True colors: A literature review on the spatial distribution of eye and hair pigmentation

Exploring Eye, Hair, and Skin Pigmentation in a Spanish Population: Insights from Hirisplex-S Predictions

BACKGROUND/OBJECTIVES

Understanding and predicting human pigmentation traits is crucial for individual identification. Genome-wide association studies have revealed numerous pigmentation-associated SNPs, indicating genetic overlap among pigmentation traits and offering the potential to develop predictive models without the need for analyzing large numbers of SNPs.

METHODS

In this study, we assessed the performance of the HIrisPlex-S system, which predicts eye, hair, and skin color, on 412 individuals from the Spanish population. Model performance was calculated using metrics including accuracy, area under the curve, sensitivity, specificity, and positive and negative predictive value.

RESULTS

Our results showed high prediction accuracies (70% to 97%) for blue and brown eyes, brown hair, and intermediate skin. However, challenges arose with the remaining categories. The model had difficulty distinguishing between intermediate eye colors and similar shades of hair and exhibited a significant percentage of individuals with incorrectly predicted dark and pale skin, emphasizing the importance of careful interpretation of final predictions. Future studies considering quantitative pigmentation may achieve more accurate predictions by not relying on categories. Furthermore, our findings suggested that not all previously established SNPs showed a significant association with pigmentation in our population. For instance, the number of markers used for eye color prediction could be reduced to four while still maintaining reasonable predictive accuracy within our population.

CONCLUSIONS

Overall, our results suggest that it may be possible to reduce the number of SNPs used in some cases without compromising accuracy. However, further validation in larger and more diverse populations is essential to draw firm conclusions and make broader generalizations.

Kafka's beautiful eyes: Forensic intelligence utilisation of phenotypic information

Franz Kafka had beautiful eyes. So striking, that many of the famous author's friends and peers commented on them - but quite variously ('dark', 'brown', 'grey' & 'blue'). Eye colour as perceived by an observer is subjective, being influenced by physiological, environmental, and even sociocultural factors. In a policing context, this does not mean that trait information such as eye colour is not valuable (far from it), but that it must be managed carefully. The Australian Federal Police has recently implemented a forensic DNA phenotyping (FDP, aka. physical trait prediction or PTP) capability, utilising massively parallel sequencing DNA technology to predict an individual's eye colour, biogeographical ancestry and sex from a crime scene sample. This information alone is not itself 'intelligence', but can be used to generate intelligence through holistic analyses undertaken within a transdisciplinary, all-source forensic intelligence (FORINT) framework. FORINT outputs posit abductive propositions typically at the activity/offence level, to provide insight and influence decision making. However, the use of predicted traits requires that they are compared to something; all Australian police databases include fields for physical traits, but no uniform standard is applied across all agencies. Moreover, collection is inconsistent and no automated systems are in place to capture such data systematically. Consider the 'Kafka problem': his peers gave multiply divergent descriptions of his eyes. If a Biology unit had predicted the eye colour of an 'unidentified author' using DNA - how would Kafka be confidently nominated as the contributor? We posit three maxims for law enforcement: (1) To expand the operational utility of forensic science in line with police demands, forensic science should operationalise FDP (e.g. operationally to rank a list of persons of interest, focus lines of enquiry in serious & organised crime, or assist with human remains identification). (2) Such advanced biological techniques are best delivered through an all-source FORINT framework, to maximise opportunities and minimise risk. (3) One cannot pursue techno-scientific advancements in isolation; it is also necessary to influence the operational posture for their implementation. In this paper we explore these issues and provide recommendations relating to (a) police practices, (b) image capture systems, and (c) research opportunities. Phenotypic trait prediction has great potential and can be operationalised effectively through a rigorous FORINT framework. However, there is (continual) work to be done to enhance the operational capabilities that are complementary to - but necessary for - effective forensic science contribution to investigations.

Predictive accuracy of genetic variants for eye color in a Kazakh population using the IrisPlex system

OBJECTIVE

This study assesses the accuracy of the IrisPlex system, a genetic eye color prediction tool for forensic analysis, in the Kazakh population. The study compares previously published genotypes of 515 Kazakh individuals from varied geographical and ethnohistorical contexts with phenotypic data on their eye color, introduced for the first time in this research.

