Predicting phenotype from genotype: normal pigmentation

Genetic landscape of forensic DNA phenotyping markers among Mediterranean populations

Forensic DNA Phenotyping can reveal the appearance of an unknown individual by predicting the External Visible Characteristics (EVC) from DNA obtained at the crime scene. Our aim is to characterize the genetic landscape of Human identification markers responsible for EVC among Mediterranean populations compared to other worldwide groups. We conducted an exhaustive search for genes involved in EVC variation. Then, variants located on these genes were extracted from public genotypic data of Mediterranean, American, African and East Asiatic populations. The genetic landscape of these Human identification markers, their allelic distribution and admixture analyses, were determined using plink, R and ADMIXTURE softwares. Our results showed that the Mediterranean populations appear close to the Mexican populations and distinguished from sub Saharan African populations living in the USA and from East Asiatic populations. We highlighted a total of 103454 common variants shared between the studied populations and among them, 25 common variants associated with EVC. Interestingly, genotype frequencies results showed that the rs17646946, rs13016869, rs977588, rs1805008 and rs2240751 variants located respectively in the TCHH, PRKCE, OCA2, MC1R and MFSD12 genes are significantly different between the Mediterranean and Asiatic populations. The genotype frequencies of the variants rs977589 and rs7179994 located in the OCA2 gene, and of rs12913832 and rs2240751 located respectively in HERC2 and MFSD12 genes are significantly different between the Mediterranean and American populations. Our work generates a large number of EVC variants that could be a valuable resource for future studies in the forensic field.

Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction

In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction.

Evaluation of Personalized Skincare Through in-silico Gene Interactive Networks and Cellular Responses to UVR and Oxidative Stress

Purpose

Personalized approaches in dermatology are designed to match the specific requirements based on the individual genetic makeup. One major factor accounting for the differences in skin phenotypes is single nucleotide polymorphism (SNP) within several genes with diverse roles that extend beyond skin tone and pigmentation. Therefore, the cellular sensitivities to the environmental stress and damage linked to extrinsic aging could also underlie the individual characteristics of the skin and dictate the unique skin care requirements. This study aimed to identify the likely biomarkers and molecular signatures expressed in skin cells of different ethnic backgrounds, which could aid further the design of personalized skin products based on specific demands.

Methods

Using data mining and in-silico modeling, the association of SNP-affected genes with three major skin types of European, Asian and African origin was analyzed and compared within the structure-function gene interaction networks. Cultured dermal fibroblasts were subsequently subjected to ultraviolet radiation and oxidative stress and analyzed for DNA damage and senescent markers. The protective applications of two cosmetic ingredients, Resveratrol and Quercetin, were validated in both cellular and in-silico models.

Results

Each skin type was characterized by the presence of SNPs in the genes controlling facultative and constitutive pigmentation, which could also underlie the major differences in responses to photodamage, such as oxidative stress, inflammation, and barrier homeostasis. Skin-type-specific dermal fibroblasts cultured in-vitro demonstrated distinctive sensitivities to ultraviolet radiation and oxidative stress, which could be modulated further by the bioactive compounds with the predicted capacities to interact with some of the genes in the in-silico models.

Conclusion

Evaluation of the SNP-affected gene networks and likely sensitivities of skin cells, defined as low threshold levels to extrinsic stress factors, can provide a valuable tool for the design and formulation of personalized skin products that match more accurately diverse ethnic backgrounds.

Predicting Physical Appearance from DNA Data-Towards Genomic Solutions

The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.

Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch

Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10⁻³). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations.

Prediction of eye, hair and skin colour in Latin Americans

Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.

Chemical and biochemical control of skin pigmentation with special emphasis on mixed melanogenesis

Melanins are widely distributed in animals and plants; in vertebrates, most melanins are present on the body surface. The diversity of pigmentation in vertebrates is mainly attributed to the quantity and ratio of eumelanin and pheomelanin synthesis. Most natural melanin pigments in animals consist of both eumelanin and pheomelanin in varying ratios, and thus, their combined synthesis is called "mixed melanogenesis." Gene expression is an established mechanism for controlling melanin synthesis; however, there are multiple factors that affect melanin synthesis besides gene expression. Due to the differential sensitivity of the eumelanin and pheomelanin synthetic pathways to pH, melanosomal pH likely plays a major role in mixed melanogenesis. Here, we focused on various factors affecting mixed melanogenesis including (1) chemical regulation of melanin synthesis, (2) melanosomal pH regulation during normal melanogenesis and effect on mixed melanogenesis, and (3) mechanisms of melanosomal pH control (proton pumps, channels, transporters, and signaling pathways).

