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Eye Color GWAS Leads to 50 New Loci, Underscoring Trait's Complexity

NEW YORK – An international research team has tracked down dozens of new eye color-associated loci in European individuals, including a subset of variants that show similar effects in individuals with Asian ancestry. The results may boost research on conditions affecting both the eye and other parts of the body.

"By describing [new] genes related to eye color, we are identifying other genes that can potentially be the cause of cases of optic disc and retinal abnormalities that have previously remained unexplained and were not understood," co-senior and corresponding author Pirro Hysi, a researcher at King's College London, said in an email.

In a paper published in Science Advances on Wednesday, Hysi and his colleagues considerably expanded the collection of genes linked to iris color, commonly referred to as eye color, with the help of a genome-wide association study that included nearly 193,000 individuals of European ancestry from 10 different populations and more than 1,600 individuals with Asian or South Asian ancestry.

The resulting set, which included 50 loci that were not linked to eye color in the past, may ultimately help in understanding diseases such as skin cancer that appear to be influenced by melanin metabolism, pigmentation, and related processes, Hysi noted. The loci are also expected to improve the understanding of conditions and biological processes that directly affect the eye, including pigmentary glaucoma and optic disc and retina development.

"We also know that, for reasons that still remain poorly understood, melanin metabolism is very important to the development of [the] optic disc and retina," he said, noting that eye color-associated genes have been linked to a lack of skin pigmentation in individuals with albinism, along with altered optic nerve development and visual impairment.

For the study, the researchers brought together array-based genotyping profiles for 157,485 participants of European ancestry enrolled in 23andMe research programs and another 35,501 Europeans enrolled through the International Visible Trait Genetics Consortium. Their initial GWAS highlighted thousands of iris color-associated SNPs clustered at 52 sites in the genome, while its replication and meta-analysis steps helped to narrow in on nine more loci.

"We find evidence for genes involved in melanin pigmentation," the authors reported, "but we also find associations with genes involved in iris morphology and structure."

The team went on to test its eye color-related variant set in 1,636 individuals with Han Chinese or Indian ancestry for replication and meta-analyses. It saw the same directional effects for 30 of the 44 lead SNPs at eye color-linked loci from the prior GWAS that could be reliably tested.

A handful of those variants also showed significant ties to eye color in the Han Chinese and Indian participants, hinting at shared eye color genetic architecture despite a broader range of eye color phenotypes in the European cohort.

"The large number of novel eye color-associated genetic loci identified here provide a valuable resource for functional studies, aiming to understand the molecular mechanisms that explain their eye floor association, and for future genetic prediction, aiming to improve DNA-based eye color prediction in anthropological and forensic applications," the authors wrote.

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