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

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.

Advancement in Human Face Prediction Using DNA

The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System

Forensic DNA Phenotyping (FDP) can reveal the appearance of an unknown individual by predicting the ancestry, phenotype (i.e., hair, eye, skin color), and age from DNA obtained at the crime scene. The HIrisPlex system has been developed to simultaneously predict eye and hair color. However, the prediction accuracy of the system needs to be assessed for the tested population before implementing FDP in casework. In this study, we evaluated the performance of the HIrisPlex system on 149 individuals from the Turkish population. We applied the single-based extension (SNaPshot chemistry) method and used the HIrisPlex online tool to test the prediction of the eye and hair colors. The accuracy of the HIrisPlex system was assessed through the calculation of the area under the receiver characteristic operating curves (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The results showed that the proposed method successfully predicted the eye and hair color, especially for blue (100%) and brown (95.60%) eye and black (95.23) and brown (98.94) hair colors. As observed in previous studies, the system failed to predict intermediate eye color, representing 25% in our cohort. The majority of incorrect predictions were observed for blond hair color (40.7%). Previous HIrisPlex studies have also noted difficulties with these phenotypes. Our study shows that the HIrisPlex system can be applied to forensic casework in Turkey with careful interpretation of the data, particularly intermediate eye color and blond hair color.

Population biobank as a basis for determining spatial variation of clinically relevant pharmacogenetic biomarkers of cardiovascular diseases

The introduction of pharmacogenetic tests among the Russian population faces a fundamental limitation  — pronounced genetic differences between populations. The genetic geography of pharmacogenetic markers of deoxyribonucleic acid (DNA) helps to remove these limitations.

Aim. To reveal the spatial variation of the gene pools of the indigenous European Russian population in terms of DNA markers that are significant for the pharmacotherapy of cardiovascular diseases (CVDs) using the population biobank collections.

Material and methods. A total of 3170 samples from 61 populations of the Biobank of Northern Eurasia, which represents the gene pools of the indigenous Eastern Europe population, were studied using two pharmacogenetic DNA marker arrays as follows: 60 most significant markers and 24 markers associated with CVDs. Using the multivariate statistics and genetic geography, a comparison of gene pool variation was made.

Results. A cartographic atlas has been created that includes maps of the distribution among the Eastern Europe population of 24 pharmacogenetic CVD markers. These cartographic models allow various specialists to analyze patterns in the distribution of pharmacogenetic markers. General patterns are supplemented by regional studies in  the  North Caucasus, the Cisurals and the Russian Plain, which identify population groups with similar pharmacogenetic status. For each region, a comparison of gene pool variation for two arrays of above-mentioned DNA markers was made.

Conclusion. The created atlas is the basis for the development of pharmacogenetic studies conducted by genetic geography methods using a single panel of markers and representative samples provided by population biobanks. The reliability of the results is ensured by a detailed genealogical and population annotation of each biobank sample and representative samples from the populations.

The constraints of racialization: How classification and valuation hinder scientific research on human variation

Human biological variation has historically been studied through the lens of racialization. Despite a general shift away from the use of overt racial terminologies, the underlying racialized frameworks used to describe and understand human variation still remain. Even in relatively recent anthropological and biomedical work, we can observe clear manifestations of such racial thinking. This paper shows how classification and valuation are two specific processes which facilitate racialization and hinder attempts to move beyond such frameworks. The bias induced by classification distorts descriptions of phenotypic variation in a way that erroneously portrays European populations as more variable than others. Implicit valuation occurs in tandem with classification and produces narratives of superiority/inferiority for certain phenotypic variants without an objective biological basis. The bias of racialization is a persistent impediment stemming from the inheritance of scientific knowledge developed under explicitly racial paradigms. It is also an internalized cognitive distortion cultivated through socialization in a world where racialization is inescapable. Though undeniably challenging, this does not present an insurmountable barrier, and this bias can be mitigated through the critical evaluation of past work, the active inclusion of marginalized perspectives, and the direct confrontation of institutional structures enforcing racialized paradigms.