Genetic makeup of human face gradually reveals underlying pattern

The genetic makeup of the human face is difficult to decipher. In 2018, Professor Peter Claes (KU Leuven) and colleagues from Penn State, the University of Pittsburgh and the Stanford University School of Medicine already identified 15 genes related to specific parts of the face . With colleagues from Indiana University – Purdue University Inidianapolis and Cardiff University, they have now identified 203 genetic sites that play a role in the development of the shape of our face. Of these, 53 have never been reported before.


The researchers used 3D images of the faces of European individuals with more than 7,000 data points on them. This allowed them to identify differences in the DNA sequence that contribute to variation in facial features.
In addition to knowledge about the formation of our face, this information can ultimately lead to new insights into craniofacial abnormalities, such as cleft lip and palate. More knowledge about the genetic makeup of our face can also help us understand the evolution of the face. In addition, this information may one day be useful for forensics, although we are still a long way from facial DNA reconstructions and their use as legal evidence.

“Your face says something about your identity, who you are related to, where your ancestors came from, and even about your health,” says Julie White of Pennsylvania State University. “However, we know very little about how faces are formed,” adds Karlijne Indencleef (KU Leuven). “The facial structure takes shape early on, and if something goes wrong in that process, you can get cleft palate or some other problem. However, we do not yet fully know how these processes are organized. ”

Moreover, not many people have facial abnormalities, which makes it difficult to locate and identify problematic genes based on a large data set. However, the researchers believe that the genetic location of normal lip formation – which can be traced back to large research populations – can also cause lip malformations.

Gridded mask

The researchers used two datasets containing the DNA code and a 3D image of the faces of thousands of people. © Shutterstock
The team used two datasets: one from the United Kingdom with 3,566 individuals, and one from the United States with 4,680 individuals. Detailed 3D photos of the face and complete DNA were available for all individuals in the datasets. On those images, the researchers placed more than 7,000 point locations using a rasterized mask that was digitally stretched to conform to the facial contours of each individual.

The researchers then divided the face into 63 segments based on data on the relationships between certain facial areas. This allowed them to view variations in small subsets of the face.

The researchers alternated between the two datasets to find genetic locations associated with facial features and then replicate them. By just looking at genetic locations that had similar associations in both datasets, they eventually identified 203 genetic locations relevant to facial structure. Of these, 89 were previously identified in other studies using either the same data or working with independent data. The researchers also identified 61 sites that had already been attributed to facial abnormalities in humans or mice. Finally, they also found 53 locations that were completely new.

“The additional epigenetic analyzes showed that the genetic regions we identified are expressed in cells relevant to craniofacial development,” said Indencleef. “It is an important initial validation of the locations we have identified. Please note: we initially only labeled these locations so that their exact functions can be validated and further investigated. ”

“In this research, it is critical to work together to jointly analyze multiple datasets using advanced analysis techniques,” said Professor Peter Claes, senior lecturer in engineering (ESAT-PSI) and human genetics and head of the Imaging Laboratory in Genetics at KU Leuven. He invented the method for the 3D analysis.

Shared genes
“If you compare this finding with previous studies, you see that our genes overlap with genes that have previously been shown to play a role in non-facial issues, such as limb development and organ and skeletal abnormalities,” explains White. “So there are common genetic elements related to the face as well as to another part of the body.”

Some facial deformities are linked to other physical problems, so it was no surprise that there are common genetic elements. More knowledge about these shared genes will help researchers understand how facial aberration comes about. Many of the identified genes are activated in the early stages of embryonic development. The researchers are now trying to find out how these genes are physically expressed in adults. However, according to the team, further research is needed to verify these links.