Prediction of Facial Phenotypic Traits by DNA: Status of Research

The article considers the current state of research aimed at predicting the human phenotypic characteristics based on genetic material. Identification of DNA markers corresponding to certain phenotypes is in demand not only in forensic practices but also in ancient DNA studies. Despite the overall relevance of this field and a large array of publications, research is currently still at its early stage. Bioinformatic analysis of genomic data collected by the scientific community in recent years made it possible to identify the key DNA markers affecting the examined physical characteristics as well as to determine the geography of the alleles. It is noted that the same appearance characteristics in the population of different regions of the world can be determined by different mutations in the ~~same genes which is also relevant when studying the population of Russia. The introduction of modern~~ techniques of whole-genome sequencing and artificial intelligence provides obvious advantages, including obtaining more accurate and practically valuable methods of forensic identification, medical genetics and paleogenetics.

1. Roginsky Y.Y., Levin M.G. Anthropology. Textbook. 3rd ed. Moscow: Higher School, 1978. 528 p. (In Russ.).

2. Khrisanfova E.N., Perevozchikov I.V. Anthropology. Textbook. Moscow: Nauka, 2005. 400 p. (In Russ.)/

3. Bogatenkov D.V. Introduction to Anthropology. Study Guide. Moscow: Moskovskii gorodskoi psikhologo-pedagogicheskii universitet, 2004. 495 p. (In Russ.).

4. Chaitanya L., Walsh S., Andersen J.D., Ansell R., Ballantyne K. et al. Collaborative EDNAP Exercise on the IrisPlex System for DNA-Based Prediction of Human Eye Colour. Forensic Science International: Genetics. 2014. Vol. 11. P. 241–251. https://doi.org/10.1016/j.fsigen.2014.04.006

5. Walsh S., Chaitanya L., Clarisse L., Wirken L., Draus-Barini J. et al. Developmental Validation of the HIrisPlex System: DNA-based Eye and Hair Colour Prediction for Forensic and Anthropological Usage. Forensic Science International: Genetics. 2014. Vol. 9. P. 150–161. https://doi.org/10.1016/j.fsigen.2013.12.006

6. Walsh S., Chaitanya L., Breslin K., Muralidharan C. et al. Global Skin Colour Prediction from DNA. Human Genetics. 2017. Vol. 136. No. 7. P. 847–863. https://doi.org/10.1007/s00439-017-1808-5

7. HIrisPlex-S Eye, Hair and Skin Colour DNA Phenotyping Webtool. https://hirisplex.erasmusmc.nl/

8. Sulem P., Gudbjartsson D.F., Stacey S.N., Helgason A., Rafnar T. et al. Genetic Determinants of Hair, Eye and Skin Pigmentation in Europeans. Nature Genetics. 2007. Vol. 39. No. 12. P. 1443–1452. https://doi.org/10.1038/ng.2007.13

9. Sulem P., Gudbjartsson D.F., Stacey S.N., Helgason A., Rafnar T. et al. Two Newly Identified Genetic Determinants of Pigmentation in Europeans. Nature Genetics.. 2008. Vol. 40. No. 7. P. 835–837. https://doi.org/10.1038/ng.160.

10. Palmal S., Adhikari K., Mendoza-Revilla J., Fuentes-Guajardo M. et al. Prediction of Eye, Hair and Skin Colour in Latin Americans. Forensic Science International: Genetics. 2021. Vol. 53. 102517. https://doi.org/10.1016/j.fsigen.2021.102517

11. Jeong C., Balanovsky O., Lukianova E., Kahbatkyzy N., Flegontov P. et al. The Genetic History of Admixture Across Inner Eurasia. Nature Ecology & Evolution. 2019. Vol. 3. No. 6. P. 966–976. https://doi.org/10.1038/s41559-019-0878-2

12. Balanovska E., Kagazezheva J., Agdzhoyan A., Pylev V., Balanovsky O., et al. Optimizing the Genetic Prediction of the Eye and Hair Color for North Eurasian Populations. BMC Genomics. 2020. Vol. 21. No. 7. P. 527.

13. Balanovskaya E.V., Gorin I.O., Balanovsky O.P. Method for Determining Probability of Eye Color in an Individual Originating from Russian Populations and Single-Nucleotide Polymorphism Panel. Patent Application No. 2020137355, November 13, 2020. (In Russ.)

