Genotype data for 60 SNP genetic markers associated with eye, hair, skin color, ABO blood group, sex, core Y-chromosome haplogroups in Kazakh population

OBJECTIVES

The collection of genotype data was conducted as an essential part of a pivotal research project with the goal of examining the genetic variability of skin, hair, and iris color among the Kazakh population. The data has practical application in the field of forensic DNA phenotyping (FDA). Due to the limited size of forensic databases from Central Asia (Kazakhstan), it is practically impossible to obtain an individual identification result based on forensic profiling of short tandem repeats (STRs). However, the pervasive use of the FDA necessitates validation of the currently employed set of genetic markers in a variety of global populations. No such data existed for the Kazakhs. The Phenotype Expert kit (DNA Research Center, LLC, Russia) was used for the first time in this study to collect data.

DATA DESCRIPTION

The present study provides genotype data for a total of 60 SNP genetic markers, which were analyzed in a sample of 515 ethnic Kazakhs. The dataset comprises a total of 41 single nucleotide polymorphisms (SNPs) obtained from the HIrisPlex-S panel. Additionally, there are 4 SNPs specifically related to the AB0 gene, 1 marker associated with the AMELX/Y genes, and 14 SNPs corresponding to the primary haplogroups of the Y chromosome. The aforementioned data could prove valuable to researchers with an interest in investigating genetic variability and making predictions about phenotype based on eye color, hair color, skin color, AB0 blood group, gender, and biogeographic origin within the male lineage.

Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology

Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.

Consistency of Eye Coloration Across Different Relationship Partners

Studies have indicated that people are attracted to partners who resemble themselves or their parents, in terms of physical traits including eye color. We might anticipate this inclination to be relatively stable, giving rise to a sequential selection of similar partners who then represent an individual's "type". We tested this idea by examining whether people's sequential partners resembled each other at the level of eye color. We gathered details of the eye colors of the partners of participants (N = 579) across their adult romantic history (N = 3250 relationships), in three samples, comprising two samples which made use of self-reports from predominantly UK-based participants, and one which made use of publicly available information about celebrity relationship histories. Recorded partner eye colors comprised black (N = 39 partners), dark brown (N = 884), light brown (N = 393), hazel (N = 224), blue (N = 936), blue green (N = 245), grey (N = 34), and green (N = 229). We calculated the proportion of identical eye colors within each participant's relationship history, and compared that to 100,000 random permutations of our dataset, using t-tests to investigate if the eye color of partners across an individual's relationship history was biased relative to chance (i.e., if there was greater consistency, represented by higher calculated proportions of identical eye colors, in the original dataset than in the permutations). To account for possible eye color reporting errors and ethnic group matching, we ran the analyses restricted to White participants and to high-confidence eye color data; we then ran the analyses again in relation to the complete dataset. We found some limited evidence for some consistency of eye color across people's relationship histories in some of the samples only when using the complete dataset. We discuss the issues of small effect sizes, partner-report bias, and ethnic group matching in investigating partner consistency across time.

The Eyes Have It-for Idiopathic Pulmonary Fibrosis: a Preliminary Observation

Introduction

The disease origins of idiopathic pulmonary fibrosis (IPF), which occurs at higher rates in certain races/ethnicities, are not understood. The highest rates occur in white persons of European descent, particularly those with light skin, who are also susceptible to lysosomal organelle dysfunction of the skin leading to fibroproliferative disease . We had observed clinically that the vast majority of patients with IPF had light-colored eyes, suggesting a phenotypic characteristic.

Methods

We pursued this observation through a research database from the USA Veterans Administration, a population that has a high occurrence of IPF due to predominance of elderly male smokers. Using this medical records database, which included facial photos, we compared the frequency of light (blue, green, hazel) and dark (light brown, brown) eyes among white patients diagnosed with IPF compared with a control group of lung granuloma only (no other radiologic evidence of interstitial lung disease).

Results

Light eye color was significantly more prevalent in patients with IPF than in the control group with lung granuloma [114/147 (77.6%) versus 129/263 (49.0%], p < 0.001), indicating that light-colored eyes are a phenotype associated with IPF .

Conclusion

We provide evidence that light eye color is predominant among white persons with IPF.

Blue Eyes Help Men Reduce the Cost of Cuckoldry

Men with light eyes lack the dominant gene allele that codes for dark-brown eyes. Pairing with a woman who lacks the same allele must increase paternity confidence in these men, because any children with dark eyes would be extremely unlikely to have been fathered by them. This notion implies that men with light (blue or green) eyes should (1) prefer light-eyed women, especially in a long-term context, and (2) feel more threatened by light-eyed than by dark-eyed rivals. Yet because choosiness is costly and paternity concerns are entirely driven by the prospect of paternal investment, any such inclinations would be adaptive only in men who expect to invest in their children. Here I test these ideas using the data of over 1000 men who rated the facial attractiveness of potential partners, and the threat of potential rivals, whose eye color had been manipulated. Light-eyed men liked light-eyed women better (particularly as long-term companions), and feared light-eyed rivals more, than did dark-eyed men. An exploratory analysis showed that these large, robust effects disappeared in men who had felt rejected by their fathers while growing up-suggesting that such men are not expecting to invest in their own children either.

