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Study Links Nearly 250 Genetic Variants Associated With Facial Features Differences

NEW YORK — A Fudan University-led team of researchers has identified nearly 250 genetic variants associated with differences in facial features.

Face shapes are highly heritable, though vary across people from different geographic areas. Previous studies have identified more than 200 genetic loci associated with facial morphology among individuals with European ancestry but only about two dozen have been reported in individuals of East Asian ancestry, and fewer among Latin American or African ancestry individuals.

In a genome-wide association study of more than 9,500 individuals of Han Chinese ancestry, the researchers uncovered both new and known genetic loci associated with facial features. As they reported Thursday in Nature Genetics, they homed in on a dozen variants related to differences in facial morphology observed between individuals of East Asian and European ancestry and found that the difference in nose shape between the two populations appears to be due to selection among Europeans.

"As a large-scale East Asian population facial GWAS using data-driven global-to-local phenotyping, our study broadens the knowledge of craniofacial genetics outside frequently investigated European ancestry populations," Fudan's Sijia Wang and colleagues wrote in their paper.

For their GWAS, the researchers relied on 3D facial surface scans and genotyping data from a discovery cohort of 6,968 individuals and a replication cohort of 2,706 individuals and used a semi-supervised phenotyping procedure to define 63 different facial segments. In the discovery dataset, they identified 153 variants that reached genome-wide significance for association with a facial feature, 119 of which reached nominal significance in the replication cohort. When they combined their datasets into a meta-analysis, the researchers uncovered 244 variants in 166 loci associated with variations in facial morphology.

These variants implicated about 206 candidate genes, many of which were enriched for related processes such as development of the skeletal system.

The researchers then compared the variants they found with 203 variants that had previously been identified in a European-ancestry cohort using similar phenotyping and analysis. Of these, 89 variants were shared across the two studies, while 155 variants were specific to East Asian individuals and 114 were specific to European individuals. Still, through a series of analyses using the polygenic population shape — a score similar to polygenic scores but for a population — the researchers found that the facial shape effects they found among the East Asian population also generally could be seen in a European population.

The researchers also homed in on 13 variants that contribute to a more East Asian ancestry facial appearance. These variants have allele frequency differences between East Asian and European ancestry populations, and a comparison of these variants as compared to both Europeans and Yorubans suggested that the variants might be under selection in East Asian populations.

In additional selection analyses, the researchers found that facial morphology has been under natural selection in both East Asian and European populations, particularly the nose. Natural selection was further stronger on the nose, the region about the nose and between the eyebrows, and cheekbones of Europeans, as compared to East Asian ancestry populations. This finding, they noted, was in line with previous work that indicated the shape of the human nose has evolved under pressure from natural selection.

"Our study identified a large number of previously unknown variants associated with normal-range facial shape variation," the researchers wrote, adding that their "findings will greatly facilitate the understanding of human facial morphology across populations."