A Genome-Wide Association Study and Machine-Learning Algorithm Analysis on the Prediction of Facial Phenotypes by Genotypes in Korean Women (2025)

Jin-Sik Bae

2022, Clinical, Cosmetic and Investigational Dermatology

visibility

description

13 pages

link

1 file

Changes in facial appearance are affected by various intrinsic and extrinsic factors, which vary from person to person. Therefore, each person needs to determine their skin condition accurately to care for their skin accordingly. Recently, genetic identification by skin-related phenotypes has become possible using genome-wide association studies (GWAS) and machinelearning algorithms. However, because most GWAS have focused on populations with American or European skin pigmentation, large-scale GWAS are needed for Asian populations. This study aimed to evaluate the correlation of facial phenotypes with candidate single-nucleotide polymorphisms (SNPs) to predict phenotype from genotype using machine learning. Materials and Methods: A total of 749 Korean women aged 30-50 years were enrolled in this study and evaluated for five facial phenotypes (melanin, gloss, hydration, wrinkle, and elasticity). To find highly related SNPs with each phenotype, GWAS analysis was used. In addition, phenotype prediction was performed using three machine-learning algorithms (linear, ridge, and linear support vector regressions) using five-fold cross-validation. Results: Using GWAS analysis, we found 46 novel highly associated SNPs (p < 1×10 −05): 3, 20, 12, 6, and 5 SNPs for melanin, gloss, hydration, wrinkle, and elasticity, respectively. On comparing the performance of each model based on phenotypes using five-fold cross-validation, the ridge regression model showed the highest accuracy (r 2 = 0.6422-0.7266) in all skin traits. Therefore, the optimal solution for personal skin diagnosis using GWAS was with the ridge regression model. Conclusion: The proposed facial phenotype prediction model in this study provided the optimal solution for accurately predicting the skin condition of an individual by identifying genotype information of target characteristics and machine-learning methods. This model has potential utility for the development of customized cosmetics.

Related papers

The genetics of the human face: identification of large effect single gene variants

In order to discover specific variants with relatively large effects on the human face we have devised an approach to identifying facial features with high heritability. This is based on using twin data to estimate the additive genetic value of each point on a face, as provided by a 3D camera system. In addition, we have used the ethnic difference between East Asian and European faces as a further source of face genetic variation. We use principal components analysis to provide a fine definition of the surface features of human faces around the eyes and of the profile, and chose upper and lower 10% extremes of the most heritable PCs for looking for genetic associations. Using this strategy for the analysis of 3D images of 1832 unique volunteers from the well characterised People of the British Isles study [1, 2] and 1567 unique twin images from the TwinsUK cohort (www.twinsuk.ac.uk), together with genetic data for 500,000 SNPs, we have identified three specific genetic variants with...

View PDFchevron_right

Genetic polymorphisms and skin aging: the identification of population genotypic groups holds potential for personalized treatments

Mireia Coma

Clinical, cosmetic and investigational dermatology, 2014

Skin changes are among the most visible signs of aging. Skin properties such as hydration, elasticity, and antioxidant capacity play a key role in the skin aging process. Skin aging is a complex process influenced by heritable and environmental factors. Recent studies on twins have revealed that up to 60% of the skin aging variation between individuals can be attributed to genetic factors, while the remaining 40% is due to non-genetic factors. Recent advances in genomics and bioinformatics approaches have led to the association of certain single nucleotide polymorphisms (SNPs) to skin properties. Our aim was to classify individuals based on an ensemble of multiple polymorphisms associated with certain properties of the skin for providing personalized skin care and anti-aging therapies. We identified the key proteins and SNPs associated with certain properties of the skin that contribute to skin aging. We selected a set of 13 SNPs in gene coding for these proteins which are potential...

View PDFchevron_right

Prediction Model Validation: Normal Human Pigmentation Variation

Shosuke Ito

Journal of Forensic Research, 2011

In a past study, we developed multiple linear regression (MLR) models that employed three single nucleotide polymorphisms (SNPs) that predicted a significant proportion of variation in pigmentation phenotypes from a large population cohort (n=789, training sample). Multiple linear regression models were developed for skin reflectance, eye color, and two aspects of hair color (log of the ratio of eumelanin-to-pheomelanin and total melanin). In this report, using an independent cohort (n=242 , test sample), we 1) externally cross-validated the prediction models, and 2) tested and refined the algorithm presented in the study by Valenzuela and colleagues, (2010). Relative shrinkage was moderate for skin reflectance (23.4%), eye color (19.4%), and the log of the ratio of eumelanin-to-pheomelanin in hair (37.3%), and largest for total melanin (67%) in hair. Independent construction of predictive models using our algorithm for the test sample set yielded the same or similar models as the training sample set. Two of the three SNPs composing the models were the same, with some variability in the third SNP of the model.