RESULTS

The IrisPlex panel's effectiveness in predicting eye color in the Kazakh population was validated. It exhibited slightly lower accuracy than in Western European populations but was higher than in Siberian populations. The sensitivity was notably high for brown-eyed individuals (0.99), but further research is needed for blue and intermediate eye colors. This study establishes IrisPlex as a useful predictive tool in the Kazakh population and provides a basis for future investigations into the genetic basis of phenotypic variations in this diverse population.

Iris Pigmented Lesions and Risk of Cutaneous Melanoma: Case-Control Study in Lithuania

The global incidence of cutaneous melanoma (CM) is rising, necessitating early detection and identification of risk factors across different populations. A case-control study with 180 patients with primary diagnosed CM and 182 healthy controls was conducted. Participants underwent ophthalmic and skin examinations, where the identification and counting of common melanocytic nevi (CMN) and atypical melanocytic nevi (AMN) was performed. During ophthalmic examination, high-resolution slit lamp iris images were taken. Images were categorized according to iris periphery, collaret, and freckles. There was no difference in iris periphery and collaret color between groups. However, blue/grey iris periphery and blue collaret with or without freckles were the most common patterns. The presence of pigmented iris lesions and 2-5 mm and ≥5 mm in diameter CMNs was strongly associated with CM risk. The evidence from this study indicates that blue or grey periphery and blue collaret iris pattern with iris freckles are 2.74 times higher in the CM group than controls. Further research is needed to explore iris patterns' association with CM risk in diverse populations.

Comparison of cycloplegia at 20- and 30-minutes following proxymetacaine and cyclopentolate instillation in white 12-13-year-olds

CLINICAL RELEVANCE

Reducing the time between drop instillation and refraction reduces the time paediatric patients and young adults spend in practice, facilitating more eye examinations daily.

BACKGROUND

The current procedure for paediatric cycloplegic refraction is to wait for at least 30-minutes post-instillation of a cycloplegic before measuring spherical equivalent refraction. This study compared cycloplegia at 20- and 30-minutes following 0.5% proxymetacaine and 1.0% cyclopentolate in 12-13-year-olds.

METHODS

Participants were 99 white 12-13-year-olds. One drop of proxymetacaine hydrochloride (Minims, 0.5% w/v, Bausch & Lomb, UK) followed by one drop of cyclopentolate hydrochloride (Minims, 1.0% w/v, Bausch & Lomb, UK) was instilled into both eyes. Spherical equivalent refraction was measured by autorefraction (Dong Yang Rekto ORK-11 Auto Ref-Keratometer) at 20- and 30-minutes post-instillation. Data were analysed through paired t-testing, correlations, and linear regression analysis.

RESULTS

There was no significant difference in level of cycloplegia achieved at 20- (Mean spherical equivalent refraction (standard deviation) 0.438 (1.404) D) and 30-minutes (0.487 (1.420) D) post-eyedrop instillation (t (98) = 1.667, p = 0.099). The mean spherical equivalent refraction difference between time points was small (0.049 (0.294) D, 95% confidence interval =-0.108 ̶ 0.009D). Agreement indices: Accuracy = 0.999, Precision = 0.973, Concordance = 0.972. Spherical equivalent refraction at 20- and 30-minutes differed by ≤0.50D in 92% of eyes, and by <1.00D in 95%.

CONCLUSIONS

There was no clinically significant difference in spherical equivalent refraction or level of cycloplegia at 20- and 30-minutes post-eyedrop instillation. The latent time between drop instillation and measurement of refractive error may be reduced to 20 minutes in White 12-13-year-olds and young adults. Further studies must determine if these results persist in younger children and non-White populations.

