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Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations

NCJ Number
PLoS Genetics Dated: August 2021
Chenxing Liu; Myoung Keun Lee; Sahin Naqvi; Hanne Hoskens; Dongjing Liu; Julie D. White; Karlijne Indencleef; Harold Matthews; Ryan J. Eller; Jiarui Li; Jaaved Mohammed; Tomek Swigut; Stephen Richmond; Mange Manyama; Benedikt Hallgrímsson; Richard A. Spritz; Eleanor Feingold; Mary L. Marazita; Joanna Wysocka; Susan Walsh; Mark D. Shriver; Peter Claes; Seth M. Weinberg; John R. Shaffer
Date Published
August 2021

Since the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown, the current study examined the genetic basis of facial morphology in an East African cohort.


Facial morphology is highly variable, both within and among human populations, and a sizable portion of this variation is attributable to genetics. Previous genome scans have revealed more than 100 genetic loci associated with various aspects of normal-range facial variation. Most of these loci have been detected in Europeans, with few studies focusing on other ancestral groups. Consequently, the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown. The current project applied an open-ended, data-driven phenotyping approach to a sample of 2,595 3D facial images collected on Tanzanian children. This approach segments the face into hierarchically arranged, multivariate features that capture the shape variation after adjusting for age, sex, height, weight, facial size and population stratification. Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10−8) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. Two of these associations were in highly conserved regions showing craniofacial-specific enhancer activity during embryological development (5q31.1 and 12q21.31). Six of the 20 loci surpassed a stricter accounting for multiple phenotypes with study-wide significance (p < 6.25 × 10−10). Cross-population comparisons indicated 10 association signals were shared with Europeans (seven sharing the same associated SNP) and facilitated fine-mapping of causal variants at previously reported loci. Taken together, these results may point to both shared and population-specific components to the genetic architecture of facial variation. (publisher abstract modified)

Date Created: September 21, 2021