Genes determine, to a large extent, the remarkable range of shapes and sizes of the human face within and among diverse populations.

Earlier genome studies have identified over a hundred genetic sites linked to facial features. But these studies mostly focused on Europeans. So, the degree to which human faces share a common genetic basis across diverse human populations is not known.

A new study published in PLOS Genetics compares genomic factors underlying facial features in East Africans and Europeans to reveal unique and common factors, enhancing our understanding of how genes shape the human face.

The study, led by Chenxing Liu, PhD, Seth Weinberg, PhD, and John Shaffer, PhD, at the University of Pittsburgh is reported in the article, “Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations.” These findings shed light on the genetic and biological basis underpinning the diversity of human facial structures and may offer insights into developmental mechanisms responsible for facial deformities.

Shaffer said, “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.”

Weinberg added, “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.”

The researchers analyzed 2,595 three-dimensional facial images of Tanzanian children and scanned their genomes to find genetic sites linked to specific features. Matching genomic features to visible traits (phenotypes) is an arduous and complex undertaking. The approach the researchers adopt in this study segments the face into hierarchically arranged, multivariate features that capture the variations in shape after adjusting for age, sex, height, weight, size, and population strata.

Through this approach, they identified 20 regions in the genome that are enriched for active chromatin elements in embryonic craniofacial tissue and human cranial neural crest cells—cells that migrating from the border of the neural plate and go on to form different cell types including the cartilage and bone of the skull and face. These genomic regions, the researchers concluded, are potentially linked to the shape of the face, consistent with the early developmental origin of specific facial nuances, three to six weeks after conception.

Ten of the genetic sites identified in the Tanzanian children were identified in European populations in earlier studies providing evidence that the genetic basis for human face shape is, at least partially, shared across populations despite gross morphological differences. Seven of the ten shared the same associated single nucleotide polymorphism (SNP). That allowed the researchers to map causal variants in previously reported loci in studies on Europeans.

The authors also identified two genomic sites linked to face shape—on the long arms of chromosomes 5 and 12—where the genomic locus is highly conserved and induced during embryonic development by a craniofacial-specific enhancer element. The authors also uncovered novel genomic sites potentially related to face shape, and advanced earlier understanding of facial genetics gleaned from studies on Europeans.

The study was funded by the National Institute of Dental and Craniofacial Research, the Center for Inherited Disease Research, National Human Genome Research Institute, Howard Hughes Medical Institute, the March of Dimes Foundation, and other agencies.