Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations

Abstract

DNA-based prediction for externally visible characteristics such as eye color is already a useful tool in forensic criminal investigations. The IrisPlex system, consisting of six single nucleotide polymorphisms (SNPs) and a prediction model, was developed based on individuals from several European populations. Other recent studies have developed a different prediction model, also based on European populations. In this study, we compared two prediction models using the data for the six IrisPlex SNPs genotyped on 905 individuals from 12 different Eurasian populations. All SNPs showed significant differences in allele frequencies among three groups of populations: European, genetically intermediate (Khanty, Uygur, and Yakut), and East Asian. The two prediction models, the FROG-kb calculation based on the formula of Walsh et al. (2011) and the Snipper calculation from Ruiz et al. (2013), gave identical predictions of brown eye color for the four East Asian populations with complete data but did not give concordant predictions for many individuals in the seven intermediate and European populations. Inconsistencies were mainly conclusive prediction by one model but not the other. Of the 714 individuals with complete 6-locus genotypes, the two models gave 22 % inconsistent predictions. Eliminating the 306 individuals in the Korean and three Chinese populations, in which the predictions were always consistent for brown eye color, the inconsistencies (among the remaining 408 individuals) were 38.7 %. We conclude that more attention should be paid to predictive uncertainty/error. Implementation of both prediction models in future forensic casework is one immediate way to highlight uncertainty.

Forensic DNA Phenotyping: A Review in Korean Perspective

“…The studies have confirmed that OCA2 gene, as well as other three genes, HERC2, SLC24A4, and SLC24A5, respectively, were discovered to have significant melanin effects in determining human iris colors by regulating melanin production and expression in the eye [1,3,8,9,12,16]. Moreover, HERC2 gene was discovered to be strongly associated with blue eye color; further analysis has presented that rs12913832 in HERC2 was responsible for determining blue and brown eye color variation [3,9,[16][17][18], and also has the highest discrimination power for predicting either light or dark iris color among various population groups [3,12].…”

“…In fact, when Yun et al [12], compared the prediction outcomes using two different methods, one being the FROG-kb used in Walsh et al [16][17][18]'s IrisPlex system and the other one being Ruiz et al [27]'s Snipper based on Bayseian form, two systems showed no contradicting predictions among East Asian samples. This finding indicates that while these platforms can be used to rule out East Asians among other population groups, these SNPs would not allow further detailed differentiation within the East Asian groups.…”

“…The drawback is that these monomorphic traits cannot provide any useful information when finding the investigative leads in Korea, which these platforms would predict every individual as brown eye with dark hair. In other words, alternate approach is required when distinguishing an individual within East Asian populations based on phenotypic traits; additional assessments would be needed to decide which markers to keep and which markers to retract for constructing Korean specific prediction tools [12,20,21].…”

“…Because of such limited phenotypic features, certain traits other than pigmentations must be taken into account in order to compensate for less diverse pigmentation variations [12,31]; that is to concentrate on certain propensity markers to be included to further narrow down the investigative pool. Incorporating the rightful propensity prediction markers could enhance the functionality and the precision rate of the prediction model.…”

“…The idea of FDP by utilizing EVC was first introduced by Grimes et al [7] using the MC1R gene to predict red hair pigmentation trait [7][8][9][10]; because human pigmentation variations were understood as inherited traits [8], EVCs were thought to be promising components to be used to differentiate individuals. Hence, using particular DNA markers that can provide phenotypical information about the unknown possible suspect and such appropriate application of FDP can help narrowing down the investigative pool and can aid in arresting the offender [2,11,12]. Nevertheless, the capacity of FDP technique is not limited to criminal investigation; it can also be used when finding missing persons or for personal identification in mass disaster cases [10].…”