Eye color and the risk of skin cancer

Melanoma, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the most common skin cancers. The incidence rates of all three types of skin cancers have increased in the past three decades. Light pigmentary traits have been recognized as one of the host risk factors for skin cancer, but findings on associations between eye colors and risk of skin cancers have been inconsistent.We performed a prospective analysis to examine the association between eye colors and risk of skin cancers using the Health Professionals Follow-up Study (HPFS). Cox proportional hazard models were applied to estimate relative risks (RRs) and their 95% confidence intervals (CIs). Effect modifications due to hair color and skin reaction to sun were also examined.The HPFS included 35,662 males. During a median follow-up of 19 years (1988-2012), 445 melanoma, 1123 SCC, and 7198 BCC cases were documented. Compared to those whose eye colors were dark or brown, participants with hazel/green/medium and blue/light colors had a 24% (RR = 1.24, 95% CI: 1.06-1.45) and a 19% (RR = 1.19, 95% CI: 1.01-1.41) higher risk of SCC, respectively. Similarly, a higher risk of BCC was observed in participants with hazel/green/medium eye colors (RR = 1.16, 95% CI: 1.09-1.23) and blue/light eye colors (RR = 1.17, 95% CI: 1.10-1.25). We did not find significant associations between eye color and risk of melanoma. Lighter eye color was associated with increased risks of SCC and BCC among those with dark hair colors (p for interaction ≤ 0.02).In conclusion, in this large prospective study of men, we found that light eye colors were associated with higher risks of SCC and BCC, but not melanoma. Further studies are needed to confirm this association in other populations.

Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods

Background

Genotype–phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the association which can be broadly categorized into two classes, statistical techniques, and machine learning. Statistical techniques are good for finding the actual SNPs causing variation where Machine Learning techniques are good where we just want to classify the people into different categories. In this article, we examined the Eye-color and Type-2 diabetes phenotype. The proposed technique is a hybrid approach consisting of some parts from statistical techniques and remaining from Machine learning.

Results

The main dataset for Eye-color phenotype consists of 806 people. 404 people have Blue-Green eyes where 402 people have Brown eyes. After preprocessing we generated 8 different datasets, containing different numbers of SNPs, using the mutation difference and thresholding at individual SNP. We calculated three types of mutation at each SNP no mutation, partial mutation, and full mutation. After that data is transformed for machine learning algorithms. We used about 9 classifiers, RandomForest, Extreme Gradient boosting, ANN, LSTM, GRU, BILSTM, 1DCNN, ensembles of ANN, and ensembles of LSTM which gave the best accuracy of 0.91, 0.9286, 0.945, 0.94, 0.94, 0.92, 0.95, and 0.96% respectively. Stacked ensembles of LSTM outperformed other algorithms for 1560 SNPs with an overall accuracy of 0.96, AUC = 0.98 for brown eyes, and AUC = 0.97 for Blue-Green eyes. The main dataset for Type-2 diabetes consists of 107 people where 30 people are classified as cases and 74 people as controls. We used different linear threshold to find the optimal number of SNPs for classification. The final model gave an accuracy of 0.97%.

Conclusion

Genotype–phenotype predictions are very useful especially in forensic. These predictions can help to identify SNP variant association with traits and diseases. Given more datasets, machine learning model predictions can be increased. Moreover, the non-linearity in the Machine learning model and the combination of SNPs Mutations while training the model increases the prediction. We considered binary classification problems but the proposed approach can be extended to multi-class classification.

Optimizing the genetic prediction of the eye and hair color for North Eurasian populations

Background

Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been verified on the West and Central Europeans only, while populations from border regions between Europe and Asia (like Caucasus and Ural) also carry the light pigmentation phenotypes.

Results

We phenotyped 286 samples collected across North Eurasia, genotyped them by the standard HIrisPlex-S markers and found that predictive power in Caucasus/Ural/West Siberian populations is reasonable but lower than that in West Europeans. As these populations have genetic ancestries different from that of West Europeans, we hypothesized they may carry a somewhat different allele spectrum. Thus, for all samples we performed the exome sequencing additionally enriched with the 53 genes and intergenic regions known to be associated with the eye/hair color. Our association analysis replicated the importance of the key previously known SNPs but also identified five new markers whose eye color prediction power for the studied populations is compatible with the two major previously well-known SNPs. Four out of these five SNPs lie within the HERС2 gene and the fifth in the intergenic region. These SNPs are found at high frequencies in most studied populations. The released dataset of exomes from Russian populations can be further used for population genetic and medical genetic studies.

