetic basis of human pigmentation, and drew attention to their potential applications, such as in forensic sciences [9,10]
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