Considering the flanking region variants of nonbinary SNP and phenotype-informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piSNPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTR^R Identifiler^R PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.

The color of normal: How a Eurocentric focus erases pigmentation complexity

OBJECTIVES

Skin pigmentation is both a highly variable and highly visible human phenotypic trait. Investigations into the biology and origins of this variation have been the focus of research in the fields of dermatology, anthropology, and forensic science, among others. This manuscript explores how much of what we know about the biology, genetics, and evolutionary origins of pigmentation has been strongly influenced by investigations and applications that focus on lighter skin.

METHODS

I reviewed literature from the fields of dermatology, anthropology and evolutionary genetics, and forensic science to assess how perceptions of lighter skin as the "normal" state in humans can shape the ways that knowledge is gathered and applied in these fields.

RESULTS

This normalization of lighter skin has impacted common tools used in dermatology and shaped the framework of dermatological education. A strong Eurocentric bias has shaped our understanding of the genetic architecture of pigmentary traits, which influences the ways in we understand the evolutionary processes leading to modern pigmentation diversity. Finally, I discuss how these biases in pigmentation genetics work in combination with phenotypic systems that privilege predicting lighter pigmentation variation to impede accurate prediction of intermediate phenotypes, particularly in individuals with ancestry from multiple populations. This can lead to a disproportionate targeting of already over-policed populations with darker skin.

CONCLUSIONS

Potential changes to how we conceptualize clinical and basic pigmentation research may help to reduce existing health disparities and improve understanding of pigmentation genetic architecture and how this knowledge is applied in forensic contexts.

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

Eye color prediction using the IrisPlex system: a limited pilot study in the Iraqi population

Background

Forensic DNA phenotyping has gained momentum in the recent past due to the prediction of externally visible characters (EVCs) from the biological sample. The most common phenotypes like eye, hair, and skin color are predicted from the biological samples using a web-based system called IrisPlex. Based on six genetic SNPs, the IrisPlex system is developed and validated for its prediction accuracy in diverse ethnic groups worldwide. In previous studies, this system proved to have significant prediction accuracy. The EVCs vary substantially based on different geographical locations. Hence, the objective of this study was to validate the accuracy of the IrisPlex system in predicting the eye colors in the Iraqi population.

Methods

Six genetic single-nucleotide polymorphisms SNPs (HERC2-rs12913832, OCA2- rs1800407, SLC24A4-rs12896399, SLC45A2- rs16891982, TYR-rs1393350, and IRF4- rs12203592) in 58 Iraqi subjects were performed using Sequenom MassARRAY Genotyping. According to Liu et al., a predicted probability of 0.7 was considered as the threshold.

Results

Participants in this study of brown color were observed in 44.83%, intermediate in 43.1%, and blue in 12.07%. Completely predictive accuracy is obtained in 1; we observed the AUC at threshold 0.7 was 0.91 for brown, 0.79 for blue, and 0.60 for intermediate eye color. The sensitivity was 42.85% for blue, 0% for intermediate eye color, and 100% for brown-colored eye. Specificity was 100% for blue, 100% for intermediate, and 78.13% for brown eye color.

Conclusion

Hence, it was concluded that the prediction accuracy of the IrisPlex system for blue and brown color eye in the Iraqi population is significant in the studied population size. However, a pivotal study with larger sample size is required to represent the prediction accuracy of the IrisPlex system in the whole Iraqi population.

Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry

Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R² = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R² = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R² = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.

A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect

Genetic variation in melanocortin-1 receptor (MC1R) is a known contributor to disease-free red hair in humans. Three loss-of-function single-nucleotide variants (rs1805007, rs1805008 and rs1805009) have been established as strongly correlated with red hair. The contribution of other loss-of-function MC1R variants (in particular rs1805005, rs2228479 and rs885479) and the extent to which other genetic loci are involved in red hair colour is less well understood. Here, we used the UK Biobank cohort to capture a comprehensive list of MC1R variants contributing to red hair colour. We report a correlation with red hair for both strong-effect variants (rs1805007, rs1805008 and rs1805009) and weak-effect variants (rs1805005, rs2228479 and rs885479) and show that their coefficients differ by two orders of magnitude. On the haplotype level, both strong- and weak-effect variants contribute to the red hair phenotype, but when considered individually, weak-effect variants show a reverse, negative association with red hair. The reversal of association direction in the single-variant analysis is facilitated by a distinguishing structure of MC1R, in which loss-of-function variants are never found to co-occur on the same haplotype. The other previously reported hair colour genes' variants do not substantially improve the MC1R red hair colour predictive model. Our best model for predicting red versus other hair colours yields an unparalleled area under the receiver operating characteristic of 0.96 using only MC1R variants. In summary, we present a comprehensive statistically derived characterization of the role of MC1R variants in red hair colour and offer a powerful, economical and parsimonious model that achieves unsurpassed performance.

