Summary: A new genetics study reveals shared genetic sites relevant to facial shapes and features between Tanzanian children and Europeans, suggesting the genetic basis for human face shape is partly shared across different populations.
A new study of the genetics underlying facial features finds that East Africans have some unique facial genetics and some that are shared with Europeans.
The findings, published August 19th in PLOS Genetics by Chenxing Liu, Seth Weinberg and John Shaffer of the University of Pittsburgh and colleagues, add to our understanding of how genetics shape the human face.
The remarkable range of shapes and sizes of the human face is largely the result of genetics. Previous studies have linked more than 100 genetic sites to facial characteristics, but most of these studies included only European or Asian populations. In the new study, Liu and colleagues focused on an East African population to expand our knowledge of the genetic factors behind human facial features.
The team analyzed 2,595 3D facial images collected from Tanzanian children and scanned their genomes to find genetic sites linked to specific features. The researchers identified 20 regions on the genome associated with face shape. Several of these genetic variants play a role in embryonic cells that give rise to facial structures very early in life – around 3 to 6 weeks after conception. Ten of the genetic sites were previously identified in European populations, suggesting that the genetic basis for human face shape is partly shared across populations.
Shaffer adds, “Our findings confirm that the genes connected to human facial features are basically the same across populations. Observed differences were mostly explained by how frequently an allele occurs in a given population. By comparing populations, we were able to uncover genetic signals that would otherwise remain obscured and narrow the field of genetic variants that are functionally impacting facial traits.”
The new study in Tanzanians uncovered novel sites and genes potentially related to face shape and also advanced the understanding of sites that were already recognized in Europeans. Overall, these findings shed light on the genetic and biological basis underpinning the diversity of human facial structures. They may also offer insights into the biological mechanisms responsible for how the face forms and the causes of facial deformities.
Weinberg adds, “Most published genetic studies of human facial traits have been limited to individuals of predominantly European ancestry, and African populations have been particularly under-represented in this field. The current study, therefore, represents an important advance in terms of diversity and provides new insights into the wide array of genes that impact facial appearance.”
Funding: Tanzania data collection was supported by the National Institute of Dental and Craniofacial Research (U01-DE020054, PD/PIs: RAS/BH/OK, http://www.nidcr.nih.gov/); Center for Inherited Disease Research (X01-HG006829, PD/PI: RAS, http://www.cidr.jhmi.edu/).
Pittsburgh personnel, data collection, and analyses were supported by the National Institute of Dental and Craniofacial Research (U01-DE020078, PD/PIs: SMW/MLM, R01-DE016148, PD/PIs: MLM/SMW, and R01-DE027023, PD/PIs: SMW/JRS/PC/JW).
Funding for genotyping by the National Human Genome Research Institute (X01-HG007821 and X01-HG007485, PD/PI: MLM) and funding for initial genomic data cleaning by the University of Washington provided by contract HHSN268201200008I from the National Institute for Dental and Craniofacial Research awarded to the Center for Inherited Disease Research.
Penn State personnel, data collection, and analyses were supported by Procter & Gamble, Company (UCRI-2015-1117-HN-532, PD/PI: HN), the Center for Human Evolution and Development at Penn State, the Science Foundation of Ireland Walton Fellowship (04.W4/B643, PD/PI: MDS), the US National Institute of Justice (2008-DN-BX-K125, PD/PI: MDS; and 2018-DU-BX-0219, PD/PI: SW), and by the US Department of Defense.
IUPUI personnel, data collection, and analyses were supported by the National Institute of Justice (2015-R2-CX-0023, 2014-DN-BX-K031, and 2018-DU-BX-0219, PD/PI: SW).
The UK Medical Research Council and Wellcome (Grant ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors and PC will serve as guarantor for the contents of this paper.
The KU Leuven research team and analyses were supported by the National Institute of Dental and Craniofacial Research (R01-DE027023, PD/PIs: SMW/JRS/PC/JW), The Research Fund KU Leuven (BOF-C1, C14/15/081 and C14/20/081, PD/PI: PC), and the Research Program of the Research Foundation – Flanders (FWO, G078518N, PD/PI: PC).
Stanford University personnel and analyses were supported by the National Institute of Dental and Craniofacial Research (R01-DE027023, PD/PIs: SMW/JRS/PC/JW; and U01-DE024430, PD/PIs: JW/LS), the Howard Hughes Medical Institute, and the March of Dimes Foundation (1-FY15-312, PD/PI: JW).
SN was supported by a Helen Hay Whitney Fellowship.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
About this genetics research news
Author: Claire Turner Source: PLOS Contact: Claire Turner – PLOS Image: The image is in the public domain
Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations
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 different 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. We therefore investigated the genetic basis of facial morphology in an East African cohort. We 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 threshold 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.