Incorporating non-genetic evidence in large scale missing person searches: A general approach beyond filtering

The search for missing persons implies several steps, from the preliminary investigation that involves collecting background data related to the case to the genetic kinship testing. Despite its crucial importance in identifications, only some approaches mathematically formalize the possibility of using preliminary investigation data. In some cases, a filtering strategy is applied, which implies selecting a subset of possible victims where some non-genetic variables perfectly match those of the missing. Through a Bayesian approach, we propose a mathematical model for computing the prior odds based on non-genetic variables usually collected during the preliminary investigation, such as biological sex, hair colour, and age. We use computational simulations to show how to incorporate these prior odds in DNA-database searches. Importantly, our results suggest that applying the proposed model leads to better search performance in underpowered cases from the genetic point of view, where few or distant relatives of the missing person are available for genotyping. Furthermore, the results are also helpful when using non-genetic data for prior odds in well-powered cases, where genetic data are enough to reach a reliable conclusion. It performs better than other approaches, such as using non-genetic data for filtering. The software mispitools, freely available on CRAN, implements all described methods (https://CRAN.R-project.org/package=mispitools).

Phenotypic Classification of Eye Colour and Developmental Validation of the Irisplex System on Population Living in Malakand Division, Pakistan

The core objective of forensic DNA typing is developing DNA profiles from biological evidence for personal identification. The present study was designed to check the validation of the IrisPlex system and the Prevalence of eye colour in the Pakhtoon population residing within the Malakand Division.

METHODS

Eye colour digital photographs and buccal swab samples of 893 individuals of different age groups were collected. Multiplexed SNaPshot single base extension chemistry was used, and the genotypic results were analysed. Snapshot data were used for eye colour prediction through the IrisPlex and FROG-kb tool.

RESULTS

The results of the present study found brown eye colour to be the most prevalent eye colour in comparison to intermediate and blue coloured. Overall, individuals with brown-coloured eyes possess CT (46.84%) and TT (53.16%) genotypes. Blue eye-coloured individuals are solely of the CC genotype, while individuals of intermediate eye colour carry CT (45.15%) and CC (53.85%) genotypes in rs12913832 SNP in the HERC2 gene. It was also revealed that brown-coloured eyes individuals were dominant among all age groups followed by intermediate and blue. Statistical analysis between particular variables and eye colour showed a significant p-value (<0.05) for rs16891982 SNP in SLC45A2 gene, rs12913832 SNP in HERC2 gene, rs1393350 SNP in SLC45A2, districts and gender. The rest of the SNPs were non-significant with eye colour, respectively. The rs12896399 SNP and SNP rs1800407 were found significant with rs16891982 SNP. The result also demonstrated that the study group differs from the world population based on eye colour. The two eye colour prediction results were compared, and it was discovered that IrisPlex and FROG-Kb had similar higher prediction ratios for Brown and Blue eye colour.

CONCLUSIONS

The results of the current study revealed brown eye colour to be the most prevalent amongst members of the local population of Pakhtoon ethnicity in the Malakand Division of northern Pakistan. A set of contemporary human DNA samples with known phenotypes are used in this research to evaluate the custom panel's prediction accuracy. With the aid of this forensic test, DNA typing can be supplemented with details about the appearance of the person from whom the sample was taken in cases involving missing persons, ancient human remains, and trace samples. This study may be helpful for future population genetics and forensics studies.

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022

This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.

Redheaded women are more sexually active than other women, but it is probably due to their suitors

Women with red hair color, i.e., 1–9% of female Europeans, tend to be the subject of various stereotypes about their sexually liberated behavior. The aim of the present case–control study was to explore whether a connection between red hair color and sexual behavior really exists using data from 110 women (34% redheaded) and 93 men (22% redheaded). Redheadedness in women, correlated with various traits related to sexual life, namely with higher sexual desire as measured by Revised Sociosexual Orientation Inventory, with higher sexual activity and more sexual partners of the preferred gender over the past year, earlier initiation of sexual life, and higher sexual submissiveness. Structural equation modelling, however, showed that sexual desire of redheaded women mediated neither their higher sexual activity nor their higher number of sexual partners. These results indirectly indicate that the apparently more liberated sexual behavior in redheaded women could be the consequence of potential mates’ frequent attempts to have sex with them. Our results contradicted the three other tested models, specifically the models based on the assumption of different physiology, faster life history strategy, and altered self-perception of redheaded women induced by stereotypes about them. Naturally, the present study cannot say anything about the validity of other potential models that were not subjects of testing.

