Abstract
BackgroundPredicting 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.ResultsWe 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.ConclusionsThis 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.
Highlights
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
It is possible that some Asian populations carry alleles of the pigmentation-related genes which are not included in HirisPlex-S but affects the appearance phenotypes in these populations
As many key Single nucleotide polymorphism (SNP) are known to be located in intronic regions, we developed the custom exome panel which includes both, exonic and intronic regions of the 53 genes and intergenic regions known to be involved in the pigmentation traits
Summary
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. The genome-wide association studies [1,2,3] identified some key genes and sites within these genes which influence the pigmentation of the eye and hair color, as well as skin color [4, 5] phenotypes These genes have been widely used for predicting pigmentation from genotype, mainly in the forensic context [6,7,8]. It is possible that some Asian populations carry alleles of the pigmentation-related genes which are not included in HirisPlex-S but affects the appearance phenotypes in these populations If this is a case, such additional alleles might be useful for eye/color prediction in these populations and have practical importance for genetic forensic investigations in Russia, or when investigating individuals of Russian ancestry in Europe
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