View PDFchevron_right

Genetic Signature of Skin Aging: A Pilot Study

Flavio Garoia

Journal of Clinical & Experimental Dermatology Research, 2018

Genetic risk assessment is becoming an important component of clinical decision-making. Recent research has focused attention on the single nucleotide polymorphisms (SNPs) involved in the aging process. The aging process is a complex interaction of genetic and environmental factors. To evaluate the contribution of individual genetic variability to skin aging we combine the relatively small effects of individual genes in a multi locus genetic risk score (GRS). This study aims to evaluate whether the genetic risk score may be linked to the evolution of skin properties and provide personalized skin care and anti-age treatments. A GRS was calculated using an additive model, based on the genotype analysis of 8 selected SNPs potentially associated with skin aging. One hundred patients were genotyped, tested for skin properties (elasticity, stratum corneum thickness, H2O content) and subjected to a questionnaire to evaluate sun exposure. ANCOVA analysis was performed to evaluate qualitative and quantitative explanatory variables. Once all the variables were taken in account, we found a significant correlation between GRS and elasticity and the thickness of the stratum corneum (SCT) suggesting that the combination of genetic signature, environmental and lifestyle information may provide a useful tool for personalized and more effective anti-aging therapies.

View PDFchevron_right

Genetics of the human face: Identification of large-effect single gene variants

Bruce Winney

2018

Significance The human face is extraordinarily variable, and the extreme similarity of the faces of identical twins indicates that most of this variability is genetically determined. We have devised an approach to increase the chance of identifying specific large genetic effects on particular facial features, by choosing features with high heritability and selecting individuals with relatively extreme facial phenotypes for comparison with a control population. This has yielded three specific and replicated genetic variants, two for features of facial profiles, and one for the region around the eyes. Further application of these methods should enable the understanding, eventually at the molecular level, of the nature of this extraordinary genetic variability, which is such an important feature of our everyday human interactions. To discover specific variants with relatively large effects on the human face, we have devised an approach to identifying facial features with high heritabil...

View PDFchevron_right

Population-specific facial traits and diagnosis accuracy of genetic and rare diseases in an admixed Colombian population

estephania candelo

ABSTRACTUp to 40% of genetic and rare disorders (RD) present facial dysmorphologies. Visual assessment of facial gestalt is commonly used for clinical diagnosis, health management and treatment monitoring. Quantitative approaches to facial phenotypes are more objective and provide first diagnoses of RD with relatively high accuracy, but are mainly based on populations of European descent, disregarding the influence of population ancestry. Here we assessed the facial phenotypes associated to four genetic disorders in a Latino-American population from Colombia. We recorded the coordinates of 18 facial landmarks in 2D images from 79 controls 51 pediatric individuals diagnosed with Down (DS), Morquio (MS), Noonan (NS) and Neurofibromatosis type 1 (NF1) syndromes. We quantified facial differences using Euclidean Distance Matrix Analysis (EDMA) and assessed the diagnostic accuracy of Face2gene, an automatic deep learning algorithm with widespread use in the clinical practice.Quantitative ...

View PDFchevron_right

Different Cosmetic Habits Can Affect the Biophysical Profile of Facial Skin: A Study of Korean and Chinese Women

Soyun Cho

Annals of Dermatology

Background: Previous studies on the age-, climate, and skin care habit-related changes of biophysical parameters have mainly focused on Caucasians, and studies on Asians are in paucity. Objective: This study was aimed to investigate the variations of cutaneous biophysical parameters in Chinese and Korean women (northeast Asians) and to assess the association between those parameters and age, climate, and cosmetic habits. Methods: A cross-sectional study included 361 healthy Chinese and Korean women between 18 and 49 years of age in 4 cities (Guangzhou, Nanjing, and Shijiazhuang in China, and Suwon in Korea). We measured skin surface temperature, hydration, transepidermal water loss (TEWL), sebum, elasticity, skin pore, wrinkle, and skin tone (brightness) using non-invasive instruments. Demographic profiles and cosmetic habits were assessed using a questionnaire. Results: Skin elasticity and tone decreased, and pore size and wrinkle increased with age. Subjects in Suwon (Korean) showed higher hydration level, lower TEWL and lower sebum, less severe wrinkle and brighter skin than those in the 3 cities in China. After adjusting for age and region, using sunscreen everyday, wearing base makeup daily, and using moisturizers improved hydration, TEWL, and elasticity significantly. Conclusion: Women in Suwon (Korea) were found to have a better profile of biophysical parameters than women in the 3 Chinese cities, which might be attributed to cosmetic habits, besides age and climatic factors. The fact that appropriate cosmetic habits are associated with favorable skin biophysical parameters underscores the importance of daily skin care routine in preserving skin functions. (Ann Dermatol 31(2) 175∼185, 2019