Investigating the genetic architecture of eye colour in a Canadian cohort

Eye color is highly variable in populations with European ancestry, ranging from low to high quantities of melanin in the iris. Polymorphisms in the HERC2/OCA2 locus have the largest effect on eye color in these populations, although other genomic regions also influence eye color. We performed genome-wide association studies of eye color in a Canadian cohort of European ancestry (N = 5,641) and investigated candidate causal variants. We uncovered several candidate causal signals in the HERC2/OCA2 region, whereas other loci likely harbor a single causal signal. We observed colocalization of eye color signals with the expression or methylation profiles of cultured primary melanocytes. Genetic correlations of eye and hair color suggest high genome-wide pleiotropy, but locus-level differences in the genetic architecture of both traits. Overall, we provide a better picture of the polymorphisms underpinning eye color variation, which may be a consequence of specific molecular processes in the iris melanocytes.

•

Genome-wide association studies of eye color in 5,641 participants

•

Multiple independent candidate causal variants were identified across HERC2/OCA2

•

Single candidate causal variants observed on or near IRF4, SLC24A4, TYR, and TYRP1

•

Colocalization of eye color signals with expression and methylation profiles

Correlation between iris color and glaucoma type

Introduction: Glaucoma is a group of diseases, etiologically very different, which is characterized by typical damage to the optic nerve and visual field defects. The most common cause of this disease is higher intraocular pressure (IOP) than the vascular system of the optic nerve head can withstand. Aim: The aim of our study was to examine the correlation between iris color and glaucoma type through a cross-sectional study. Material and methods: Total of 117 patients with glaucoma that were treated at the Clinic for Ophthalmology of the University Clinical Center of Serbia, in the glaucoma clinic, relevant data was recorded, including iris color and the type of glaucoma that was diagnosed and under therapy. The correlation between iris color and sex of patients, age, type of glau-coma, values of IOP of both eyes (IOP OD/OS) and central corneal thickness of both eyes (CCT OD/OS) was examined. Results: The population of our patients consisted of 38.5% men and 61.5% women. Primary open angle glaucoma (POAG) was present in 34.2% and primary angle closure glaucoma (PCAG) in 28.2% of patients. Blue iris was found in 16.2%, green in 6.8%, light brown in 29.9% and dark brown in 47% of patients. The mean IOP is 17.6 ± 6.5mmHg for the right and 16.9 ± 6.1mmHg for the left eye, and for CCT 547.6 ± 69.3mm for the right and 546.6 ± 64.2mm for left eye. Statistically significant correlations were found between glaucoma type and sex (p = 0.001), glaucoma type and iris color (p = 0.031) and CCT and iris color (p = 0.027). Conclusion: A statistically significant correlation of iris color and glaucoma type was confirmed , indicating that people with darker irises develop glaucoma more often than people with lighter irises. The relationship between sex and IOP with iris color was not determined. Results show a higher incidence of glaucoma in females, as well as higher values of CCT in people with darker irises.

A genome-wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans

BACKGROUND

Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans.

OBJECTIVES

To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America.

METHODS

Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome.

RESULTS

Genome-wide significant association was observed at four genome regions: two were associated with wrinkling (in 1p13·3 and 21q21·2), one with mole count (in 1q32·3) and one with both wrinkling and mole count (in 5p13·2). Associated SNPs in 5p13·2 and in 1p13·3 are intronic within SLC45A2 and VAV3, respectively, while SNPs in 1q32·3 are near the SLC30A1 gene, and those in 21q21·2 occur in a gene desert. Analyses of SNPs in IRF4 and MC1R are consistent with a role of these genes in skin ageing.

CONCLUSIONS

We replicate the association of wrinkling with variants in SLC45A2, IRF4 and MC1R reported in Europeans. We identify VAV3 and SLC30A1 as two novel candidate genes impacting on wrinkling and mole count, respectively. We provide the first evidence that SLC45A2 influences mole count, in addition to variants in this gene affecting melanoma risk in Europeans.

