Validation of candidate SNPs and CpGs for human face prediction

Wojciech Branicki; Maria Wrobel; Balakrishnan Subramanian; Beata Cienkosz-Stepanczak; Katarzyna Urbanelis; Aleksandra Pisarek-Pacek; Weronika Flis; Danuta Piniewska-Rog; Kamila Marszalek; Andrzej Ossowski; Aneta Sitek; Bozena Wysocka; Iwona Wronka; Manfred Kayser; Susan Walsh; Ewelina Pospiech

doi:10.20330/AnthropKozl.2026.67s.67

Wojciech Branicki Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland; Institute of Forensic Research, Krakow, Poland
Maria Wrobel Institute of Forensic Research, Krakow, Poland; Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
Balakrishnan Subramanian Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland
Beata Cienkosz-Stepanczak Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland
Katarzyna Urbanelis Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland
Aleksandra Pisarek-Pacek Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland
Weronika Flis Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland
Danuta Piniewska-Rog Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Krakow, Poland
Kamila Marszalek Pomeranian Medical University, Department of Forensic Genetics, Szczecin, Poland
Andrzej Ossowski Pomeranian Medical University, Department of Forensic Genetics, Szczecin, Poland
Aneta Sitek University of Lodz, Faculty of Biology and Environmental Protection, Institute of Ecology and Environmental Protection, Department of Anthropology, Lodz, Poland
Bozena Wysocka Central Forensic Laboratory of the Police, Warsaw, Poland
Iwona Wronka Jagiellonian University, Faculty of Biology, Institute of Zoology and Biomedical Sciences, Laboratory of Anthropology, Krakow, Poland
Manfred Kayser Erasmus MC University Medical Center, Department of Pathology and Clinical Bioinformatics, Rotterdam, The Netherlands
Susan Walsh Indiana University Indianapolis, Department of Biology, Indianapolis, USA
Ewelina Pospiech Pomeranian Medical University, Department of Forensic Genetics, Szczecin, Poland

DOI: https://doi.org/10.20330/AnthropKozl.2026.67s.67

Keywords: Human face morphology, BMI, Phenotyping, DNA-based prediction

Abstract

Background: Human facial genetics remains challenging due to the complexity of facial morphology, its highly polygenic basis, and the combined influence of genetics, environment, age, and lifestyle on facial appearance.

Objective: To develop predictors of human facial appearance that could aid facial reconstruction in forensic anthropology and predict facial appearance using DNA-based methods alone.

Subjects and methods: Data from ~800 individuals, including Illumina GSA genotypes, EPIC methylation profiles, metadata, and 3D facial scans, were analyzed. Candidate facial SNPs were evaluated using MeshMonk with facial segmentation and landmark-based phenotyping. Associations were tested between 747 DNA variants and facial traits in 658 individuals. In addition, BMI-predictive CpG sites were validated, and a compact BMI prediction model was developed using Elastic Net regression on methylation data from 624 individuals.

Results: Using global-to-local segmentation approach we found 29 SNPs to be significantly associated with 22 segments of the faces. The facial landmarking approach identified 27 candidate SNPs to be significantly associated with 60 facial distances. Elastic Net regression yielded 30 CpG BMI predictors. In the validation set, the model achieved a mean absolute error of 2.9 kg/m². The current results represent a step forward in our research on facial prediction.

References

References: None.