DNA-based Eye Color Prediction of Pakhtun Population Living in District Swat KP Pakistan

Background:  Forensic DNA Phenotyping (FDP) or the prediction of Externally Visible Characteristics (EVCs) from a DNA sample has gained importance in the last decade or so in the forensic community. If and when the traditional forensic DNA typing via Short Tandem Repeats (STR) fails due to the absence of a reference sample, an individual can be traced by a DNA sample using FDP. Amongst the many available EVCs, eye color is one such character that can be predicted by employing previously developed IrisPlex system using Single Nucleotide Polymorphism (SNP) assay. In this study, we applied the IrisPlex system to samples collected from population of District Swat for prediction of eye colours from DNA. Method:  Eye colour digital photographs and buccal swab samples were collected from 267 Pakhtun individuals of District Swat. Any person with eye disease was excluded from the study. Genomic DNA was extracted through Phenol-Chloroform extraction method. The amplified SNPs were typed using Multiplexed Single Base Extension (SBE). The genotypes were checked for eye color phenotypes through IrisPlex online tool and correlation were checked between SNPs, Gender, pie score and eye color. Result:  Brown eye color was found prevalent as compared to intermediate and blue. Females have highly brown eye color compared to males while males have intermediate and blue. Three SNPs rs12913832 (in the  HERC2 ), rs1393350 ( TYR  gene), rs1800407 ( OCA2  gene) were strongly significant to eye color. Pie score was also significant to eye color and rs12913832 SNP. IrisPlex analysis in 20 individuals of District Swat was performed. The prediction accuracy of IrisPlex for blue or brown was 100% in the studied individuals. However, the IrisPlex tool predicted the intermediate phenotype incorrectly as brown or blue. Conclusion:  It is concluded from the data that intermediate eye colour was not predicted accurately, therefore, inclusion of more SNPs in the IrisPlex system is needed to predict intermediate eye colour accurately. Keywords: Eye colour, IrisPlex, SNPs, Multiplex genotyping, DNA, District Swat