14. Balanovska E.V., Gorin I.O., Koshel S.M., Balanovsky O.P. Gene Geographic Atlas of Dna Markers Controlling Human Eye and Hair Color. Russian Journal of Genetics. 2021. Vol. 57. No. 12. P. 1356–1375. (In Russ.). https://doi.org/10.31857/S0016675821120031

15. Lazaridis I., Nadel D., Rollefson G., Merrett D.C., Rohland N. et al. Genomic Insights into the Origin of Farming in the Ancient Near East. Nature. 2016. Vol. 25. No. 536 (7617). P. 419–424. https://doi.org/10.1038/nature19310

16. Clemente F., Unterl nder M., Dolgova O. et al. The Genomic History of the Aegean Palatial Civilizations. Cell. 2021. Vol. 184. No. 10. P. 2565–2586.e21. https://doi.org/10.1016/j.cell.2021.03.039

17. Brunel S., Bennett A., Cardin L., Pruvost M. Ancient Genomes from Present-Day France Unveil 7000 Years of Its Demographic History. Proceedings of the National Academy of Sciences. 2020. Vol. 117. No. 23. P. 12791–12798. https://doi.org/10.1073/pnas.1918034117

18. Feldman M., Fern ndez-Dom nguez E., Reynolds L. et al. Late Pleistocene Human Genome Suggests a Local Origin for the First Farmers of Central Anatolia. Nature Communications. 2019. Vol. 10. St. 1218. https://doi.org/10.1038/s41467-019-09209-7

19. Spichenok O., Budimlija Z. M., Mitchell A. A., JennyA.,KovacevicL.,MarjanovicD.,CaragineT., Prinz M., Wurmbach E. Prediction of Eye and Skin Color in Diverse Populations Using Seven SNPs. Forensic Science International: Genetics. 2011. Vol. 5. No. 5. P. 472-478. https://doi.org/10.1016/j.fsigen.2010.10.005

20. Liu F., Visser M., Duffy D.L., Hysi P.G., Jacobs L.C. et al. Genetics of Skin Color Variation in Europeans: Genome-Wide Association Studies with Functional Follow-Up. Human Genetics. 2015. Vol. 134. No. 8. P. 823–835. https://doi.org/10.1007/s00439-015-1559-0

21. Fesenko D.O., Ivanovsky P.L., Ivanov P.L., Zemskova E.Yu., Agapitova A.S., Polyakov S.A., Fesenko O.E., Filippova M.A., Zasedatelev A.S. Biochip for Genotyping Polymorphisms Associated with Eye, Hair, Skin Color, Abo Blood Groupe, Sex, Core Y-Chromosome Haplo-groups, and its Using for a Study of the Slavic Population. Molecule Biology. 2022. Vol. 56. No. 5. P. 860–880. (In Russ.). https://doi.org/10.31857/S0026898422050056

22. Bukayev A., Aidarov B., Fesenko D., Saidamarova V., Ivanovsky I. et al. Genotype Data for 60 SNP Genetic Markers Associated with Eye, Hair, Skin Color, ABO Blood Group, Sex, Core Y-chromosome Haplogroups in Kazakh Population. BMC Research Notes. 2024. Vol. 17. No. 51. https://doi.org/10.1186/s13104-024-06712-z

23. Lippert C., Sabatini R., Maher M.C. et al. Identification of Individuals by Trait Prediction Using Whole-Genome Sequencing Data. Proceed-ings of the National Academy of Sciences of the United States of America. 2017. Vol. 114. No. 38. P. 10166–10171. https://doi.org/10.1073/pnas.1716166114

24. Du S., Chen J., Li J., Qian W. et al. A Multi-Ancestry GWAS Meta-Analysis of Facial Features and its Application in Predicting Archaic Human Features. Journal of Genetics and Genomics. 2025. Vol. 52. No. 4. P. 513–524. https://doi.org/10.1016/j.jgg.2024.07.005

25. Alshehhi A., Mousa M., Tay G.K., Werghi N., AlSafar H. Genome Wide Association Study Reveals Novel Associations with Face Morphology. PLoS One. 2025. Vol. 10. https://doi.org/10.1371/journal.pone.0299660

26. Jiao M., Li J., Zhong B., Du S., Li S., Zhang M., Zhang Q., Liang Z., Liu F., Zuo C., Wang S., Chen L. De Novo Reconstruction of 3D Human Facial Images from DNA Sequence. Advanced Science. 2025. Vol. 12. No. 10. https://doi.org/10.1002/advs.202414507

27. Adhikari K., Fuentes-Guajardo M., QuintoSánchez M., Mendoza-Revilla J., Camilo Chacón-Duque J. et al. A Genome-Wide Association Scan Implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in Human Facial Variation. Natural Communication. 2016. Vol. 7. 11616. https://doi.org/10.1038/ncomms11616

28. Pantel J.T., Hajjir N., Danyel M., Elsner J., AbadPerez A.T. et al. Efficiency of Computer-Aided Facial Phenotyping (DeepGestalt) in Individuals with and without a Genetic Syndrome: Diagnostic Accuracy Study. Journal of Medical Internet Research. 2020. Vol. 10. No. 22. https://doi.org/10.2196/19263