Prediction of eye, hair and skin colour in Latin Americans

Palmal, Sagnik; Adhikari, Kaustubh; Mendoza‐Revilla, Javier; Fuentes-Guajardo, Macarena; Cerqueira, Caio César Silva de; Bonfante, Betty; Chacón-Duque, Juan Camilo; Sohail, Anood; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Jaramillo, Claudia; Arias, William; Lozano, Rodrigo Barquera; Everardo-Martínez, Paola; Gómez-Valdés, Jorge; Villamil‐Ramírez, Hugo; Hünemeier, Tábita; Ramallo, Virgínia; Parolín, María Laura; González‐José, Rolando; Schüler‐Faccini, Lavínia; Bortolini, Maria-Cátira; Acuña-Alonzo, Víctor; Canizales‐Quinteros, Samuel; Gallo, Carla; Poletti, Giovanni; Bedoya, Gabriel; Rothhammer, Francisco; Balding, David J.; Faux, Pierre; Ruiz-Linares, Andrés

doi:10.1016/j.fsigen.2021.102517

Cited by 7 publications

(15 citation statements)

References 53 publications

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“…When analyzing eye color prediction made with the IrisPlex system, the prediction of intermediate colors in our population was inaccurate. In fact, none of the samples were predicted to be of intermediate color, showing concordance with other studies of mixed populations (Carratto et al, 2021;Marano et al, 2019;Palmal et al, 2021). It can be observed that in our predictions, intermediate colors show a considerable lack of definition when we use…”

Section: Discussionsupporting

confidence: 91%

“…We extracted DNA using Proteinase K (Promega, USA) and LiCl (Gemmell & Akiyama, 1996), and quantified it by using the Nanodrop spectrophotometer (Thermofisher). Then, we genotyped the samples for the six SNPs of the IrisPlex: rs12913832:A>G, rs1800407:C>T, rs12896399:G>T, rs16891982:C>G, rs1393350:G>A, and rs12203592:C>T, and additionally, another four SNPs: rs1129038:C>T, rs7183877:C>A, rs1800410:G>A and rs4778232:T>C. These polymorphisms are located in genes associated with eye color (HERC2, OCA2, LOC105370627, SLC45A2, TYR, and IRF4) (Duffy et al, 2007;Eiberg et al, 2008;Eriksson et al, 2010;Frudakis et al, 2003;Han et al, 2008;Lippert et al, 2017;Liu et al, 2009;Palmal et al, 2021;Ruiz et al, 2013;Visser et al, 2012;Wollstein et al, 2017). We designed oligonucleotides with Primer-BLAST (Ye et al, 2012) and performed polymerase chain reaction (PCR) using recombinant Taq polymerase (T-Plus, Inbio-Highway, Tandil, Argentina), as well as the thermocyclers MPI (La Plata, Argentina) and Biometra T3000 (Biosciences, Dublin, Ireland).…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

“…This way of prediction can be helpful for individual identification in certain criminal investigations, and it is known as forensic DNA phenotyping (FDP) (Koops & Schellekens, 2008). However, the bulk of available studies on EVC genetics is mainly focused on European populations (Liu et al, 2009;Mengel-From et al, 2009;Shapturenko et al, 2019;Sulem et al, 2007;Walsh et al, 2012), and only more recently, the scientific community began to analyze this topic in admixed populations (Beleza et al, 2013;Edwards et al, 2015;Lloyd-Jones et al, 2017), especially from Latin America (Carratto et al, 2019(Carratto et al, , 2020(Carratto et al, , 2021Hohl et al, 2018;Marano et al, 2019;Palmal et al, 2021;Silva de Cerqueira et al, 2014). Considering that differences in the genetic pool of a population can influence phenotype predictions based on genotype information (Beleza et al, 2013;Carratto et al, 2019Carratto et al, , 2020Carratto et al, , 2021Frudakis et al, 2003;Popejoy & Fullerton, 2016;Sirugo et al, 2019), there is a need for these comprehensive studies in admixed populations.…”

Section: Introductionmentioning

confidence: 99%

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Applicability of the IrisPlex system for eye color prediction in an admixed population from Argentina

Hohl

González

Meztler

et al. 2022

Annals of Human Genetics

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Eye color prediction based on an individual's genetic information is of interest in the field of forensic genetics. In recent years, researchers have studied different genes and markers associated with this externally visible characteristic and have developed methods for its prediction. The IrisPlex represents a validated tool for homogeneous populations, though its applicability in populations of mixed ancestry is limited, mainly regarding the prediction of intermediate eye colors. With the aim of validating the applicability of this system in an admixed population from Argentina (n = 302), we analyzed the six single nucleotide variants used in that multiplex for eye color and four additional SNPs, and evaluated its prediction ability. We also performed a genotype-phenotype association analysis. This system proved to be useful when dealing with the extreme ends of the eye color spectrum (blue and brown) but presented difficulties in determining the intermediate phenotypes (green), which were found in a large proportion of our population. We concluded that these genetic tools should be used with caution in admixed populations and that more studies are required in order to improve the prediction of intermediate phenotypes.

