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

Abstract

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.

Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics

“…IRF4 has not been included in an eye colour classification tree developed by Allwood et al based on a population sample from New Zealand while the model involves rs1393350 in TYR [ 10 ]. Lack of association for these two SNPs has also been revealed in a recent study performed on a Portuguese population [ 14 ]. The examination of rs12203592 in IRF4 in 12 European and Asian populations has revealed very weak effect of this SNP for iris colour prediction [ 12 ].…”

“…Pietroni et al, for instance, argued that three SNPs: rs12913832, rs1800407 and rs16891982 are the only informative markers among the six IrisPlex polymorphisms [ 13 ]. Position rs12203592 is regarded as the weakest predictor, and its association with eye colour has not been confirmed in several study samples [ 8 , 10 , 12 , 14 ]. In our population sample of 718 individuals from Poland, only four IrisPlex SNPs have been found to be associated with eye colour, with IRF4 and TYR unimportant for prediction [ 11 ].…”

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

“…They were: (a) rs12913832 in hect domain and RCC1 - like domain 2 ( HERC2 ) gene, (b) rs1800407, (c) rs7495174, (d) rs4778241 and (e) rs4778138 in the oculocutaneous albinism II ( OCA2 ) gene, (f) rs12896399 in solute carrier family 24 , member 4 ( SLC24A4 ) gene, (g) rs16891982 in solute carrier family 45 , member 2 ( SLC45A2 ) gene, (h) rs12203592 in interferon regulatory factor 4 ( IRF4 ) gene, (i) rs1393350 in tyrosinase ( TYR ) gene, (j) rs731236 in vitamin D receptor ( VDR ) gene, (k) rs6058017, (l) rs1015362 and (m) rs4911414 in Agouti signaling protein ( ASIP ) gene, (n) rs1805007 in melanocortin 1 receptor ( MC1R ) gene. We chose the SNPs based on their documented association with pigmentation traits within Europe and not the ones that have been reported as an Ancestry Informative Markers (AIM) that correlated more with an ethnic descent rather than with a visible trait, e.g., rs1426654 in SLC24A5 (Dario et al 2015 ; Bouakaze et al 2009 ; Lao et al 2007 ). All marker details including primer sequences and concentrations can be found in Supplementary Table 1.…”

“…Most of the EVCs, e.g., human pigmentation or hair and facial morphology, are complex polygenic and multifactorial traits, yet they are highly heritable and can be classified into easily described categories (Pulker et al 2007 ; Kastelic and Drobnič 2012 ; Walsh et al 2013 ; Liu et al 2012 ). Though EVC prediction of a human phenotype’s characteristics from DNA markers requires a probabilistic method, it provides an important and very useful tool in both criminal network as well as in archeological anthropology studies and it refers to as “DNA intelligence” (Kayser and Schneider 2009 ; Dario et al 2015 ). There is an increasing knowledge on genetic factors that explain differences in human morphological traits and SNPs are considered to affect human phenotypic variation the most (Kayser and de Kniff 2011 ; Wei et al 2014 ).…”

DNA Fingerprinting: A substantial and imperative aid to forensic investigation

“…There has been increasing interest in the determination of externally visible characteristics ("EVCs") such as age, eye color, hair color, and skin color, a newly emerging forensic technique [66][67][68][69][70], now more commonly known as FDP. FDP refers to the prediction of appearance traits of unknown sample donors, or unknown deceased (missing) persons, directly from biological materials found at the scene.…”