Evaluation of supervised machine-learning methods for predicting appearance traits from DNA

The prediction of human externally visible characteristics (EVCs) based solely on DNA information has become an established approach in forensic and anthropological genetics in recent years. While for a large set of EVCs, predictive models have already been established using multinomial logistic regression (MLR), the prediction performances of other possible classification methods have not been thoroughly investigated thus far. Motivated by the question to identify a potential classifier that outperforms these specific trait models, we conducted a systematic comparison between the widely used MLR and three popular machine learning (ML) classifiers, namely support vector machines (SVM), random forest (RF) and artificial neural networks (ANN), that have shown good performance outside EVC prediction. As examples, we used eye, hair and skin color categories as phenotypes and genotypes based on the previously established IrisPlex, HIrisPlex, and HIrisPlex-S DNA markers. We compared and assessed the performances of each of the four methods, complemented by detailed hyperparameter tuning that was applied to some of the methods in order to maximize their performance. Overall, we observed that all four classification methods showed rather similar performance, with no method being substantially superior to the others for any of the traits, although performances varied slightly across the different traits and more so across the trait categories. Hence, based on our findings, none of the ML methods applied here provide any advantage on appearance prediction, at least when it comes to the categorical pigmentation traits and the selected DNA markers used here.

Forensic determination of hair deposition time in crime scenes using electron paramagnetic resonance

Several types of biological samples, including hair strands, are found at crime scenes. Apart from the identification of the value and the contributor of the probative evidence, it is important to prove that the time of shedding of hair belonging to a suspect or victim matches the crime window. To this end, to estimate the ex vivo aging of hair, we evaluated time-dependent changes in melanin-derived free radicals in blond, brown, and black hairs by using electron paramagnetic resonance spectroscopy (EPR). Hair strands aged under controlled conditions (humidity 40%, temperature 20-22°C, indirect light, with 12/12 hour of light/darkness cycles) showed a time-dependent decay of melanin-derived radicals. The half-life of eumelanin-derived radicals in hair under our experimental settings was estimated at 22 ± 2 days whereas that of pheomelanin was about 2 days suggesting better stabilization of unpaired electrons by eumelanin. Taken together, this study provides a reference for future forensic studies on determination of degradation of shed hair in a crime scene by following eumelanin radicals by utilizing the non-invasive, non-destructive, and highly specific EPR technique.

Testing the impact of trait prevalence priors in Bayesian-based genetic prediction modeling of human appearance traits

The prediction of appearance traits by use of solely genetic information has become an established approach and a number of statistical prediction models have already been developed for this purpose. However, given limited knowledge on appearance genetics, currently available models are incomplete and do not include all causal genetic variants as predictors. Therefore such prediction models may benefit from the inclusion of additional information that acts as a proxy for this unknown genetic background. Use of priors, possibly informed by trait category prevalence values in biogeographic ancestry groups, in a Bayesian framework may thus improve the prediction accuracy of previously predicted externally visible characteristics, but has not been investigated as of yet. In this study, we assessed the impact of using trait prevalence-informed priors on the prediction performance in Bayesian models for eye, hair and skin color as well as hair structure and freckles in comparison to the respective prior-free models. Those prior-free models were either similarly defined either very close to the already established ones by using a reduced predictive marker set. However, these differences in the number of the predictive markers should not affect significantly our main outcomes. We observed that such priors often had a strong effect on the prediction performance, but to varying degrees between different traits and also different trait categories, with some categories barely showing an effect. While we found potential for improving the prediction accuracy of many of the appearance trait categories tested by using priors, our analyses also showed that misspecification of those prior values often severely diminished the accuracy compared to the respective prior-free approach. This emphasizes the importance of accurate specification of prevalence-informed priors in Bayesian prediction modeling of appearance traits. However, the existing literature knowledge on spatial prevalence is sparse for most appearance traits, including those investigated here. Due to the limitations in appearance trait prevalence knowledge, our results render the use of trait prevalence-informed priors in DNA-based appearance trait prediction currently infeasible.

Interpol review of forensic biology and forensic DNA typing 2016-2019

This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.