View PDFchevron_right

A Genome-Wide Association Study Identifies the Skin Color Genes IRF4, MC1R, ASIP, and BNC2 Influencing Facial Pigmented Spots

Diana Van Heemst

The Journal of investigative dermatology, 2015

Facial pigmented spots are a common skin aging feature, but genetic predisposition has yet to be thoroughly investigated. We conducted a genome-wide association study (GWAS) for pigmented spots in 2844 Dutch Europeans from the Rotterdam Study (mean age: 66.9±8.0; 47% male). Using semi-automated image analysis of high resolution digital facial photographs, facial pigmented spots were quantified as the percentage of affected skin area (mean women: 2.0%±0.9, men: 0.9%±0.6). We identified genome-wide significant association with pigmented spots at 3 genetic loci: IRF4 (rs12203592, P=1.8 × 10(-27)), MC1R (compound heterozygosity score, P=2.3 × 10(-24)), and RALY/ASIP (rs6059655, P=1.9 × 10(-9)). Additionally, after adjustment for the other 3 top associated loci the BNC2 locus demonstrated significant association (rs62543565, P=2.3 × 10(-8)). The association signals observed at all four loci were successfully replicated (P&lt;0.05) in an independent Dutch cohort (Leiden Longevity Study N=...

View PDFchevron_right

Prediction of eye, hair and skin color in admixed populations of Latin America

Paola Everardo

Forensic Science International , 2021

We report an evaluation of prediction accuracy for eye, hair and skin pigmentation based on genomic and phenotypic data for over 6,500 admixed Latin Americans (the CANDELA dataset). We examined the impact on prediction accuracy of three main factors: (i) The methods of prediction, including classical statistical methods and machine learning approaches, (ii) The inclusion of non-genetic predictors, continental genetic ancestry and pigmentation SNPs in the prediction models, and (iii) Compared two sets of pigmentation SNPs: the commonly-used HIrisPlex-S set (developed in Europeans) and novel SNP sets we defined here based on genome-wide association results in the CANDELA sample. We find that Random Forest or regression are globally the best performing methods. Although continental genetic ancestry has substantial power for prediction of pigmentation in Latin Americans, the inclusion of pigmentation SNPs increases prediction accuracy considerably, particularly for skin color. For hair and eye color, HIrisPlex-S has a similar performance to the CANDELA-specific prediction SNP sets. However, for skin pigmentation the performance of HIrisPlex-S is markedly lower than the SNP set defined here, including predictions in an independent dataset of Native American data. These results reflect the relatively high variation in hair and eye color among Europeans for whom HIrisPlex-S was developed, whereas their variation in skin pigmentation is comparatively lower. Furthermore, we show that the dataset used in the training of prediction models strongly impacts on the portability of these models across Europeans and Native Americans.

View PDFchevron_right

Predicting Phenotype from Genotype: Normal Pigmentation

Keith Cheng

Journal of Forensic Sciences, 2010

Abstract: Genetic information in forensic studies is largely limited to CODIS data and the ability to match samples and assign them to an individual. However, there are circumstances, in which a given DNA sample does not match anyone in the CODIS database, and no other information about the donor is available. In this study, we determined 75 SNPs in 24 genes (previously implicated in human or animal pigmentation studies) for the analysis of single- and multi-locus associations with hair, skin, and eye color in 789 individuals of various ethnic backgrounds. Using multiple linear regression modeling, five SNPs in five genes were found to account for large proportions of pigmentation variation in hair, skin, and eyes in our across-population analyses. Thus, these models may be of predictive value to determine an individual’s pigmentation type from a forensic sample, independent of ethnic origin.

View PDFchevron_right

A Genome-Wide Association Study and Machine-Learning Algorithm Analysis on the Prediction of Facial Phenotypes by Genotypes in Korean Women (2025)
Top Articles
Latest Posts
Recommended Articles
Article information

Author: Lakeisha Bayer VM

Last Updated:

Views: 5856

Rating: 4.9 / 5 (69 voted)

Reviews: 84% of readers found this page helpful

Author information

Name: Lakeisha Bayer VM

Birthday: 1997-10-17

Address: Suite 835 34136 Adrian Mountains, Floydton, UT 81036

Phone: +3571527672278

Job: Manufacturing Agent

Hobby: Skimboarding, Photography, Roller skating, Knife making, Paintball, Embroidery, Gunsmithing

Introduction: My name is Lakeisha Bayer VM, I am a brainy, kind, enchanting, healthy, lovely, clean, witty person who loves writing and wants to share my knowledge and understanding with you.