A Genome-Wide Association Study of Skin and Iris Pigmentation among Individuals of South Asian Ancestry

South Asia has a complex history of migrations and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta-analysis of two genome-wide association studies (GWASs) of skin pigmentation using skin reflectance (M-index) as a quantitative phenotype. The meta-analysis includes a sample of individuals of South Asian descent living in Canada (N = 348), and a sample of individuals from two caste and four tribal groups from West Maharashtra, India (N = 480). We also present the first GWAS of iris color in South Asian populations. This GWAS was based on quantitative measures of iris color obtained from high-resolution iris pictures. We identified genome-wide significant associations of variants within the well-known gene SLC24A5, including the nonsynonymous rs1426654 polymorphism, with both skin pigmentation and iris color, highlighting the pleiotropic effects of this gene on pigmentation. Variants in the HERC2 gene (e.g., rs12913832) were also associated with iris color and iris heterochromia. Our study emphasizes the usefulness of quantitative methods to study iris color variation. We also identified novel genome-wide significant associations with skin pigmentation and iris color, but we could not replicate these associations due to the lack of independent samples. It will be critical to expand the number of studies in South Asian populations in order to better understand the genetic variation driving the diversity of skin pigmentation and iris color observed in this region.

RECENT TECHNIQUES BASED ON THE UTILIZATION OF DNA AND AUTOSOMAL SINGLE NUCLEOTIDE POLYMORPHISMS FOR IDENTIFYING HUMANS

The biological samples used in forensics can contain DNA which is highly fragmented as a consequence of exposure to any of the numerous degrading factors. Analysis of the sequence or size of the products of Polymerase chain reaction is at present responsible for the analysis of remains of humans in forensics. Despite the effectiveness of protocols based on PCR, there are certain limitations that are presented by the low numbers of copies of the template and the variations that are imposed by the decaying process to the template. The primary aim of this research is to explore the significance of autosomal SNPs in forensic science through the identification of humans at a crime scene. This study provides an exploration of the applicability of autosomal SNPs for the identification of humans at crime scene. This would fill the gap present in the current literature regarding the significance of autosomal SNPs in the identification of humans during crime scene investigation. It will also enable the identification of the criminals involved in several types of the crimes ranging from general theft to rape and sexual assault, murder, and robberies. It will also allow the identification of dead bodies in cases where it is difficult to identify the dead person due to unrecognizable condition of the body. This study will facilitate the improvement of the investigation of crime scene investigators. It will provide a significant way for the incorporation of recent techniques of the molecular genetics into forensics. Reduction in the workload of the crime scene investigators would also occur through the implementation of outcomes of this study into the field of forensic science. There are several studies which have demonstrated the applicability of SNPs in forensic investigations for identifying the humans at crime scene. Several effective and efficient technological systems have been developed by the researchers which are capable of performing analysis of biological samples containing degraded DNA because SNPs can be obtained from these samples. Physical characteristics of the individuals can be predicted through the analysis of SNPs. This can provide significant information about the color of eye, hair and skin of the individuals involved in crime.

Prediction of skin color, tanning and freckling from DNA in Polish population: linear regression, random forest and neural network approaches