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Section: Discussionsupporting

confidence: 91%

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Applicability of the IrisPlex system for eye color prediction in an admixed population from Argentina

Hohl

González

Meztler

et al. 2022

Annals of Human Genetics

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“…A set of 41 SNPs in a total of 19 genes (the HIrisPlex-S system [53]) now allows estimation of individual probabilities for five skin, four hair and three eye colour categories from genotypes. The predictive models were developed and validated in a set of individuals (80% of them European) from indigenous populations [53][54][55]; in admixed populations, while SNP-based eye and hair colour prediction perform well [56,57], skin colour prediction is less accurate [57,58], reflecting the more complex nature of this trait, and possible epistatic interactions between alleles [56].…”

Section: No-suspect Cases: Dna-based Intelligence On Phenotype Predic...mentioning

confidence: 99%

Forensic genetics through the lens of Lewontin: population structure, ancestry and race

Jobling

2022

Phil. Trans. R. Soc. B

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In his famous 1972 paper, Richard Lewontin used ‘classical’ protein-based markers to show that greater than 85% of human genetic diversity was contained within, rather than between, populations. At that time, these same markers also formed the basis of forensic technology aiming to identify individuals. This review describes the evolution of forensic genetic methods into DNA profiling, and how the field has accounted for the apportionment of genetic diversity in considering the weight of forensic evidence. When investigative databases fail to provide a match to a crime-scene profile, specific markers can be used to seek intelligence about a suspect: these include inferences on population of origin (biogeographic ancestry) and externally visible characteristics, chiefly pigmentation of skin, hair and eyes. In this endeavour, ancestry and phenotypic variation are closely entangled. The markers used show patterns of inter- and intrapopulation diversity that are very atypical compared to the genome as a whole, and reinforce an apparent link between ancestry and racial divergence that is not systematically present otherwise. Despite the legacy of Lewontin's result, therefore, in a major area in which genetics coincides with issues of public interest, methods tend to exaggerate human differences and could thereby contribute to the reification of biological race. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

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“…which are more frequent in these groups [60][61][62][63]64,65 . Future research that addresses these shortcomings will not only advance the field of forensics but also will facilitate geneticallyinformed studies such as this one in admixed populations.…”

Section: Limitationsmentioning

confidence: 99%

The skin we live in: pigmentation traits and tanning behaviour in British young adults, an observational and genetically-informed study

Bonilla

Mejía-Lancheros

2022

Preprint

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Background: Skin cancer incidence has been increasing worldwide, representing a particularly high burden for populations of European ancestry. Outdoor and indoor tanning using ultraviolet radiation (UVR) devices are major risk factors for skin cancer. While tanning behaviours can be modified by targeted interventions to reduce skin cancer rates, there is insufficient evidence on the motivations for tanning preferences and their relationship with pigmentation phenotypes. The present observational and genetically-informed study investigates motives for tanning and the role that pigmentation phenotypes play on outdoor and indoor tanning behaviour in British young adults. Methods: This study included 3722 participants from the Avon Longitudinal Study of Parents and Children in South West England. Skin, hair and eye colour features, and tanning ability and preferences were collected using a questionnaire applied when participants were ~25 years of age. Genotypes for 41 single nucleotide polymorphisms (SNPs) associated with pigmentation were obtained from a subset of participants who provided a biological sample, and used to estimate the probability of having particular pigmentation traits with the HIrisPlex-S system. Results: Liking to tan and outdoor tanning were strongly influenced by skin, hair and eye pigmentation, and tanning ability. However, the association of these traits with UV indoor tanning was weaker. Conversely, females, participants of lower socioeconomic position, individuals who were unhappy with their pigmentation phenotype during adolescence, and participants who believed that tanning helps prevent sunburn were more likely to have used UVR-based tanning devices. Conclusion: Our results provide evidence to support the implementation of skin cancer preventative interventions that consider individual biological characteristics and motives for undergoing outdoor and indoor tanning.

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Prediction of eye, hair and skin colour in Latin Americans

Cited by 7 publications

References 53 publications

Applicability of the IrisPlex system for eye color prediction in an admixed population from Argentina

Applicability of the IrisPlex system for eye color prediction in an admixed population from Argentina

Forensic genetics through the lens of Lewontin: population structure, ancestry and race

The skin we live in: pigmentation traits and tanning behaviour in British young adults, an observational and genetically-informed study

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