A single-nucleotide polymorphism (SNP) multiplex system: the association of five SNPs with human eye and hair color in the Slovenian population and comparison using a Bayesian network and logistic regression model

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

Forensic DNA databasesin Western Balkan region:retrospectives, perspectives, and initiatives

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations

What comes after caring? The impact of family care on women's employment

Previous research has shown that women providing family care tend to decrease paid work. We take the opposite perspective and examine how current and previous family care tasks influence women’s likelihood to (re-)enter employment or to increase working hours. Family care is defined as caring for an ill, disabled or frail elderly partner, parent, or other family member. Using German Socio-Economic Panel data, we apply Cox shared frailty regression modeling to analyze transitions (1) into paid work and (2) from part-time to full-time work among women aged 25–59. The results indicate that in the German policy context, part-time working women providing extensive family care have a lower propensity to increase working hours. When family care ends, the likelihood that part-time working women change to full-time does not increase. Homemaking women’s likelihood of entering the workforce is not influenced by either current or previous family care tasks

Prediction of eye color in the Slovenian population using the IrisPlex SNPs

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 human

FORENSIC SCIENCE 382

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 TYRrs1393350, 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. -14). Variation of iris color depends on the content of eumelanine, a brown light-absorbing biopolymer, which is present in higher concentrations in brown-eyed individuals (15, Several prediction models have already been proposed to be useful in eye color prediction MatErial anD MEthoDs sample collection, Dna extraction, and quantification The study population comprised 105 unrelated Slovenian volunteers, 70 male and 35 female, who signed a written consent for their DNA to be used in the project. The study was approved by the National Medical Ethics Committee of the Republic of Slovenia. The eye color was defined according to descriptions provided by the volunteers and our own grading. For confirmation and in order to prevent bias, photographs of each donor&apos;s eyes were taken. Participants were divided into three categories according to eye color: blue, intermediate, and brown. The intermediate group included individuals with green eyes (lighter phenotype), hazel eyes (darker phenotype), and with combination of two or more pigments within the iris, such as blue or green eye color with brown peripupillary rings. The blue and the brown group included the individuals with the eye color that was clearly composed of only one color including all the shades of this particular color. Buccal swabs were collected from all volunteers using a SAFE ® Box kit (ForensiX, Prionics AG, Zurich, Switzerland). DNA was extracted from the samples using Chelex extraction (25). DNA extracts were quantified using the Quantifiler Human DNA Quantification Kit (Applied Biosystems Inc., Foster City, CA, USA) in accordance with the manufacturer&apos;s guidelines. single nucleotide polymorphisms (snP) genotyping Four SNPs (HERC2 -rs12913832, OCA2 -rs1800407, SLC45A2 -rs16891982, and TYR -rs1393350) were genotyped previously as described in Kastelic et al (26). The remaining two IrisPlex SNPs (SLC24A4 -rs12896399 and IRF4 -rs12203592) were genotyped for the purpose of this study using the protocol described by Walsh et al (17). Marker details and primer sequences are listed in Model-based prediction of eye color and evaluation of its accuracy On the basis of the formula provided by Liu et al (4) and implemented in the eye color prediction model of the IrisPlex system, three prediction probability values were generated for each of the three phenotype categories (blue, intermediate, and brown) (Supplementary rEsults Characteristics of the study population The frequency of blue eye color in the studied sample was 44.7% (47 samples) and the frequency of brown eye color was much lower and reached 29.6% (31 samples). The individuals were categorized in these two eye color groups only when the color was homogenous, regardless of the intensity. The frequency of individuals in the intermediate eye color group was relatively high, 25.7% (27 samples). Prediction accuracy of the irisPlex model Prediction accuracy expressed by the AUC DisCussion In the studied population sample, blue eye color was present with the frequency 44.7%, while according to the Eupedia (http://www.eupedia.com/europe/maps_of_euro pe.shtml#eye_colour), the expected frequency of light eyed individuals in Slovenia should be between 50% and 79%. However, most of the individuals included in the intermediate category had green irises and blue irises with brown spots or peripupillary rings and therefore could be included in the group of light eyed people. Taking this into account, it can be said that the percentage of light-eyed individuals in the study was 56%, which is in accordance with the Eupedia. FORENSIC SCIENCE 384 Croat Med J. 2013;54:381-6 www.cmj.hr The IrisPlex system includes six SNPs located on six genes (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 rs16891982, TYR rs1393350, and IRF4 rs12203592), which are considered to be major genetic predictors of eye color OCA2 SNP rs1800407, which ranked second among the best eye color predictors, has very low frequency of allele A (11.9%) and therefore may have had weak overall influence on variation in eye color in our population sample (4,12,13). The remaining IrisPlex predictors have been shown to have smaller effect on iris color variation but all six are implemented in the IrisPlex macro (13). It has been pointed out that IrisPlex can accurately predict blue and brown eye color while it is inefficient in the prediction of intermediate eye color and thus one should expect considerably lower prediction accuracy for this eye color category In conclusion, our study contributed to the body of evidence on eye color phenotype variation across Europe, as well as on genotype distribution in the six eye color informative IrisPlex SNPs, providing data for Slovenian population sample. The obtained results confirmed the utility of the IrisPlex prediction model for accurate prediction of blue and brown eye colors. Further studies are needed to explain the remaining variation in human eye color and open up possibility for prediction of a complete spectrum of eye colors in humans. acknowledgments We thank the volunteers who provided DNA samples and eye photographs for this study