Predicting phenotypes from DNA has recently become extensively studied field in forensic research and is referred to as Forensic DNA Phenotyping. Systems based on single nucleotide polymorphisms for accurate prediction of iris, hair and skin color in global population, independent of bio-geographical ancestry, have recently been introduced. Here, we analyzed 14 SNPs for distinct skin pigmentation traits in a homogeneous cohort of 222 Polish subjects. We compared three different algorithms: General Linear Model based on logistic regression, Random Forest and Neural Network in 18 developed prediction models. We demonstrate Random Forest to be the most accurate algorithm for 3- and 4-category estimations (total of 58.3% correct calls for skin color prediction, 47.2% for tanning prediction, 50% for freckling prediction). Binomial Logistic Regression was the best approach in 2-category estimations (total of 69.4% correct calls, AUC = 0.673 for tanning prediction; total of 52.8% correct calls, AUC = 0.537 for freckling prediction). Our study confirms the association of rs12913832 (HERC2) with all three skin pigmentation traits, but also variants associated solely with certain pigmentation traits, namely rs6058017 and rs4911414 (ASIP) with skin sensitivity to sun and tanning abilities, rs12203592 (IRF4) with freckling and rs4778241 and rs4778138 (OCA2) with skin color and tanning. Finally, we assessed significant differences in allele frequencies in comparison with CEU data and our study provides a starting point for the development of prediction models for homogeneous populations with less internal differentiation than in the global predictive testing.

Shades of complexity: New perspectives on the evolution and genetic architecture of human skin

Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.

Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource

With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.

Reliability of genomic predictions of complex human phenotypes

Genome-wide association studies have helped us identify a wealth of genetic variants associated with complex human phenotypes. Because most variants explain a small portion of the total phenotypic variation, however, marker-based studies remain limited in their ability to predict such phenotypes. Here, we show how modern statistical genetic techniques borrowed from animal breeding can be employed to increase the accuracy of genomic prediction of complex phenotypes and the power of genetic mapping studies. Specifically, using the triglyceride data of the GAW20 data set, we apply genomic-best linear unbiased prediction (G-BLUP) methods to obtain empirical genetic values (EGVs) for each triglyceride phenotype and each individual. We then study 2 different factors that influence the prediction accuracy of G-BLUP for the analysis of human data: (a) the choice of kinship matrix, and (b) the overall level of relatedness. The resulting genetic values represent the total genetic component for the phenotype of interest and can be used to represent a trait without its environmental component. Finally, using empirical data, we demonstrate how this method can be used to increase the power of genetic mapping studies. In sum, our results show that dense genome-wide data can be used in a wider scope than previously anticipated.

Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA

Human head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.

Four-dimensional, dynamic mosaicism is a hallmark of normal human skin that permits mapping of the organization and patterning of human epidermis during terminal differentiation

Recent findings of mosaicism (DNA sequence variation) challenge the dogma that each person has a stable genetic constitution. Copy number variations, point mutations and chromosome abnormalities in normal or diseased tissues have been described. We studied normal skin mosaicism of a single nucleotide polymorphism (SNP) [rs1426654, p.Thr111Ala] in SLC24A5, an ion transporter gene. This SNP is unusual in that more than 90% of people of European descent have homozygous germline A/A alleles, while more than 90% of East Asians and Blacks have homozygous germline G/G alleles. We found mosaicism in neonatal foreskins as well as in 69% of nearly 600 skin surface scraping samples from 114 donors of different ages. Strikingly, donors with germline (buccal or blood) A/A, A/G or G/G genotypes had all three sequences (A/A, A/G or G/G) in the skin surface scrapings. SNP sequence differences extended within the epidermis in the vertical dimension from basal cell layer to the stratum corneum at the surface, as well as across the two-dimensions of the skin surface. Furthermore, repeated scrapings in the same location revealed variation in the sequences in the same individuals over time, adding a fourth dimension to this variation. We then used this mosaicism to track the movement of epidermal cells during normal differentiation and characterize the patterning of epidermal cells during terminal differentiation. In this coordinated proliferation model of epidermal differentiation, the skin surface is alternatively populated by synchronous, cycling of waves of cells, with each group having a different DNA sequence. These groups of cells abruptly flatten into large sheets at the surface providing patches of uniform SNP sequence. This four-dimensional mosaicism is a normal, previously unrecognized form of dynamic mosaicism in human skin.

Hair Color and Skin Color Together Influence Perceptions of Age, Health, and Attractiveness in Lightly-Pigmented, Young Women

OBJECTIVE

Research documents that even subtle changes in visible skin condition affect perceptions of age, health, and attractiveness. There is evidence that hair quality also affects the assessment of physical appearance, as variations in hair diameter, hair density, and hair style have systematic effects on perception. Here, we consider combined effects of hair color and skin color on the perception of female physical appearance.

METHODS

In two experiments, we digitally manipulated facial skin color of lightly-pigmented, young women, both between-subjects (Experiment 1) and within-subjects (Experiment 2), and investigated possible interactions with hair color in regard to age, health, and attractiveness perception.

