Determination of Phenotype Associated SNPs in the MC1R Gene*
Jagiellonian University, Cracovia, Lesser Poland Voivodeship, Poland Journal of Forensic Sciences
(Impact Factor: 1.16).
02/2007; 52(2):349 - 354. DOI: 10.1111/j.1556-4029.2006.00361.x
Prediction of physical appearance based on genetic analysis is a very attractive prospect for forensic investigations. Recent studies have proved that there is a significant association between some genetic variants of the melanocortin 1 receptor (MC1R) gene and red hair color. The present study focuses on the potential forensic applicability of variation within this pigment-related gene. Sequencing of the complete MC1R gene was performed on a group of red-haired individuals and controls with different pigmentation. A major role in determination of red hair color is played by two MC1R variants—C451T and C478T. The optimized minisequencing assay for genotyping of the above positions and three other important red hair-related MC1R polymorphisms, C252A, G425A, and G880C was successfully applied to analyze typical forensic specimens. Determination of a homozygous or heterozygous combination can be a good predictor of both red hair color and fair skin of a subject.
Available from: PubMed Central
- "The genome-wide association study (GWAS), a linkage analysis and candidate gene study, has been used to identify genetic variants influencing such EVCs. Variations in the MC1R gene have been associated with red hair . The red hair prediction method, based on a combination of non-synonymous SNPs in MC1R, was already developed for forensic science more than 10 years ago , and its accuracy was 84% in the prediction of red-haired individuals. "
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ABSTRACT: The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.
Available from: ncbi.nlm.nih.gov
- "From the 105 Slovenian samples we eliminated only one person, this being the only person with red hair in our population (0.9% of the Slovenian population). This low frequency of red hair color was expected for the general Slovenian population and additionally confirmed that red haired individuals were more prevalent in the Baltic region and Northern Europe populations (28). "
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To analyze two phenotype characteristics – eye and hair color – using single-nucleotide polymorphisms (SNPs) and evaluate their prediction accuracy in Slovenian population.
Twelve SNPs (OCA2 – rs1667394, rs7170989, rs1800407, rs7495174; HERC2 – rs1129038, rs12913832; MC1R – rs1805005, rs1805008; TYR – rs1393350; SLC45A2 – rs16891982, rs26722; SLC24A5 – rs1426654) were used for the development of a single multiplex assay. The single multiplex assay was based on SNaPshot chemistry and capillary electrophoresis. In order to evaluate the accuracy of the prediction of eye and hair color, we used the logistic regression model and the Bayesian network model, and compared the parameters of both.
The new single multiplex assay displayed high levels of genotyping sensitivity with complete profiles generated from as little as 62 pg of DNA. Based on a prior evaluation of all SNPs in a single multiplex, we focused on the five most statistically significant in our population in order to investigate the predictive value. The two prediction models performed reliably without prior ancestry information, and revealed very good accuracy for both eye and hair color. Both models determined the highest predictive value for rs12913832 (P < 0.0001), while the other four SNPs (rs1393350, rs1800407, rs1805008, and rs7495174) showed additional association for color prediction.
We developed a sensitive and reliable single multiplex genotyping assay. More samples from different populations should be analyzed before this assay could be used as one of the supplemental tools in tracing unknown individuals in more complicated crime investigations.
Available from: Fan Liu
- "First, we tested the genotyped SNPs for hair color association in our study sample. Although variation in MC1R is usually attributed to red hair color (Branicki et al. 2007; Grimes et al. 2001; Valverde et al. 1995), the compound variant MC1R-R in our study was significantly associated with all but one (auburn) hair color category, albeit its association was strongest with red hair (allelic OR: 12.6; 95% CI: [7.0–22.7]; P = 2.5910 -17 ; Table 1). "
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ABSTRACT: Predicting complex human phenotypes from genotypes is the central concept of widely advocated personalized medicine, but so far has rarely led to high accuracies limiting practical applications. One notable exception, although less relevant for medical but important for forensic purposes, is human eye color, for which it has been recently demonstrated that highly accurate prediction is feasible from a small number of DNA variants. Here, we demonstrate that human hair color is predictable from DNA variants with similarly high accuracies. We analyzed in Polish Europeans with single-observer hair color grading 45 single nucleotide polymorphisms (SNPs) from 12 genes previously associated with human hair color variation. We found that a model based on a subset of 13 single or compound genetic markers from 11 genes predicted red hair color with over 0.9, black hair color with almost 0.9, as well as blond, and brown hair color with over 0.8 prevalence-adjusted accuracy expressed by the area under the receiver characteristic operating curves (AUC). The identified genetic predictors also differentiate reasonably well between similar hair colors, such as between red and blond-red, as well as between blond and dark-blond, highlighting the value of the identified DNA variants for accurate hair color prediction.
Electronic supplementary material
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