Conclusions

This study demonstrated that precision of the established systems for eye/hair color prediction from a genotype is slightly lower for the populations from the border regions between Europe and Asia that for the West Europeans. However, this precision can be improved if some newly revealed predictive SNPs are added into the panel. We discuss that the replication of these pigmentation-associated SNPs on the independent North Eurasian sample is needed in the future studies.

Assessment of Predictors of Sun Sensitivity as Defined by Fitzpatrick Skin Phototype in an Ecuadorian Population and Its Correlation with Skin Damage

BACKGROUND

The Fitzpatrick skin phototype scale (FSPTS) is a widely used instrument to assess skin type.

METHODS

A cross-sectional survey collected responses from 254 subjects from Quito regarding self-reported FSPTS, gender, age, education, and tobacco and alcohol consumption. Univariate and multivariate logistic regression analyses were performed to determine if ethnicity, hair color, and eye color significantly predict FSPTS. In addition, we studied the correlation between FSPTS and the SCINEXA scale with Pearson's correlation coefficient.

RESULTS

Ethnicity, eye color, and hair color are significant independent predictors of FSPTS (p < 0.0001).

CONCLUSIONS

Patient self-reported race and pigmentary phenotypes are inaccurate predictors of sun sensitivity as defined by Fitzpatrick skin phototype. Our study does not fully represent the population of the country. There are limitations to using patient-reported race and appearance in predicting individual sunburn risk.

["Blue eyes"-case report about the risks of cosmetic iris implants]

A 24-year-old Iranian woman presented to our department for routine eye control. She had had cosmetic iris implants (BrightOcular©) implanted 5 years before in a Tunisian eye clinic in order to change the color of her eyes. Despite subjective freedom of symptoms, a dramatically reduced corneal endothelial cell count was measured in the left eye. Therefore, surgical removal of the angle-supported cosmetic iris implants was necessary. Cosmetic iris implants are associated with sight-threatening complications-even years after their implantation. We report on a case of cosmetic iris implants inserted for alteration of eye color only, which gave rise to serious complications for our patient.

Importance of nonsynonymous OCA2 variants in human eye color prediction

Background

The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single‐nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G.

Methods

In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region.

Results

We identified three nonsynonymous OCA2 variants as important for eye color, including rs1800407:G>A (p.Arg419Gln) and two variants, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile), not previously described as important for eye color variation. It was shown that estimated haplotypes consisting of four variants (rs12913832:A>G, rs1800407:G>A (p.Arg419Gln), rs74653330:A>T (p.Ala481Thr), and rs121918166:G>A (p.Val443Ile)) explained 75.6% (adjusted R² = 0.76) of normal eye color variation, whereas rs12913832:A>G alone explained 68.8% (adjusted R² = 0.69). Moreover, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) had a measurable effect on quantitative skin color (P = 0.008).

Conclusion

Our data showed that rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) have a measurable effect on normal pigmentation variation.

A Practical Guide to the HIrisPlex System: Simultaneous Prediction of Eye and Hair Color from DNA

The HIrisPlex system, which consists of two parts, allows the simultaneous prediction of eye and hair color from DNA, e.g., samples extracted from crime scene evidence. The first part is a highly sensitive multiplex genotyping assay consisting of 24 DNA markers using SNaPshot™ chemistry, for analysis on all Capillary Electrophoresis machines. The second part consists of statistical models that respectively establish eye and hair color prediction probabilities from complete and incomplete genotype profiles using parameters generated from large genotype and phenotype databases. This combined prediction tool constitutes the online system freely available to users. Here we provide a practical guide on how to use the HIrisPlex system for forensic and other DNA applications.

Eye darkening as a reliable, easy and inexpensive indicator of stress in fish

We expand the use of eye darkening (ED) to indicate non-social stress in the fish Nile tilapia Oreochromis niloticus (L.). ED is easily estimated, not requiring any sophisticated equipment, and is non-invasive, facilitating the collection of several measures of stress over time. In the current study, we showed the following: (i) high- and low-ED occur spontaneously, indicating different fish reactions to adjustments to a novel environment; (ii) fish confinement or air exposure clearly increases ED (air exposure is a stronger stressor than confinement), and the time to restore basal values indicates the severity of the impact of the stressor on the fish (this response is not affected by period of the day, e.g., morning or afternoon); and (iii) in adults, females were more responsive (slower recovery) to 2-min air exposure than to 30-min confinement.