RESULTS

In both experiments, we detected hair color and skin color interaction effects on men's and women's assessments. For between-subjects comparisons, participants with lighter hair color were judged to be younger than those with darker shades; this effect was more pronounced in women with light skin color. No such effect was observed for within-subjects variation in skin color. Both experiments showed that smaller perceived contrast between hair color and skin color resulted in more positive responses.

CONCLUSION

We conclude that hair color and facial skin color together have an effect on perceptions of female age, health, and attractiveness in young women, and we discuss these findings with reference to the literature on the role of hair and skin in the assessment of female physical appearance. This article is protected by copyright. All rights reserved.

Genetic and phenotypic variability of iris color in Buenos Aires population

The aim of this work was to describe the phenotypic and genotypic variability related to iris color for the population of Buenos Aires province (Argentina), and to assess the usefulness of current methods of analysis for this country. We studied five Single Nucleotide Polymorphisms (SNPs) included in the IrisPlex kit, in 118 individuals, and we quantified eye color with Digital Iris Analysis Tool. The markers fit Hardy-Weinberg equilibrium for the whole sample, but not for rs12913832 within the group of brown eyes (LR=8.429; p=0.004). We found a remarkable association of HERC2 rs12913832 GG with blue color (p < 0.01) but the other markers did not show any association with iris color. The results for the Buenos Aires population differ from those of other populations of the world for these polymorphisms (p < 0,01). The differences we found might respond to the admixed ethnic composition of Argentina; therefore, methods of analysis used in European populations should be carefully applied when studying the population of Argentina. These findings reaffirm the importance of this investigation in the Argentinian population for people identification based on iris color.

Global skin colour prediction from DNA

Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.

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.

MC1R diversity in Northern Island Melanesia has not been constrained by strong purifying selection and cannot explain pigmentation phenotype variation in the region

BACKGROUND

Variation in human skin pigmentation evolved in response to the selective pressure of ultra-violet radiation (UVR). Selection to maintain darker skin in high UVR environments is expected to constrain pigmentation phenotype and variation in pigmentation loci. Consistent with this hypothesis, the gene MC1R exhibits reduced diversity in African populations from high UVR regions compared to low-UVR non-African populations. However, MC1R diversity in non-African populations that have evolved under high-UVR conditions is not well characterized.

METHODS

In order to test the hypothesis that MC1R variation has been constrained in Melanesians the coding region of the MC1R gene was sequenced in 188 individuals from Northern Island Melanesia. The role of purifying selection was assessed using a modified McDonald Kreitman's test. Pairwise FST was calculated between Melanesian populations and populations from the 1000 Genomes Project. The SNP rs2228479 was genotyped in a larger sample (n = 635) of Melanesians and tested for associations with skin and hair pigmentation.

RESULTS

We observe three nonsynonymous and two synonymous mutations. A modified McDonald Kreitman's test failed to detect a significant signal of purifying selection. Pairwise FST values calculated between the four islands sampled here indicate little regional substructure in MC1R. When compared to African, European, East and South Asian populations, Melanesians do not exhibit reduced population divergence (measured as FST) or a high proportion of haplotype sharing with Africans, as one might expect if ancestral haplotypes were conserved across high UVR populations in and out of Africa. The only common nonsynonymous polymorphism observed, rs2228479, is not significantly associated with skin or hair pigmentation in a larger sample of Melanesians.

CONCLUSIONS

The pattern of sequence diversity here does not support a model of strong selective constraint on MC1R in Northern Island Melanesia This absence of strong constraint, as well as the recent population history of the region, may explain the observed frequencies of the derived rs2228479 allele. These results emphasize the complex genetic architecture of pigmentation phenotypes, which are controlled by multiple, possibly interacting loci. They also highlight the role that population history can play in influencing phenotypic diversity in the absence of strong natural selection.

