ABSTRACT
AIM: To evaluate the accuracy of eye color prediction based on six IrisPlex single nucleotide polymorphisms (SNP) in a Slovenian population sample. METHODS: Six IrisPlex predictor SNPs (HERC2 - rs12913832, OCA2 - rs1800407, SLC45A2 - rs16891982 and TYR - rs1393350, SLC24A4 - rs12896399, and IRF4 - rs12203592) of 105 individuals were analyzed using single base extension approach and SNaPshot chemistry. The IrisPlex multinomial regression prediction model was used to infer eye color probabilities. The accuracy of the IrisPlex was assessed through the calculation of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and the area under the receiver characteristic operating curves (AUC). RESULTS: Blue eye color was observed in 44.7%, brown in 29.6%, and intermediate in 25.7% participants. Prediction accuracy expressed by the AUC was 0.966 for blue, 0.913 for brown, and 0.796 for intermediate eye color. Sensitivity was 93.6% for blue, 58.1% for brown, and 0% for intermediate eye color. Specificity was 93.1% for blue, 89.2% for brown, and 100% for intermediate eye color. PPV was 91.7% for blue and 69.2% for brown color. NPV was 94.7% for blue and 83.5% for brown eye color. These values indicate prediction accuracy comparable to that established in other studies. CONCLUSION: Blue and brown eye color can be reliably predicted from DNA samples using only six polymorphisms, while intermediate eye color defies prediction, indicating that more research is needed to genetically predict the whole variation of eye color in humans.
Subject(s)
Eye Color/genetics , Genotype , Polymorphism, Single Nucleotide , White People/genetics , Adult , Antigens, Neoplasm/genetics , Antiporters/genetics , Area Under Curve , DNA/genetics , DNA Primers/genetics , False Positive Reactions , Female , Guanine Nucleotide Exchange Factors/genetics , Humans , Interferon Regulatory Factors/genetics , Male , Membrane Transport Proteins/genetics , Monophenol Monooxygenase/genetics , Predictive Value of Tests , ROC Curve , Reproducibility of Results , Sensitivity and Specificity , Slovenia , Ubiquitin-Protein LigasesABSTRACT
AIM: To analyze two phenotype characteristics--eye and hair color--using single-nucleotide polymorphisms (SNPs) and evaluate their prediction accuracy in Slovenian population. METHODS: Twelve SNPs (OCA2 - rs1667394, rs7170989, rs1800407, rs7495174; HERC2 - rs1129038, rs12913832; MC1R - rs1805005, rs1805008; TYR - rs1393350; SLC45A2 - rs16891982, rs26722; SLC24A5 - rs1426654) were used for the development of a single multiplex assay. The single multiplex assay was based on SNaPshot chemistry and capillary electrophoresis. In order to evaluate the accuracy of the prediction of eye and hair color, we used the logistic regression model and the Bayesian network model, and compared the parameters of both. RESULTS: The new single multiplex assay displayed high levels of genotyping sensitivity with complete profiles generated from as little as 62 pg of DNA. Based on a prior evaluation of all SNPs in a single multiplex, we focused on the five most statistically significant in our population in order to investigate the predictive value. The two prediction models performed reliably without prior ancestry information, and revealed very good accuracy for both eye and hair color. Both models determined the highest predictive value for rs12913832 (P<0.0001), while the other four SNPs (rs1393350, rs1800407, rs1805008, and rs7495174) showed additional association for color prediction. CONCLUSION: We developed a sensitive and reliable single multiplex genotyping assay. More samples from different populations should be analyzed before this assay could be used as one of the supplemental tools in tracing unknown individuals in more complicated crime investigations.
Subject(s)
Eye Color/genetics , Genetics, Population , Hair Color/genetics , Polymorphism, Single Nucleotide , Adult , Bayes Theorem , DNA/genetics , DNA Primers/genetics , Female , Genotype , Humans , Male , Membrane Transport Proteins/genetics , Multiplex Polymerase Chain Reaction , Phenotype , Receptor, Melanocortin, Type 1/genetics , SloveniaABSTRACT
Determining the gender of the source of forensic DNA evidence is based on the amelogenin test. However, at times the assay may not be indicative of gender assignment, because of deletions at the amelogenin site. Previously, we described successful coamplification of a marker residing within the SRY gene with the short tandem repeat markers from two commercially available human identification kits. The study herein addresses the validation of primers for the target SRY gene regarding specificity, sensitivity, and robustness. Among 115 unrelated male Slovenians no null allele was observed. Repeatable and reliable results were obtained from as little as 25 pg of template DNA, indicating a high sensitivity of detection for the assay. No polymerase chain reaction product was observed even at a concentration of 10 ng/microL of template female DNA. Additionally, the male specific marker could be detected in mixed male and female samples down to a ratio of 1:16.