Assessment of IrisPlex-based multiplex for eye and skin color prediction with application to a Portuguese population

DNA phenotyping research is one of the most emergent areas of forensic genetics. Predictions of externally visible characteristics are possible through analysis of single nucleotide polymorphisms. These tools can provide police with "intelligence" in cases where there are no obvious suspects and unknown biological samples found at the crime scene do not result in any criminal DNA database hits. IrisPlex, an eye color prediction assay, revealed high prediction rates for blue and brown eye color in European populations. However, this is less predictive in some non-European populations, probably due to admixing. When compared to other European countries, Portugal has a relatively admixed population, resulting from a genetic influx derived from its proximity to and historical relations with numerous African territories. The aim of this work was to evaluate the utility of IrisPlex in the Portuguese population. Furthermore, the possibility of supplementing this multiplex with additional markers to also achieve skin color prediction within this population was evaluated. For that, IrisPlex was augmented with additional SNP loci. Eye and skin color prediction was estimated using the multinomial logistic regression and binomial logistic regression models, respectively. The results demonstrated eye color prediction accuracies of the IrisPlex system of 90 and 60% for brown and blue eye color, respectively, and 77% for intermediate eye color, after allele frequency adjustment. With regard to skin color, it was possible to achieve a prediction accuracy of 93%. In the future, phenotypic determination multiplexes must include additional loci to permit skin color prediction as presented in this study as this can be an advantageous tool for forensic investigation.

Exploration of SNP variants affecting hair colour prediction in Europeans

DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.

Assay Development and Validation of an 8-SNP Multiplex Test to Predict Eye and Skin Coloration

Identifying human remains is one of the many responsibilities of forensic scientists. An eye- and skin-color predictor translates genotypic information into phenotypic description. Eight single nucleotide polymorphisms (SNPs) are utilized for this predictor, five for eye, and six for skin coloration. Here, we describe the development and validation of an 8-SNP multiplex assay that consists of a multiplex PCR, followed by a multiplexed single-base primer extension reaction generating fluorescently labeled oligonucleotides of distinct length that are detected by multicolor capillary electrophoresis. Validation of this assay included tests for reproducibility, reliability, sensitivity, species specificity, its performance on degraded DNA, and on forensic samples. It can be concluded that the 8-SNP multiplex assay is robust and can be used on challenging samples, including bones, to reliably determine the genotypes to predict eye and skin color of individuals. This information can assist in the identification of human remains and missing persons.

SLC24A5 and ASIP as phenotypic predictors in Brazilian population for forensic purposes

Pigmentation is a variable and complex trait in humans and it is determined by the interaction of environmental factors, age, disease, hormones, exposure to ultraviolet radiation and genetic factors, including pigmentation genes. Many polymorphisms of these genes have been associated with phenotypic diversity of skin, eyes and hair color in homogeneous populations. Phenotype prediction from biological samples using genetic information has benefited forensic area in some countries, leading some criminal investigations. Herein, we evaluated the association between polymorphisms in the genes SLC24A5 (rs1426654) and ASIP (rs6058017) with skin, eyes and hair colors, in 483 healthy individuals from Brazilian population for attainable use in forensic practice. The volunteers answered a questionnaire where they self-reported their skin, eye and hair colors. The polymorphic homozygous genotype of rs1426654∗A and rs6058017∗A in SLC24A5 and ASIP respectively, showed strongest association with fairer skin (OR 47.8; CI 14.1-161.6 and OR 8.6; CI 2.5-29.8); SLC24A5 alone showed associations with blue eyes (OR 20.7; CI 1.2-346.3) and blond hair (OR 26.6; CI 1.5-460.9). Our data showed that polymorphic genotypes (AA), in both genes, are correlated with characteristics of light pigmentation, while the ancestral genotype (GG) is related to darker traits, corroborating with previous studies in European and African populations. These associations show that specific molecular information of an individual may be useful to access some phenotypic features in an attempt to help forensic investigations, not only on crime scene samples but also in cases of face reconstructions in unknown bodies.

Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics

SNPs that are molecularly very close (<10kb) will generally have extremely low recombination rates, much less than 10(-4). Multiple haplotypes will often exist because of the history of the origins of the variants at the different sites, rare recombinants, and the vagaries of random genetic drift and/or selection. Such multiallelic haplotype loci are potentially important in forensic work for individual identification, for defining ancestry, and for identifying familial relationships. The new DNA sequencing capabilities currently available make possible continuous runs of a few hundred base pairs so that we can now determine the allelic combination of multiple SNPs on each chromosome of an individual, i.e., the phase, for multiple SNPs within a small segment of DNA. Therefore, we have begun to identify regions, encompassing two to four SNPs with an extent of <200bp that define multiallelic haplotype loci. We have identified candidate regions and have collected pilot data on many candidate microhaplotype loci. Here we present 31 microhaplotype loci that have at least three alleles, have high heterozygosity, are globally informative, and are statistically independent at the population level. This study of microhaplotype loci (microhaps) provides proof of principle that such markers exist and validates their usefulness for ancestry inference, lineage-clan-family inference, and individual identification. The true value of microhaplotypes will come with sequencing methods that can establish alleles unambiguously, including disentangling of mixtures, because a single sequencing run on a single strand of DNA will encompass all of the SNPs.

Implications of the admixture process in skin color molecular assessment

The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice.

Association of genetic variants with self-assessed color categories in Brazilians

The Brazilian population was formed by extensive admixture of three different ancestral roots: Amerindians, Europeans and Africans. Our previous work has shown that at an individual level, ancestry, as estimated using molecular markers, was a poor predictor of color in Brazilians. We now investigate if SNPs known to be associated with human skin pigmentation can be used to predict color in Brazilians. For that, we studied the association of fifteen SNPs, previously known to be linked with skin color, in 243 unrelated Brazilian individuals self-identified as White, Browns or Blacks from Rio de Janeiro and 212 unrelated Brazilian individuals self-identified as White or Blacks from São Paulo. The significance of association of SNP genotypes with self-assessed color was evaluated using partial regression analysis. After controlling for ancestry estimates as covariates, only four SNPs remained significantly associated with skin pigmentation: rs1426654 and rs2555364 within SLC24A5, rs16891982 at SLC45A2 and rs1042602 at TYR. These loci are known to be involved in melanin synthesis or transport of melanosomes. We found that neither genotypes of these SNPs, nor their combination with biogeographical ancestry in principal component analysis, could predict self-assessed color in Brazilians at an individual level. However, significant correlations did emerge at group level, demonstrating that even though elements other than skin, eye and hair pigmentation do influence self-assessed color in Brazilians, the sociological act of self-classification is still substantially dependent of genotype at these four SNPs.

Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage

Forensic DNA Phenotyping or 'DNA intelligence' tools are expected to aid police investigations and find unknown individuals by providing information on externally visible characteristics of unknown suspects, perpetrators and missing persons from biological samples. This is especially useful in cases where conventional DNA profiling or other means remain non-informative. Recently, we introduced the HIrisPlex system, capable of predicting both eye and hair colour from DNA. In the present developmental validation study, we demonstrate that the HIrisPlex assay performs in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines providing an essential prerequisite for future HIrisPlex applications to forensic casework. The HIrisPlex assay produces complete profiles down to only 63 pg of DNA. Species testing revealed human specificity for a complete HIrisPlex profile, while only non-human primates showed the closest full profile at 20 out of the 24 DNA markers, in all animals tested. Rigorous testing of simulated forensic casework samples such as blood, semen, saliva stains, hairs with roots as well as extremely low quantity touch (trace) DNA samples, produced complete profiles in 88% of cases. Concordance testing performed between five independent forensic laboratories displayed consistent reproducible results on varying types of DNA samples. Due to its design, the assay caters for degraded samples, underlined here by results from artificially degraded DNA and from simulated casework samples of degraded DNA. This aspect was also demonstrated previously on DNA samples from human remains up to several hundreds of years old. With this paper, we also introduce enhanced eye and hair colour prediction models based on enlarged underlying databases of HIrisPlex genotypes and eye/hair colour phenotypes (eye colour: N = 9188 and hair colour: N = 1601). Furthermore, we present an online web-based system for individual eye and hair colour prediction from full and partial HIrisPlex DNA profiles. By demonstrating that the HIrisPlex assay is fully compatible with the SWGDAM guidelines, we provide the first forensically validated DNA test system for parallel eye and hair colour prediction now available to forensic laboratories for immediate casework application, including missing person cases. Given the robustness and sensitivity described here and in previous work, the HIrisPlex system is also suitable for analysing old and ancient DNA in anthropological and evolutionary studies.

Evaluation of the IrisPlex DNA-based eye color prediction assay in a United States population

DNA phenotyping is a rapidly developing area of research in forensic biology. Externally visible characteristics (EVCs) can be determined based on genotype data, specifically based on single nucleotide polymorphisms (SNPs). These SNPs are chosen based on their association with genes related to the phenotypic expression of interest, with known examples in eye, hair, and skin color traits. DNA phenotyping has forensic importance when unknown biological samples at a crime scene do not result in a criminal database hit; a phenotypic profile of the sample can therefore be used to develop investigational leads. IrisPlex, an eye color prediction assay, has previously shown high prediction rates for blue and brown eye color in a Dutch European population. The objective of this work was to evaluate its utility in a North American population. We evaluated six SNPs included in the IrisPlex assay in population sample collected from a USA college campus. We used a quantitative method of eye color classification based on (RGB) color components of digital photographs of the eye taken from each study volunteer so that each eye was placed in one of three eye color categories: brown, intermediate, or blue. Objective color classification was shown to correlate with basic human visual determination making it a feasible option for use in future prediction assay development. Using these samples and various models, the maximum prediction accuracies of the IrisPlex system after allele frequency adjustment was 58% and 95% brown and blue eye color predictions, respectively, and 11% for intermediate eye colors. Future developments should include incorporation of additional informative SNPs, specifically related to the intermediate eye color, and we recommend the use of a Bayesian approach as a prediction model as likelihood ratios can be determined for reporting purposes.

Improved eye- and skin-color prediction based on 8 SNPs

Aim

To improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions.

Methods

Analysis of an eighth single nucleotide polymorphism (SNP), rs12896399 (SLC24A4), showed a statistically significant association with human eye color (P = 0.007) but a rather poor strength of agreement (κ = 0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2, rs1545397 at OCA2, rs16891982 at SLC45A2, rs1426654 at SLC24A5, rs885479 at MC1R, rs6119471 at ASIP, and rs12203592 at IRF4). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color.

Results

The 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly (P = 6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set).

Conclusions

We can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.

Epidemiological and investigative study of premature graying of hair in higher secondary and pre-university school children

BACKGROUND

Hair pigmentation is one of the most conspicuous phenotypes in humans ranging from black, brown, and blonde to red. Premature graying of hair occurs more commonly without any underlying pathology but is said to be inherited in autosomal dominant pattern. Premature graying has been shown to be associated with a few of the autoimmune disorders. A role for environmental factors and nutritional deficiencies has also been postulated. However, to date the exact etiology of premature graying has not been established.

AIM

The objective of our study was to conduct an epidemiological and investigative study of premature graying of hair in higher secondary and pre-university school children of the semi-urban area.

MATERIALS AND METHODS

A total of 35 cases and controls were investigated for various parameter such as Hemoglobin, total iron binding capacity, serum ferritin (S. Ferritin), serum calcium (S. Ca), serum iron (S. Iron), vitamin B12, and vitamin D3 after taking informed consent. Epidemiological and investigations correlation was established using the Chi-square and Mann Whitney test and P < 0.05 values were considered significant.

RESULT

Among the various laboratory parameters S. Ca, S. Ferritin and vitamin D3 were low in patients with premature graying of hair. There was significant high number of vitamin D3 deficient and insufficient among the cases compared to the controls.

CONCLUSION

According to our study S. Ca, S. Ferritin, vitamin D3 may play a role in premature graying of hair in our society.

Neutral pH and copper ions promote eumelanogenesis after the dopachrome stage

The diversity of pigmentation in the skin, hair, and eyes of humans has been largely attributed to the diversity of pH in melanosomes with acidic pH being proposed to suppress melanin production. Tyrosinase has an optimum pH of 7.4 and its activity is suppressed greatly at lower pH values. The first step of eumelanogenesis is the oxidation of tyrosine to dopachrome (DC) via dopaquinone. However, how eumelanogenesis is controlled by pH beyond this stage is not known. In this study, we examined the effects of pH (5.3-7.3) on the conversion of DC to 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and the subsequent oxidation of DHI and DHICA to form eumelanin. The effects of Cu(2+) ions on those reactions were also compared. The results indicate that an acidic pH greatly suppresses the late stages of eumelanogenesis and that Cu(2+) ions accelerate the conversion of DC to DHICA and its subsequent oxidation.

A single-nucleotide polymorphism (SNP) multiplex system: the association of five SNPs with human eye and hair color in the Slovenian population and comparison using a Bayesian network and logistic regression model

AIM

To analyze two phenotype characteristics--eye and hair color--using single-nucleotide polymorphisms (SNPs) and evaluate their prediction accuracy in Slovenian population.

METHODS

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.

RESULTS

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.

CONCLUSION

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.

Colorful DNA polymorphisms in humans

In this review article we summarize current knowledge on how variation on the DNA level influences human pigmentation including color variation of iris, hair, and skin. We review recent progress in the field of human pigmentation genetics by focusing on the genes and DNA polymorphisms discovered to be involved in determining human pigmentation traits, their association with diseases particularly skin cancers, and their power to predict human eye, hair, and skin colors with potential utilization in forensic investigations.